MIRI MRS Pipeline Notebook#
Authors: David Law, Kirsten Larson; MIRI branch
Last Updated: July 27, 2026
Pipeline Version: 3.0.0 (Build 13.0)
Purpose:
This notebook provides a framework for processing generic Mid-Infrared
Instrument (MIRI) Medium Resolution Spectroscopy (MRS) data through all
three James Webb Space Telescope (JWST) pipeline stages. Data is assumed
to be located in two observation folders (science and background)
according to paths set up below. It should not be necessary to edit any
cells other than in the Configuration section
unless modifying the standard pipeline processing options.
Data:
This example is set up to use observations of the LMC planetary nebula
SMP LMC 058 obtained by Proposal ID (PID) 1523 Observation 3. This is a
point source that uses a standard 4-point dither in all three grating
settings. It incorporates a dedicated background in observation 4.
Example input data to use will be downloaded automatically unless
disabled (i.e., to use local files instead).
JWST pipeline version and CRDS context:
This notebook was written for the
calibration pipeline version given above. If you use it with a different pipeline
version or specify a non-default reference file context please see the relevant
release notes
(here for pipeline,
here for CRDS) for possibly relevant
changes.
Updates:
This notebook is regularly updated as improvements are made to the
pipeline. Find the most up to date version of this notebook at:
https://github.com/spacetelescope/jwst-pipeline-notebooks/
Recent Changes:
Jan 16 2025: Update to Build 11.2 (jwst 1.17.1); no significant changes.
May 5 2025: Update to Build 11.3 (jwst 1.18.0); add optional command to remove residual showers, plot spectra from updated x1d.fits data model with rf-corrected columns.
May 22 2025: Update example plot use of regular and rf-corrected spectra.
July 16 2025: No significant updates.
Sep 03 2025: Minor update to remove mrs_imatch step
December 10 2025: No significant updates.
April 17, 2026: Updated to jwst 2.0.0; add Adaptive Trace Model option to spec3.
July 27, 2026: Updated to jwst 3.0.0 (no significant changes)
Table of Contents#
1.-Configuration#
Set basic parameters to use with notebook. These will affect what data is used, where data is located (if already in disk), pipeline modules run in this data, and type of background subtraction (if any). The list of parameters are:
demo_mode
channel
band
directories with data
pipeline modules
Backgroud subtraction method
# Basic import necessary for configuration
import os
Note that
demo_mode must be set appropriately below.
Set demo_mode = True to run in demonstration mode. In this mode this
notebook will download example data from the
Barbara A. Mikulski Archive for Space Telescopes (MAST) and process it through the pipeline.
This will all happen in a local directory unless modified
in Section 3 below.
Set demo_mode = False if you want to process your own data that has already
been downloaded and provide the location of the data.
# Set parameters for demo_mode, channel, band, data mode directories, and
# processing steps.
# -----------------------------Demo Mode---------------------------------
demo_mode = True
if demo_mode:
print('Running in demonstration mode using online example data!')
# --------------------------User Mode Directories------------------------
# If demo_mode = False, look for user data in these paths
if not demo_mode:
# Set directory paths for processing specific data; these will need
# to be changed to your local directory setup (below are given as
# examples)
user_home_dir = os.path.expanduser('~')
# Point to where science observation data are
# Assumes uncalibrated data in sci_dir/uncal/ and results in stage1,
# stage2, stage3 directories
sci_dir = os.path.join(user_home_dir, 'FlightData/APT1523/data/Obs003/')
# Point to where background observation data are
# Assumes uncalibrated data in bg_dir/uncal/ and results in stage1,
# stage2, stage3 directories
bg_dir = os.path.join(user_home_dir, 'FlightData/APT1523/data/Obs004/')
#bg_dir = '' # If no background observation, use an empty string
# --------------------------Set Processing Steps--------------------------
# Whether or not to process only data from a given MRS band/channel (useful
# if overriding reference files)
# Note that BOTH parameters must be set in order to work
use_ch = '' # '12' or '34'
use_band = '' # 'SHORT', 'MEDIUM', or 'LONG'
# Individual pipeline stages can be turned on/off here. Note that a later
# stage won't be able to run unless data products have already been
# produced from the prior stage.
# Science processing
dodet1 = True # calwebb_detector1
dospec2 = True # calwebb_spec2
dospec3 = True # calwebb_spec3
doviz = True # Visualize calwebb_spec3 results
# Background processing
dodet1bg = True # calwebb_detector1
dospec2bg = True # calwebb_spec2 (needed for Master Background subtraction)
# How should background subtraction using any dedicated backgrounds be done?
# If none are selected, cubes will not be background subtracted. 1d spectra
# will always use local annular background subtraction for point sources.
# Note that if using master-background subtraction, background observations
# must be selected above to process through spec2 (dospec2bg = True).
master_bg = True # Master-background subtraction in spec3 (subtract spectrum generated from the backgrounds). This is the default pipeline setting.
pixel_bg = False # Pixel-based background subtraction in spec2 (direct pixel subtraction).
Running in demonstration mode using online example data!
Set CRDS context and server#
Before importing CRDS and JWST modules, we need to configure our environment. This includes defining a CRDS cache directory in which to keep the reference files that will be used by the calibration pipeline.
If the root directory for the local CRDS cache directory has not been set already, it will be set to create one in the home directory.
# ------------------------Set CRDS context and paths----------------------
# Set CRDS reference file context. Leave commented-out to use the default context
# (latest reference files associated with the calibration pipeline version)
# or set a specific context here.
#%env CRDS_CONTEXT jwst_1295.pmap
# Check whether the local CRDS cache directory has been set.
# If not, set it to the user home directory
if (os.getenv('CRDS_PATH') is None):
os.environ['CRDS_PATH'] = os.path.join(os.path.expanduser('~'), 'crds')
# Check whether the CRDS server URL has been set. If not, set it.
if (os.getenv('CRDS_SERVER_URL') is None):
os.environ['CRDS_SERVER_URL'] = 'https://jwst-crds.stsci.edu'
# Echo CRDS path and context in use
print('CRDS local filepath:', os.environ['CRDS_PATH'])
print('CRDS file server:', os.environ['CRDS_SERVER_URL'])
CRDS local filepath: /home/runner/crds
CRDS file server: https://jwst-crds.stsci.edu
2.-Package Imports#
# Use the entire available screen width for this notebook
from IPython.display import display, HTML
display(HTML("<style>.container { width:95% !important; }</style>"))
# Basic system utilities for interacting with files
# ----------------------General Imports------------------------------------
import glob
import copy
import time
from pathlib import Path
from collections import defaultdict
# Numpy for doing calculations
import numpy as np
# -----------------------Astropy Imports-----------------------------------
# Astropy utilities for opening FITS and ASCII files, and downloading demo files
from astropy.io import fits
from astroquery.mast import Observations
# -----------------------Plotting Imports----------------------------------
# Matplotlib for making plots
import matplotlib.pyplot as plt
from matplotlib import rc
# --------------JWST Calibration Pipeline Imports---------------------------
# Import the base JWST and calibration reference data packages
import jwst
import crds
# JWST pipelines (each encompassing many steps)
from jwst.pipeline import Detector1Pipeline
from jwst.pipeline import Spec2Pipeline
from jwst.pipeline import Spec3Pipeline
# JWST pipeline utilities
from jwst import datamodels # JWST datamodels
from jwst.associations import asn_from_list as afl # Tools for creating association files
from jwst.associations.lib.rules_level2_base import DMSLevel2bBase # Definition of a Lvl2 association file
from jwst.associations.lib.rules_level3_base import DMS_Level3_Base # Definition of a Lvl3 association file
from jwst.stpipe import Step # Import the wrapper class for pipeline steps
# Echo pipeline version and CRDS context in use
print("JWST Calibration Pipeline Version = {}".format(jwst.__version__))
print("Using CRDS Context = {}".format(crds.get_context_name('jwst')))
JWST Calibration Pipeline Version = 3.0.0
CRDS - INFO - Calibration SW Found: jwst 3.0.0 (/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst-3.0.0.dist-info)
Using CRDS Context = jwst_1584.pmap
Define convenience functions#
# Define a convenience function to select only files of a given channel/band from an input set
def select_ch_band_files(files, use_ch, use_band):
if ((use_ch != '') & (use_band != '')):
keep = np.zeros(len(files))
for ii in range(0, len(files)):
with fits.open(files[ii]) as hdu:
hdu.verify()
hdr = hdu[0].header
if ((hdr['CHANNEL'] == use_ch) & (hdr['BAND'] == use_band)):
keep[ii] = 1
indx = np.where(keep == 1)
files_culled = files[indx]
else:
files_culled = files
return files_culled
# Start a timer to keep track of runtime
time0 = time.perf_counter()
3.-Demo Mode Setup (ignore if not using demo data)#
If running in demonstration mode, set up the program information to
retrieve the uncalibrated data automatically from MAST using
astroquery.
MAST allows for flexibility of searching by the proposal ID and the
observation ID instead of just filenames.
More information about the JWST file naming conventions can be found at: https://jwst-pipeline.readthedocs.io/en/latest/jwst/data_products/file_naming.html
# Set up the program information and paths for demo program
if demo_mode:
print('Running in demonstration mode and will download example data from MAST!')
program = "01523"
sci_observtn = "003"
back_observtn = "004"
visit = "001"
basedir = os.path.join('.', 'mrs_demo_data')
download_dir = basedir
sci_dir = os.path.join(basedir, 'Obs' + sci_observtn)
bg_dir = os.path.join(basedir, 'Obs' + back_observtn)
uncal_dir = os.path.join(sci_dir, 'uncal')
uncal_bgdir = os.path.join(bg_dir, 'uncal')
# Ensure filepaths for input data exist
if not os.path.exists(uncal_dir):
os.makedirs(uncal_dir)
if not os.path.exists(uncal_bgdir):
os.makedirs(uncal_bgdir)
Running in demonstration mode and will download example data from MAST!
Identify list of science (SCI) and background (BG) uncalibrated files associated with visits.
Selects only mirifu data (ignores MIRI imager).
# Obtain a list of observation IDs for the specified demo program
if demo_mode:
# Science data
sci_obs_id_table = Observations.query_criteria(instrument_name=["MIRI/IFU"],
provenance_name=["CALJWST"], # Executed observations
obs_id=['jw' + program + '-o' + sci_observtn + '*']
)
# Background data
bg_obs_id_table = Observations.query_criteria(instrument_name=["MIRI/IFU"],
provenance_name=["CALJWST"], # Executed observations
obs_id=['jw' + program + '-o' + back_observtn + '*']
)
# Turn the list of visits into a list of uncalibrated data files
if demo_mode:
# Define types of files to select
file_dict = {'uncal': {'product_type': 'SCIENCE', 'productSubGroupDescription': 'UNCAL', 'calib_level': [1]}}
# Science files
sci_files_to_download = []
# Loop over visits identifying uncalibrated files that are associated with them
for exposure in (sci_obs_id_table):
products = Observations.get_product_list(exposure)
for filetype, query_dict in file_dict.items():
filtered_products = Observations.filter_products(products, productType=query_dict['product_type'],
productSubGroupDescription=query_dict['productSubGroupDescription'],
calib_level=query_dict['calib_level'])
sci_files_to_download.extend(filtered_products['dataURI'])
# Background files
bg_files_to_download = []
# Loop over visits identifying uncalibrated files that are associated with them
for exposure in (bg_obs_id_table):
products = Observations.get_product_list(exposure)
for filetype, query_dict in file_dict.items():
filtered_products = Observations.filter_products(products, productType=query_dict['product_type'],
productSubGroupDescription=query_dict['productSubGroupDescription'],
calib_level=query_dict['calib_level'])
bg_files_to_download.extend(filtered_products['dataURI'])
# Cull to a unique list of files that contain 'mirifu' in the filename
# (i.e., not MIRI imager)
sci_files_to_download = np.unique([i for i in sci_files_to_download if 'mirifu' in i])
bg_files_to_download = np.unique([i for i in bg_files_to_download if 'mirifu' in i])
print("Science files selected for downloading: ", len(sci_files_to_download))
print("Background selected for downloading: ", len(bg_files_to_download))
Science files selected for downloading: 24
Background selected for downloading: 12
Download all the uncal files and place them into the appropriate directories.
Warning: If this notebook is halted during this step the downloaded file may be incomplete, and cause crashes later on!
if demo_mode:
for filename in sci_files_to_download:
sci_manifest = Observations.download_file(filename, local_path=os.path.join(uncal_dir, Path(filename).name))
for filename in bg_files_to_download:
bg_manifest = Observations.download_file(filename, local_path=os.path.join(uncal_bgdir, Path(filename).name))
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03102_00001_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00001_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03102_00001_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00001_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03102_00002_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00002_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03102_00002_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00002_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03102_00003_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00003_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03102_00003_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00003_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03102_00004_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00004_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03102_00004_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00004_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03104_00001_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00001_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03104_00001_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00001_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03104_00002_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00002_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03104_00002_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00002_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03104_00003_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00003_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03104_00003_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00003_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03104_00004_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00004_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03104_00004_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00004_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03106_00001_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00001_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03106_00001_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00001_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03106_00002_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00002_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03106_00002_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00002_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03106_00003_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00003_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03106_00003_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00003_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03106_00004_mirifulong_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00004_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523003001_03106_00004_mirifushort_uncal.fits to ./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00004_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02101_00001_mirifulong_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00001_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02101_00001_mirifushort_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00001_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02101_00002_mirifulong_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00002_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02101_00002_mirifushort_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00002_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02103_00001_mirifulong_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00001_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02103_00001_mirifushort_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00001_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02103_00002_mirifulong_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00002_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02103_00002_mirifushort_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00002_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02105_00001_mirifulong_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00001_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02105_00001_mirifushort_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00001_mirifushort_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02105_00002_mirifulong_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00002_mirifulong_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01523004001_02105_00002_mirifushort_uncal.fits to ./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00002_mirifushort_uncal.fits ...
[Done]
4.-Directory Setup#
Set up detailed paths to input/output stages here.
# Define output subdirectories to keep science data products organized
uncal_dir = os.path.join(sci_dir, 'uncal') # Uncalibrated pipeline inputs should be here
det1_dir = os.path.join(sci_dir, 'stage1') # calwebb_detector1 pipeline outputs will go here
spec2_dir = os.path.join(sci_dir, 'stage2') # calwebb_spec2 pipeline outputs will go here
spec3_dir = os.path.join(sci_dir, 'stage3') # calwebb_spec3 pipeline outputs will go here
# Output subdirectories to keep background data products organized
uncal_bgdir = os.path.join(bg_dir, 'uncal') # Uncalibrated pipeline inputs should be here
det1_bgdir = os.path.join(bg_dir, 'stage1') # calwebb_detector1 pipeline outputs will go here
spec2_bgdir = os.path.join(bg_dir, 'stage2') # calwebb_spec2 pipeline outputs will go here
# We need to check that the desired output directories exist, and if not create them
if not os.path.exists(det1_dir):
os.makedirs(det1_dir)
if not os.path.exists(spec2_dir):
os.makedirs(spec2_dir)
if not os.path.exists(spec3_dir):
os.makedirs(spec3_dir)
if (bg_dir != ''):
if not os.path.exists(det1_bgdir):
os.makedirs(det1_bgdir)
if not os.path.exists(spec2_bgdir):
os.makedirs(spec2_bgdir)
If there is no background folder, ensure we don't try to process it.
if (bg_dir == ''):
dodet1bg = False
dospec2bg = False
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime so far: {time1 - time0:0.4f} seconds")
Runtime so far: 135.0872 seconds
5.-Detector1 Pipeline#
In this section we process our data through the calwebb_detector1
pipeline to create Stage 1 data products (i.e., uncalibrated slope
images of the form *rate.fits). These data products have units of DN/s.
See https://jwst-docs.stsci.edu/jwst-science-calibration-pipeline/stages-of-jwst-data-processing/calwebb_detector1
To override certain steps and reference files, use the examples provided below.
E.g., turn on detection of cosmic ray showers.
E.g., turn on detection of cosmic ray showers.
# Set up a dictionary to define how the Detector1 pipeline should be configured
# Boilerplate dictionary setup
det1dict = defaultdict(dict)
# Overrides for whether or not certain steps should be skipped (example)
#det1dict['emicorr']['skip'] = True
# Option to use the first frame for very bright MIRI data that otherwise saturates fast enough to provide no slope
#det1dict['firstframe']['bright_use_group1'] = True
# Overrides for various reference files
# Files should be in the base local directory or provide full path
#det1dict['dq_init']['override_mask'] = 'myfile.fits' # Bad pixel mask
#det1dict['saturation']['override_saturation'] = 'myfile.fits' # Saturation
#det1dict['reset']['override_reset'] = 'myfile.fits' # Reset
#det1dict['linearity']['override_linearity'] = 'myfile.fits' # Linearity
#det1dict['rscd']['override_rscd'] = 'myfile.fits' # RSCD
#det1dict['dark_current']['override_dark'] = 'myfile.fits' # Dark current subtraction
#det1dict['jump']['override_gain'] = 'myfile.fits' # Gain used by jump step
#det1dict['ramp_fit']['override_gain'] = 'myfile.fits' # Gain used by ramp fitting step
#det1dict['jump']['override_readnoise'] = 'myfile.fits' # Read noise used by jump step
#det1dict['ramp_fit']['override_readnoise'] = 'myfile.fits' # Read noise used by ramp fitting step
# Turn on multi-core processing for jump step (off by default). Choose what fraction of cores to use (quarter, half, or all)
det1dict['jump']['maximum_cores'] = 'half'
# Toggle detection of cosmic ray showers if desired (on by default)
#det1dict['jump']['find_showers'] = True
Below an example of how to insert custom pipeline steps using the
pre-hook/post-hook framework.
For more information see Tips and Trick for working with the JWST Pipeline
# Define a new step called XplyStep that multiplies everything by 1.0
# I.e., it does nothing, but could be changed to do something more interesting.
class XplyStep(Step):
spec = '''
'''
class_alias = 'xply'
def process(self, input_data):
with datamodels.open(input_data) as model:
result = model.copy()
sci = result.data
sci = sci * 1.0
result.data = sci
self.log.info('Multiplied everything by one in custom step!')
return result
# And here we'll insert it into our pipeline dictionary to be run at the end right after the gain_scale step
det1dict['gain_scale']['post_hooks'] = [XplyStep]
Calibrating Science Files#
Look for input science files and run calwebb_detector1 pipeline using the call method.
# Look for input files of the form *uncal.fits from the science observation
sstring = os.path.join(uncal_dir, 'jw*mirifu*uncal.fits')
uncal_files = np.array(sorted(glob.glob(sstring)))
# Check that these are the band/channel to use
uncal_files = select_ch_band_files(uncal_files, use_ch, use_band)
print('Found ' + str(len(uncal_files)) + ' science input files')
Found 24 science input files
# Run the pipeline on these input files by a simple loop over files using
# our custom parameter dictionary
if dodet1:
for file in uncal_files:
Detector1Pipeline.call(file, steps=det1dict, save_results=True, output_dir=det1_dir)
else:
print('Skipping Detector1 processing for SCI data')
2026-07-28 16:36:28,406 - CRDS - INFO - Syncing 225 files
2026-07-28 16:36:28,424 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_system_datalvl_0002.rmap 694 bytes (1 / 225 files) (0 / 804.1 K bytes)
2026-07-28 16:36:28,634 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_system_calver_0075.rmap 6.0 K bytes (2 / 225 files) (694 / 804.1 K bytes)
2026-07-28 16:36:28,834 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_system_0068.imap 385 bytes (3 / 225 files) (6.7 K / 804.1 K bytes)
2026-07-28 16:36:29,056 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_wavelengthrange_0024.rmap 1.4 K bytes (4 / 225 files) (7.1 K / 804.1 K bytes)
2026-07-28 16:36:29,258 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_wavecorr_0005.rmap 884 bytes (5 / 225 files) (8.5 K / 804.1 K bytes)
2026-07-28 16:36:29,477 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_superbias_0090.rmap 39.5 K bytes (6 / 225 files) (9.3 K / 804.1 K bytes)
2026-07-28 16:36:29,793 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_sirskernel_0002.rmap 704 bytes (7 / 225 files) (48.9 K / 804.1 K bytes)
2026-07-28 16:36:29,984 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_sflat_0027.rmap 20.6 K bytes (8 / 225 files) (49.6 K / 804.1 K bytes)
2026-07-28 16:36:30,239 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_saturation_0018.rmap 2.0 K bytes (9 / 225 files) (70.2 K / 804.1 K bytes)
2026-07-28 16:36:30,455 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_refpix_0015.rmap 1.6 K bytes (10 / 225 files) (72.2 K / 804.1 K bytes)
2026-07-28 16:36:30,694 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_readnoise_0025.rmap 2.6 K bytes (11 / 225 files) (73.8 K / 804.1 K bytes)
2026-07-28 16:36:30,894 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_psf_0002.rmap 687 bytes (12 / 225 files) (76.3 K / 804.1 K bytes)
2026-07-28 16:36:31,094 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pictureframe_0002.rmap 886 bytes (13 / 225 files) (77.0 K / 804.1 K bytes)
2026-07-28 16:36:31,278 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_photom_0013.rmap 958 bytes (14 / 225 files) (77.9 K / 804.1 K bytes)
2026-07-28 16:36:31,460 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pathloss_0011.rmap 1.2 K bytes (15 / 225 files) (78.9 K / 804.1 K bytes)
2026-07-28 16:36:31,655 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-whitelightstep_0001.rmap 777 bytes (16 / 225 files) (80.0 K / 804.1 K bytes)
2026-07-28 16:36:31,843 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-tso3pipeline_0001.rmap 786 bytes (17 / 225 files) (80.8 K / 804.1 K bytes)
2026-07-28 16:36:32,031 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-spec2pipeline_0016.rmap 2.4 K bytes (18 / 225 files) (81.6 K / 804.1 K bytes)
2026-07-28 16:36:32,215 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-resamplespecstep_0002.rmap 709 bytes (19 / 225 files) (84.0 K / 804.1 K bytes)
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2026-07-28 16:36:32,634 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-pixelreplacestep_0001.rmap 818 bytes (21 / 225 files) (85.6 K / 804.1 K bytes)
2026-07-28 16:36:32,826 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-pictureframestep_0001.rmap 818 bytes (22 / 225 files) (86.4 K / 804.1 K bytes)
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2026-07-28 16:36:33,199 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-jumpstep_0006.rmap 810 bytes (24 / 225 files) (88.4 K / 804.1 K bytes)
2026-07-28 16:36:33,384 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-image2pipeline_0008.rmap 1.0 K bytes (25 / 225 files) (89.2 K / 804.1 K bytes)
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2026-07-28 16:36:33,952 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-darkpipeline_0003.rmap 872 bytes (28 / 225 files) (92.8 K / 804.1 K bytes)
2026-07-28 16:36:34,149 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-darkcurrentstep_0003.rmap 1.8 K bytes (29 / 225 files) (93.7 K / 804.1 K bytes)
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2026-07-28 16:36:34,603 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-cleanflickernoisestep_0003.rmap 1.1 K bytes (31 / 225 files) (96.4 K / 804.1 K bytes)
2026-07-28 16:36:34,803 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_pars-adaptivetracemodelstep_0002.rmap 997 bytes (32 / 225 files) (97.5 K / 804.1 K bytes)
2026-07-28 16:36:34,989 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_ote_0030.rmap 1.3 K bytes (33 / 225 files) (98.5 K / 804.1 K bytes)
2026-07-28 16:36:35,187 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_msaoper_0019.rmap 1.7 K bytes (34 / 225 files) (99.8 K / 804.1 K bytes)
2026-07-28 16:36:35,391 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_msa_0027.rmap 1.3 K bytes (35 / 225 files) (101.4 K / 804.1 K bytes)
2026-07-28 16:36:35,572 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_mask_0045.rmap 4.9 K bytes (36 / 225 files) (102.7 K / 804.1 K bytes)
2026-07-28 16:36:35,762 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_linearity_0017.rmap 1.6 K bytes (37 / 225 files) (107.6 K / 804.1 K bytes)
2026-07-28 16:36:35,946 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_ipc_0006.rmap 876 bytes (38 / 225 files) (109.2 K / 804.1 K bytes)
2026-07-28 16:36:36,129 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_ifuslicer_0018.rmap 1.5 K bytes (39 / 225 files) (110.1 K / 804.1 K bytes)
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2026-07-28 16:36:36,699 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_gain_0023.rmap 1.8 K bytes (42 / 225 files) (114.6 K / 804.1 K bytes)
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2026-07-28 16:36:37,257 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_flat_0015.rmap 3.8 K bytes (45 / 225 files) (122.6 K / 804.1 K bytes)
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2026-07-28 16:36:40,722 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_superbias_0037.rmap 8.6 K bytes (63 / 225 files) (209.3 K / 804.1 K bytes)
2026-07-28 16:36:40,921 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_specwcs_0017.rmap 3.1 K bytes (64 / 225 files) (217.9 K / 804.1 K bytes)
2026-07-28 16:36:41,136 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_specprofile_0010.rmap 2.5 K bytes (65 / 225 files) (221.0 K / 804.1 K bytes)
2026-07-28 16:36:41,351 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_speckernel_0006.rmap 1.0 K bytes (66 / 225 files) (223.5 K / 804.1 K bytes)
2026-07-28 16:36:41,547 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_sirskernel_0002.rmap 700 bytes (67 / 225 files) (224.5 K / 804.1 K bytes)
2026-07-28 16:36:41,743 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_saturation_0015.rmap 829 bytes (68 / 225 files) (225.2 K / 804.1 K bytes)
2026-07-28 16:36:41,933 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_readnoise_0011.rmap 987 bytes (69 / 225 files) (226.1 K / 804.1 K bytes)
2026-07-28 16:36:42,126 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_photom_0042.rmap 1.3 K bytes (70 / 225 files) (227.1 K / 804.1 K bytes)
2026-07-28 16:36:42,313 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_persat_0007.rmap 674 bytes (71 / 225 files) (228.3 K / 804.1 K bytes)
2026-07-28 16:36:42,504 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pathloss_0003.rmap 758 bytes (72 / 225 files) (229.0 K / 804.1 K bytes)
2026-07-28 16:36:42,698 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pastasoss_0006.rmap 818 bytes (73 / 225 files) (229.7 K / 804.1 K bytes)
2026-07-28 16:36:42,894 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-wfsscontamstep_0001.rmap 797 bytes (74 / 225 files) (230.6 K / 804.1 K bytes)
2026-07-28 16:36:43,092 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-undersamplecorrectionstep_0001.rmap 904 bytes (75 / 225 files) (231.4 K / 804.1 K bytes)
2026-07-28 16:36:43,275 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-tweakregstep_0012.rmap 3.1 K bytes (76 / 225 files) (232.3 K / 804.1 K bytes)
2026-07-28 16:36:43,483 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-spec2pipeline_0009.rmap 1.2 K bytes (77 / 225 files) (235.4 K / 804.1 K bytes)
2026-07-28 16:36:43,675 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-sourcecatalogstep_0004.rmap 2.3 K bytes (78 / 225 files) (236.6 K / 804.1 K bytes)
2026-07-28 16:36:43,865 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-resamplestep_0002.rmap 687 bytes (79 / 225 files) (239.0 K / 804.1 K bytes)
2026-07-28 16:36:44,054 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-outlierdetectionstep_0004.rmap 2.7 K bytes (80 / 225 files) (239.6 K / 804.1 K bytes)
2026-07-28 16:36:44,244 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-jumpstep_0007.rmap 6.4 K bytes (81 / 225 files) (242.3 K / 804.1 K bytes)
2026-07-28 16:36:44,429 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-image2pipeline_0005.rmap 1.0 K bytes (82 / 225 files) (248.7 K / 804.1 K bytes)
2026-07-28 16:36:44,614 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-detector1pipeline_0005.rmap 1.5 K bytes (83 / 225 files) (249.7 K / 804.1 K bytes)
2026-07-28 16:36:44,798 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-darkpipeline_0002.rmap 868 bytes (84 / 225 files) (251.2 K / 804.1 K bytes)
2026-07-28 16:36:44,995 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-darkcurrentstep_0001.rmap 591 bytes (85 / 225 files) (252.1 K / 804.1 K bytes)
2026-07-28 16:36:45,178 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-cleanflickernoisestep_0003.rmap 1.2 K bytes (86 / 225 files) (252.7 K / 804.1 K bytes)
2026-07-28 16:36:45,365 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-chargemigrationstep_0005.rmap 5.7 K bytes (87 / 225 files) (253.9 K / 804.1 K bytes)
2026-07-28 16:36:45,549 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-backgroundstep_0003.rmap 822 bytes (88 / 225 files) (259.6 K / 804.1 K bytes)
2026-07-28 16:36:45,738 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_nrm_0005.rmap 663 bytes (89 / 225 files) (260.4 K / 804.1 K bytes)
2026-07-28 16:36:45,924 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_mask_0025.rmap 1.6 K bytes (90 / 225 files) (261.1 K / 804.1 K bytes)
2026-07-28 16:36:46,115 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_linearity_0022.rmap 961 bytes (91 / 225 files) (262.7 K / 804.1 K bytes)
2026-07-28 16:36:46,317 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_ipc_0007.rmap 651 bytes (92 / 225 files) (263.6 K / 804.1 K bytes)
2026-07-28 16:36:46,515 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_gain_0011.rmap 797 bytes (93 / 225 files) (264.3 K / 804.1 K bytes)
2026-07-28 16:36:46,705 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_flat_0023.rmap 5.9 K bytes (94 / 225 files) (265.1 K / 804.1 K bytes)
2026-07-28 16:36:46,900 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_filteroffset_0010.rmap 853 bytes (95 / 225 files) (270.9 K / 804.1 K bytes)
2026-07-28 16:36:47,099 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_extract1d_0007.rmap 905 bytes (96 / 225 files) (271.8 K / 804.1 K bytes)
2026-07-28 16:36:47,286 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_drizpars_0004.rmap 519 bytes (97 / 225 files) (272.7 K / 804.1 K bytes)
2026-07-28 16:36:47,479 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_distortion_0025.rmap 3.4 K bytes (98 / 225 files) (273.2 K / 804.1 K bytes)
2026-07-28 16:36:47,677 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_dark_0041.rmap 8.7 K bytes (99 / 225 files) (276.6 K / 804.1 K bytes)
2026-07-28 16:36:47,872 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_bkg_0005.rmap 3.1 K bytes (100 / 225 files) (285.3 K / 804.1 K bytes)
2026-07-28 16:36:48,059 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_area_0014.rmap 2.7 K bytes (101 / 225 files) (288.4 K / 804.1 K bytes)
2026-07-28 16:36:48,245 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_apcorr_0010.rmap 4.3 K bytes (102 / 225 files) (291.1 K / 804.1 K bytes)
2026-07-28 16:36:48,426 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_abvegaoffset_0004.rmap 1.4 K bytes (103 / 225 files) (295.4 K / 804.1 K bytes)
2026-07-28 16:36:48,610 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_0313.imap 6.0 K bytes (104 / 225 files) (296.7 K / 804.1 K bytes)
2026-07-28 16:36:48,795 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_wavelengthrange_0014.rmap 996 bytes (105 / 225 files) (302.7 K / 804.1 K bytes)
2026-07-28 16:36:48,986 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_tsophot_0003.rmap 896 bytes (106 / 225 files) (303.7 K / 804.1 K bytes)
2026-07-28 16:36:49,172 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_trappars_0003.rmap 1.6 K bytes (107 / 225 files) (304.6 K / 804.1 K bytes)
2026-07-28 16:36:49,357 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_trapdensity_0003.rmap 1.6 K bytes (108 / 225 files) (306.2 K / 804.1 K bytes)
2026-07-28 16:36:49,555 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_superbias_0022.rmap 25.5 K bytes (109 / 225 files) (307.8 K / 804.1 K bytes)
2026-07-28 16:36:49,794 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_specwcs_0027.rmap 8.0 K bytes (110 / 225 files) (333.3 K / 804.1 K bytes)
2026-07-28 16:36:49,980 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_sirskernel_0003.rmap 671 bytes (111 / 225 files) (341.3 K / 804.1 K bytes)
2026-07-28 16:36:50,164 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_saturation_0011.rmap 2.8 K bytes (112 / 225 files) (342.0 K / 804.1 K bytes)
2026-07-28 16:36:50,358 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_regions_0003.rmap 3.4 K bytes (113 / 225 files) (344.8 K / 804.1 K bytes)
2026-07-28 16:36:50,553 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_readnoise_0028.rmap 27.1 K bytes (114 / 225 files) (348.2 K / 804.1 K bytes)
2026-07-28 16:36:50,810 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_psfmask_0008.rmap 28.4 K bytes (115 / 225 files) (375.4 K / 804.1 K bytes)
2026-07-28 16:36:51,052 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_photom_0031.rmap 3.4 K bytes (116 / 225 files) (403.7 K / 804.1 K bytes)
2026-07-28 16:36:51,244 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_persat_0005.rmap 1.6 K bytes (117 / 225 files) (407.2 K / 804.1 K bytes)
2026-07-28 16:36:51,434 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-whitelightstep_0004.rmap 2.0 K bytes (118 / 225 files) (408.7 K / 804.1 K bytes)
2026-07-28 16:36:51,620 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-wfsscontamstep_0001.rmap 797 bytes (119 / 225 files) (410.7 K / 804.1 K bytes)
2026-07-28 16:36:51,804 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-tweakregstep_0003.rmap 4.5 K bytes (120 / 225 files) (411.5 K / 804.1 K bytes)
2026-07-28 16:36:51,990 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-tsophotometrystep_0003.rmap 1.1 K bytes (121 / 225 files) (416.0 K / 804.1 K bytes)
2026-07-28 16:36:52,182 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-spec2pipeline_0009.rmap 984 bytes (122 / 225 files) (417.1 K / 804.1 K bytes)
2026-07-28 16:36:52,365 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-sourcecatalogstep_0002.rmap 4.6 K bytes (123 / 225 files) (418.1 K / 804.1 K bytes)
2026-07-28 16:36:52,546 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-resamplestep_0002.rmap 687 bytes (124 / 225 files) (422.7 K / 804.1 K bytes)
2026-07-28 16:36:52,742 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-outlierdetectionstep_0003.rmap 940 bytes (125 / 225 files) (423.4 K / 804.1 K bytes)
2026-07-28 16:36:52,946 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-jumpstep_0005.rmap 806 bytes (126 / 225 files) (424.3 K / 804.1 K bytes)
2026-07-28 16:36:53,130 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-image2pipeline_0004.rmap 1.1 K bytes (127 / 225 files) (425.1 K / 804.1 K bytes)
2026-07-28 16:36:53,325 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-detector1pipeline_0008.rmap 1.9 K bytes (128 / 225 files) (426.3 K / 804.1 K bytes)
2026-07-28 16:36:53,510 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-darkpipeline_0002.rmap 868 bytes (129 / 225 files) (428.1 K / 804.1 K bytes)
2026-07-28 16:36:53,705 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-darkcurrentstep_0001.rmap 618 bytes (130 / 225 files) (429.0 K / 804.1 K bytes)
2026-07-28 16:36:53,894 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-backgroundstep_0003.rmap 822 bytes (131 / 225 files) (429.6 K / 804.1 K bytes)
2026-07-28 16:36:54,080 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_mask_0015.rmap 6.0 K bytes (132 / 225 files) (430.4 K / 804.1 K bytes)
2026-07-28 16:36:54,276 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_linearity_0011.rmap 2.4 K bytes (133 / 225 files) (436.4 K / 804.1 K bytes)
2026-07-28 16:36:54,462 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_ipc_0003.rmap 2.0 K bytes (134 / 225 files) (438.8 K / 804.1 K bytes)
2026-07-28 16:36:54,659 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_gain_0016.rmap 2.1 K bytes (135 / 225 files) (440.8 K / 804.1 K bytes)
2026-07-28 16:36:54,858 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_flat_0028.rmap 51.7 K bytes (136 / 225 files) (442.9 K / 804.1 K bytes)
2026-07-28 16:36:55,167 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_filteroffset_0004.rmap 1.4 K bytes (137 / 225 files) (494.6 K / 804.1 K bytes)
2026-07-28 16:36:55,363 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_extract1d_0007.rmap 2.2 K bytes (138 / 225 files) (496.0 K / 804.1 K bytes)
2026-07-28 16:36:55,553 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_drizpars_0001.rmap 519 bytes (139 / 225 files) (498.2 K / 804.1 K bytes)
2026-07-28 16:36:55,742 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_distortion_0034.rmap 53.4 K bytes (140 / 225 files) (498.7 K / 804.1 K bytes)
2026-07-28 16:36:56,039 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_dark_0054.rmap 33.9 K bytes (141 / 225 files) (552.1 K / 804.1 K bytes)
2026-07-28 16:36:56,286 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_bkg_0002.rmap 7.0 K bytes (142 / 225 files) (585.9 K / 804.1 K bytes)
2026-07-28 16:36:56,468 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_area_0012.rmap 33.5 K bytes (143 / 225 files) (592.9 K / 804.1 K bytes)
2026-07-28 16:36:56,717 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_apcorr_0009.rmap 4.3 K bytes (144 / 225 files) (626.4 K / 804.1 K bytes)
2026-07-28 16:36:56,897 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_abvegaoffset_0004.rmap 1.3 K bytes (145 / 225 files) (630.7 K / 804.1 K bytes)
2026-07-28 16:36:57,084 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_0358.imap 5.8 K bytes (146 / 225 files) (632.0 K / 804.1 K bytes)
2026-07-28 16:36:57,275 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_wavelengthrange_0031.rmap 1.0 K bytes (147 / 225 files) (637.8 K / 804.1 K bytes)
2026-07-28 16:36:57,461 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_tsophot_0004.rmap 882 bytes (148 / 225 files) (638.8 K / 804.1 K bytes)
2026-07-28 16:36:57,643 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_straymask_0009.rmap 987 bytes (149 / 225 files) (639.7 K / 804.1 K bytes)
2026-07-28 16:36:57,827 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_specwcs_0051.rmap 6.4 K bytes (150 / 225 files) (640.7 K / 804.1 K bytes)
2026-07-28 16:36:58,021 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_saturation_0015.rmap 1.2 K bytes (151 / 225 files) (647.1 K / 804.1 K bytes)
2026-07-28 16:36:58,205 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_rscd_0012.rmap 1.0 K bytes (152 / 225 files) (648.2 K / 804.1 K bytes)
2026-07-28 16:36:58,400 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_resol_0006.rmap 790 bytes (153 / 225 files) (649.2 K / 804.1 K bytes)
2026-07-28 16:36:58,601 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_reset_0027.rmap 3.8 K bytes (154 / 225 files) (650.0 K / 804.1 K bytes)
2026-07-28 16:36:58,788 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_regions_0036.rmap 4.4 K bytes (155 / 225 files) (653.8 K / 804.1 K bytes)
2026-07-28 16:36:58,973 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_readnoise_0026.rmap 1.9 K bytes (156 / 225 files) (658.2 K / 804.1 K bytes)
2026-07-28 16:36:59,171 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_psfmask_0009.rmap 2.1 K bytes (157 / 225 files) (660.1 K / 804.1 K bytes)
2026-07-28 16:36:59,370 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_psf_0008.rmap 2.6 K bytes (158 / 225 files) (662.2 K / 804.1 K bytes)
2026-07-28 16:36:59,559 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_photom_0068.rmap 4.0 K bytes (159 / 225 files) (664.9 K / 804.1 K bytes)
2026-07-28 16:36:59,750 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pathloss_0006.rmap 866 bytes (160 / 225 files) (668.8 K / 804.1 K bytes)
2026-07-28 16:36:59,956 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-whitelightstep_0003.rmap 912 bytes (161 / 225 files) (669.7 K / 804.1 K bytes)
2026-07-28 16:37:00,145 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-wfsscontamstep_0001.rmap 787 bytes (162 / 225 files) (670.6 K / 804.1 K bytes)
2026-07-28 16:37:00,327 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-tweakregstep_0003.rmap 1.8 K bytes (163 / 225 files) (671.4 K / 804.1 K bytes)
2026-07-28 16:37:00,521 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-tsophotometrystep_0003.rmap 2.7 K bytes (164 / 225 files) (673.2 K / 804.1 K bytes)
2026-07-28 16:37:00,727 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-spec3pipeline_0011.rmap 886 bytes (165 / 225 files) (675.9 K / 804.1 K bytes)
2026-07-28 16:37:00,921 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-spec2pipeline_0015.rmap 1.5 K bytes (166 / 225 files) (676.8 K / 804.1 K bytes)
2026-07-28 16:37:01,109 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-sourcecatalogstep_0004.rmap 1.9 K bytes (167 / 225 files) (678.3 K / 804.1 K bytes)
2026-07-28 16:37:01,291 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-resamplestep_0002.rmap 677 bytes (168 / 225 files) (680.2 K / 804.1 K bytes)
2026-07-28 16:37:01,476 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-resamplespecstep_0002.rmap 706 bytes (169 / 225 files) (680.9 K / 804.1 K bytes)
2026-07-28 16:37:01,687 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-outlierdetectionstep_0020.rmap 3.4 K bytes (170 / 225 files) (681.6 K / 804.1 K bytes)
2026-07-28 16:37:01,882 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-jumpstep_0011.rmap 1.6 K bytes (171 / 225 files) (685.0 K / 804.1 K bytes)
2026-07-28 16:37:02,077 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-image2pipeline_0010.rmap 1.1 K bytes (172 / 225 files) (686.5 K / 804.1 K bytes)
2026-07-28 16:37:02,264 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-extract1dstep_0003.rmap 807 bytes (173 / 225 files) (687.6 K / 804.1 K bytes)
2026-07-28 16:37:02,472 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-emicorrstep_0003.rmap 796 bytes (174 / 225 files) (688.4 K / 804.1 K bytes)
2026-07-28 16:37:02,658 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-detector1pipeline_0012.rmap 1.6 K bytes (175 / 225 files) (689.2 K / 804.1 K bytes)
2026-07-28 16:37:02,854 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-darkpipeline_0002.rmap 860 bytes (176 / 225 files) (690.8 K / 804.1 K bytes)
2026-07-28 16:37:03,040 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-darkcurrentstep_0002.rmap 683 bytes (177 / 225 files) (691.7 K / 804.1 K bytes)
2026-07-28 16:37:03,235 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-backgroundstep_0003.rmap 814 bytes (178 / 225 files) (692.3 K / 804.1 K bytes)
2026-07-28 16:37:03,419 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-adaptivetracemodelstep_0002.rmap 979 bytes (179 / 225 files) (693.2 K / 804.1 K bytes)
2026-07-28 16:37:03,600 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_mrsxartcorr_0002.rmap 2.2 K bytes (180 / 225 files) (694.1 K / 804.1 K bytes)
2026-07-28 16:37:03,793 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_mrsptcorr_0005.rmap 2.0 K bytes (181 / 225 files) (696.3 K / 804.1 K bytes)
2026-07-28 16:37:03,978 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_mask_0037.rmap 9.3 K bytes (182 / 225 files) (698.3 K / 804.1 K bytes)
2026-07-28 16:37:04,167 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_linearity_0018.rmap 2.8 K bytes (183 / 225 files) (707.6 K / 804.1 K bytes)
2026-07-28 16:37:04,371 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_ipc_0008.rmap 700 bytes (184 / 225 files) (710.4 K / 804.1 K bytes)
2026-07-28 16:37:04,566 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_gain_0013.rmap 3.9 K bytes (185 / 225 files) (711.1 K / 804.1 K bytes)
2026-07-28 16:37:04,750 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_fringefreq_0003.rmap 1.4 K bytes (186 / 225 files) (715.0 K / 804.1 K bytes)
2026-07-28 16:37:04,951 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_fringe_0019.rmap 3.9 K bytes (187 / 225 files) (716.5 K / 804.1 K bytes)
2026-07-28 16:37:05,142 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_flat_0079.rmap 17.1 K bytes (188 / 225 files) (720.4 K / 804.1 K bytes)
2026-07-28 16:37:05,376 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_filteroffset_0029.rmap 2.4 K bytes (189 / 225 files) (737.5 K / 804.1 K bytes)
2026-07-28 16:37:05,577 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_extract1d_0022.rmap 1.0 K bytes (190 / 225 files) (739.9 K / 804.1 K bytes)
2026-07-28 16:37:05,770 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_emicorr_0007.rmap 663 bytes (191 / 225 files) (740.9 K / 804.1 K bytes)
2026-07-28 16:37:05,954 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_drizpars_0002.rmap 511 bytes (192 / 225 files) (741.6 K / 804.1 K bytes)
2026-07-28 16:37:06,138 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_distortion_0043.rmap 4.8 K bytes (193 / 225 files) (742.1 K / 804.1 K bytes)
2026-07-28 16:37:06,333 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_dark_0043.rmap 5.6 K bytes (194 / 225 files) (746.9 K / 804.1 K bytes)
2026-07-28 16:37:06,529 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_cubepar_0017.rmap 800 bytes (195 / 225 files) (752.4 K / 804.1 K bytes)
2026-07-28 16:37:06,720 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_bkg_0006.rmap 712 bytes (196 / 225 files) (753.2 K / 804.1 K bytes)
2026-07-28 16:37:06,910 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_area_0015.rmap 866 bytes (197 / 225 files) (753.9 K / 804.1 K bytes)
2026-07-28 16:37:07,101 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_apcorr_0024.rmap 5.0 K bytes (198 / 225 files) (754.8 K / 804.1 K bytes)
2026-07-28 16:37:07,292 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_abvegaoffset_0003.rmap 1.3 K bytes (199 / 225 files) (759.8 K / 804.1 K bytes)
2026-07-28 16:37:07,473 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_0517.imap 6.1 K bytes (200 / 225 files) (761.1 K / 804.1 K bytes)
2026-07-28 16:37:07,668 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_trappars_0004.rmap 903 bytes (201 / 225 files) (767.2 K / 804.1 K bytes)
2026-07-28 16:37:07,864 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_trapdensity_0006.rmap 930 bytes (202 / 225 files) (768.1 K / 804.1 K bytes)
2026-07-28 16:37:08,063 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_superbias_0017.rmap 3.8 K bytes (203 / 225 files) (769.0 K / 804.1 K bytes)
2026-07-28 16:37:08,257 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_saturation_0009.rmap 779 bytes (204 / 225 files) (772.8 K / 804.1 K bytes)
2026-07-28 16:37:08,450 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_readnoise_0014.rmap 1.3 K bytes (205 / 225 files) (773.6 K / 804.1 K bytes)
2026-07-28 16:37:08,635 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_photom_0014.rmap 1.1 K bytes (206 / 225 files) (774.8 K / 804.1 K bytes)
2026-07-28 16:37:08,828 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_persat_0006.rmap 884 bytes (207 / 225 files) (776.0 K / 804.1 K bytes)
2026-07-28 16:37:09,012 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-tweakregstep_0002.rmap 850 bytes (208 / 225 files) (776.8 K / 804.1 K bytes)
2026-07-28 16:37:09,208 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-sourcecatalogstep_0001.rmap 636 bytes (209 / 225 files) (777.7 K / 804.1 K bytes)
2026-07-28 16:37:09,403 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-outlierdetectionstep_0001.rmap 654 bytes (210 / 225 files) (778.3 K / 804.1 K bytes)
2026-07-28 16:37:09,588 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-image2pipeline_0005.rmap 974 bytes (211 / 225 files) (779.0 K / 804.1 K bytes)
2026-07-28 16:37:09,786 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-detector1pipeline_0002.rmap 1.0 K bytes (212 / 225 files) (779.9 K / 804.1 K bytes)
2026-07-28 16:37:09,980 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-darkpipeline_0002.rmap 856 bytes (213 / 225 files) (781.0 K / 804.1 K bytes)
2026-07-28 16:37:10,174 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_mask_0023.rmap 1.1 K bytes (214 / 225 files) (781.8 K / 804.1 K bytes)
2026-07-28 16:37:10,362 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_linearity_0015.rmap 925 bytes (215 / 225 files) (782.9 K / 804.1 K bytes)
2026-07-28 16:37:10,546 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_ipc_0003.rmap 614 bytes (216 / 225 files) (783.8 K / 804.1 K bytes)
2026-07-28 16:37:10,734 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_gain_0010.rmap 890 bytes (217 / 225 files) (784.4 K / 804.1 K bytes)
2026-07-28 16:37:10,919 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_flat_0009.rmap 1.1 K bytes (218 / 225 files) (785.3 K / 804.1 K bytes)
2026-07-28 16:37:11,118 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_distortion_0011.rmap 1.2 K bytes (219 / 225 files) (786.4 K / 804.1 K bytes)
2026-07-28 16:37:11,318 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_dark_0017.rmap 4.3 K bytes (220 / 225 files) (787.7 K / 804.1 K bytes)
2026-07-28 16:37:11,519 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_area_0010.rmap 1.2 K bytes (221 / 225 files) (792.0 K / 804.1 K bytes)
2026-07-28 16:37:11,709 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_apcorr_0004.rmap 4.0 K bytes (222 / 225 files) (793.1 K / 804.1 K bytes)
2026-07-28 16:37:11,905 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_abvegaoffset_0002.rmap 1.3 K bytes (223 / 225 files) (797.1 K / 804.1 K bytes)
2026-07-28 16:37:12,092 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_0126.imap 5.2 K bytes (224 / 225 files) (798.4 K / 804.1 K bytes)
2026-07-28 16:37:12,285 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_1584.pmap 580 bytes (225 / 225 files) (803.5 K / 804.1 K bytes)
2026-07-28 16:37:13,031 - CRDS - INFO - Syncing 1 files
2026-07-28 16:37:13,032 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf 1.0 K bytes (1 / 1 files) (0 / 1.0 K bytes)
2026-07-28 16:37:13,220 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:37:13,240 - CRDS - INFO - Syncing 1 files
2026-07-28 16:37:13,241 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf 936 bytes (1 / 1 files) (0 / 936 bytes)
2026-07-28 16:37:13,433 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:37:13,444 - CRDS - INFO - Syncing 1 files
2026-07-28 16:37:13,445 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf 1.4 K bytes (1 / 1 files) (0 / 1.4 K bytes)
2026-07-28 16:37:13,649 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:37:13,664 - CRDS - INFO - Syncing 1 files
2026-07-28 16:37:13,664 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf 1.8 K bytes (1 / 1 files) (0 / 1.8 K bytes)
2026-07-28 16:37:13,854 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:37:13,872 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:37:13,873 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:37:13,875 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:37:13,876 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:37:13,877 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:37:13,878 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:37:13,879 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:37:13,880 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:37:13,881 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:37:13,882 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:37:13,883 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:37:13,884 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:37:13,886 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:37:13,887 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:37:13,888 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:37:13,890 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:37:13,892 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:37:13,893 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:37:13,894 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:37:13,895 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:37:13,896 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:37:13,898 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:37:14,055 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00001_mirifulong_uncal.fits'),).
2026-07-28 16:37:14,075 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:37:14,101 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:37:14,105 - CRDS - INFO - Syncing 8 files
2026-07-28 16:37:14,105 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits 3.1 G bytes (1 / 8 files) (0 / 3.3 G bytes)
2026-07-28 16:38:21,234 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits 8.5 M bytes (2 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:38:22,260 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits 21.2 M bytes (3 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:38:23,579 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits 4.2 M bytes (4 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:38:24,497 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits 4.2 M bytes (5 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:38:25,454 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits 173.3 M bytes (6 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:38:29,809 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits 8.6 K bytes (7 / 8 files) (3.3 G / 3.3 G bytes)
2026-07-28 16:38:30,002 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits 8.5 M bytes (8 / 8 files) (3.3 G / 3.3 G bytes)
2026-07-28 16:38:30,987 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:38:30,987 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2026-07-28 16:38:30,988 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2026-07-28 16:38:30,989 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:38:30,989 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:38:30,990 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:38:30,991 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:38:30,991 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:38:30,992 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:38:30,992 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:38:31,422 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:31,423 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:38:31,423 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:38:31,430 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:38:31,580 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:31,698 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:38:31,738 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:31,792 - CRDS - INFO - Calibration SW Found: jwst 3.0.0 (/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst-3.0.0.dist-info)
2026-07-28 16:38:33,388 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:38:33,544 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:33,544 - stpipe.step - INFO - Step skipped.
2026-07-28 16:38:33,708 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:33,719 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:38:33,720 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:38:33,760 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:33,763 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:33,776 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:33,784 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:38:34,146 - stcal.saturation.saturation - INFO - Detected 373 saturated pixels
2026-07-28 16:38:34,180 - stcal.saturation.saturation - INFO - Detected 23 A/D floor pixels
2026-07-28 16:38:34,197 - stpipe.step - INFO - Step saturation done
2026-07-28 16:38:34,349 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:34,349 - stpipe.step - INFO - Step skipped.
2026-07-28 16:38:34,505 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:34,506 - stpipe.step - INFO - Step skipped.
2026-07-28 16:38:34,661 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:34,668 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:38:34,819 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:34,829 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:38:34,914 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:34,915 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:34,928 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:34,967 - stpipe.step - INFO - Step reset done
2026-07-28 16:38:35,118 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:35,125 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2026-07-28 16:38:35,164 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:35,165 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:35,178 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:35,421 - stpipe.step - INFO - Step linearity done
2026-07-28 16:38:35,570 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:35,578 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:38:35,592 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:38:35,593 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:38:35,595 - jwst.rscd.rscd_sub - INFO - There are 24 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:38:35,601 - jwst.rscd.rscd_sub - INFO - Flagged 24 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:38:35,652 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 24
2026-07-28 16:38:35,660 - stpipe.step - INFO - Step rscd done
2026-07-28 16:38:35,818 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:35,826 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:38:36,905 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:38:36,946 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:38:36,947 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:38:36,948 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:38:37,869 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:38:38,022 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:38,022 - stpipe.step - INFO - Step skipped.
2026-07-28 16:38:38,180 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:38,181 - stpipe.step - INFO - Step skipped.
2026-07-28 16:38:38,343 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:38,344 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:38:38,345 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:38:38,354 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:38:38,358 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:38:38,452 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:38:38,453 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:38:40,224 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:38:48,374 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:38:48,375 - stcal.jump.jump - INFO - Total elapsed time = 9.92189 sec
2026-07-28 16:38:48,394 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.050331
2026-07-28 16:38:48,402 - stpipe.step - INFO - Step jump done
2026-07-28 16:38:48,549 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:48,550 - stpipe.step - INFO - Step skipped.
2026-07-28 16:38:48,704 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:48,705 - stpipe.step - INFO - Step skipped.
2026-07-28 16:38:48,862 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:48,863 - stpipe.step - INFO - Step skipped.
2026-07-28 16:38:49,019 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:49,034 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:38:49,035 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:38:49,062 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:38:49,063 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:38:49,147 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:38:49,148 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:38:49,149 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:38:52,228 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.077030658721924
2026-07-28 16:38:52,419 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:38:52,571 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:52,579 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:38:52,594 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:38:52,595 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:38:52,745 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:52,770 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:38:52,770 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:38:52,778 - stpipe.step - INFO - Step xply done
2026-07-28 16:38:52,785 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:38:52,935 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:52,940 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:38:52,955 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:38:52,956 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:38:53,106 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2026-07-28 16:38:53,130 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:38:53,138 - stpipe.step - INFO - Step xply done
2026-07-28 16:38:53,145 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:38:53,224 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rateints.fits
2026-07-28 16:38:53,225 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:38:53,226 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:38:53,303 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits
2026-07-28 16:38:53,303 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:38:53,304 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:38:53,330 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:38:53,345 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:38:53,356 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:38:53,370 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:38:53,386 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:38:53,387 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:38:53,388 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:38:53,389 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:38:53,390 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:38:53,391 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:38:53,392 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:38:53,393 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:38:53,394 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:38:53,395 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:38:53,396 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:38:53,397 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:38:53,397 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:38:53,398 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:38:53,399 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:38:53,400 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:38:53,401 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:38:53,402 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:38:53,403 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:38:53,404 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:38:53,405 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:38:53,406 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:38:53,559 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00001_mirifushort_uncal.fits'),).
2026-07-28 16:38:53,579 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:38:53,605 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:38:53,609 - CRDS - INFO - Syncing 8 files
2026-07-28 16:38:53,609 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits 3.1 G bytes (1 / 8 files) (0 / 3.3 G bytes)
2026-07-28 16:40:01,344 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits 4.2 M bytes (2 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:40:02,311 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits 21.2 M bytes (3 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:40:03,546 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits 4.2 M bytes (4 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:40:04,462 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits 4.2 M bytes (5 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:40:05,365 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits 173.3 M bytes (6 / 8 files) (3.1 G / 3.3 G bytes)
2026-07-28 16:40:09,143 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits 8.6 K bytes (7 / 8 files) (3.3 G / 3.3 G bytes)
2026-07-28 16:40:09,345 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits 8.5 M bytes (8 / 8 files) (3.3 G / 3.3 G bytes)
2026-07-28 16:40:10,383 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:40:10,384 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:40:10,385 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:40:10,386 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:40:10,386 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:40:10,387 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:40:10,387 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:40:10,388 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:40:10,388 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:40:10,389 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:40:10,809 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:10,810 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:40:10,811 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:40:10,813 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:40:10,963 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:10,966 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:40:10,997 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:11,051 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:40:11,204 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:11,204 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:11,357 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:11,360 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:40:11,361 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:40:11,396 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:11,397 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:11,409 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:11,418 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:40:11,754 - stcal.saturation.saturation - INFO - Detected 1739 saturated pixels
2026-07-28 16:40:11,787 - stcal.saturation.saturation - INFO - Detected 16 A/D floor pixels
2026-07-28 16:40:11,801 - stpipe.step - INFO - Step saturation done
2026-07-28 16:40:11,951 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:11,952 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:12,107 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:12,108 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:12,260 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:12,263 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:40:12,416 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:12,419 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:40:12,502 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:12,503 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:12,516 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:12,553 - stpipe.step - INFO - Step reset done
2026-07-28 16:40:12,709 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:12,712 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:40:12,749 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:12,749 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:12,762 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:13,005 - stpipe.step - INFO - Step linearity done
2026-07-28 16:40:13,157 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:13,160 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:40:13,174 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:40:13,174 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:40:13,177 - jwst.rscd.rscd_sub - INFO - There are 37 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:40:13,182 - jwst.rscd.rscd_sub - INFO - Flagged 37 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:40:13,232 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 37
2026-07-28 16:40:13,235 - stpipe.step - INFO - Step rscd done
2026-07-28 16:40:13,386 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:13,389 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:40:15,084 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:15,131 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:40:15,132 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:40:15,133 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:40:16,034 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:40:16,187 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:16,188 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:16,341 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:16,342 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:16,497 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:16,498 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:40:16,498 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:40:16,501 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:40:16,504 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:40:16,600 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:40:16,601 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:40:18,336 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:40:25,261 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:40:25,262 - stcal.jump.jump - INFO - Total elapsed time = 8.6614 sec
2026-07-28 16:40:25,281 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.783776
2026-07-28 16:40:25,285 - stpipe.step - INFO - Step jump done
2026-07-28 16:40:25,437 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:25,438 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:25,593 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:25,594 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:25,746 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:25,747 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:25,899 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:25,905 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:40:25,905 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:40:25,930 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:40:25,930 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:40:26,012 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:40:26,013 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:40:26,014 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:40:28,905 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.8884952068328857
2026-07-28 16:40:29,060 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:40:29,217 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:29,220 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:40:29,233 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:40:29,234 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:40:29,387 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:29,411 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:40:29,412 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:40:29,415 - stpipe.step - INFO - Step xply done
2026-07-28 16:40:29,418 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:40:29,570 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:29,574 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:40:29,587 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:40:29,587 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:40:29,739 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2026-07-28 16:40:29,763 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:40:29,766 - stpipe.step - INFO - Step xply done
2026-07-28 16:40:29,770 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:40:29,835 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rateints.fits
2026-07-28 16:40:29,836 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:40:29,836 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:40:29,898 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits
2026-07-28 16:40:29,899 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:40:29,900 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:40:29,927 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:40:29,942 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:40:29,952 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:40:29,966 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:40:29,982 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:40:29,984 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:40:29,985 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:40:29,986 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:40:29,987 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:40:29,987 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:40:29,989 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:40:29,989 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:40:29,990 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:40:29,991 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:40:29,992 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:40:29,993 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:40:29,993 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:40:29,994 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:40:29,995 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:40:29,996 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:40:29,998 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:40:30,000 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:40:30,001 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:40:30,001 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:40:30,002 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:40:30,003 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:40:30,155 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00002_mirifulong_uncal.fits'),).
2026-07-28 16:40:30,174 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:40:30,200 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:40:30,203 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:40:30,204 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2026-07-28 16:40:30,205 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2026-07-28 16:40:30,205 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:40:30,206 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:40:30,206 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:40:30,207 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:40:30,208 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:40:30,208 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:40:30,209 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:40:30,641 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:30,642 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:40:30,642 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:40:30,644 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:40:30,793 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:30,796 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:40:30,827 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:30,881 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:40:31,033 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:31,033 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:31,187 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:31,191 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:40:31,191 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:40:31,226 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:31,227 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:31,239 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:31,247 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:40:31,590 - stcal.saturation.saturation - INFO - Detected 354 saturated pixels
2026-07-28 16:40:31,623 - stcal.saturation.saturation - INFO - Detected 25 A/D floor pixels
2026-07-28 16:40:31,637 - stpipe.step - INFO - Step saturation done
2026-07-28 16:40:31,789 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:31,790 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:31,944 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:31,945 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:32,101 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:32,104 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:40:32,257 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:32,260 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:40:32,344 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:32,345 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:32,358 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:32,396 - stpipe.step - INFO - Step reset done
2026-07-28 16:40:32,550 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:32,553 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2026-07-28 16:40:32,590 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:32,591 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:32,605 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:32,850 - stpipe.step - INFO - Step linearity done
2026-07-28 16:40:33,002 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:33,005 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:40:33,019 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:40:33,019 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:40:33,022 - jwst.rscd.rscd_sub - INFO - There are 23 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:40:33,027 - jwst.rscd.rscd_sub - INFO - Flagged 23 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:40:33,079 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 23
2026-07-28 16:40:33,082 - stpipe.step - INFO - Step rscd done
2026-07-28 16:40:33,237 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:33,240 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:40:34,034 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:34,075 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:40:34,075 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:40:34,076 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:40:34,809 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:40:34,964 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:34,964 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:35,121 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:35,122 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:35,279 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:35,279 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:40:35,280 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:40:35,283 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:40:35,285 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:40:35,377 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:40:35,378 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:40:37,071 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:40:45,355 - stcal.jump.jump - INFO - Total showers= 6
2026-07-28 16:40:45,356 - stcal.jump.jump - INFO - Total elapsed time = 9.97787 sec
2026-07-28 16:40:45,375 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.095088
2026-07-28 16:40:45,378 - stpipe.step - INFO - Step jump done
2026-07-28 16:40:45,529 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:45,530 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:45,684 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:45,685 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:45,839 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:45,840 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:45,993 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:45,998 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:40:45,998 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:40:46,025 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:40:46,025 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:40:46,097 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:40:46,098 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:40:46,099 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:40:49,135 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.0339126586914062
2026-07-28 16:40:49,292 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:40:49,451 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:49,454 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:40:49,469 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:40:49,470 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:40:49,623 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:49,647 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:40:49,648 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:40:49,651 - stpipe.step - INFO - Step xply done
2026-07-28 16:40:49,654 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:40:49,809 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:49,812 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:40:49,828 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:40:49,829 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:40:49,982 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2026-07-28 16:40:50,006 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:40:50,009 - stpipe.step - INFO - Step xply done
2026-07-28 16:40:50,013 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:40:50,080 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rateints.fits
2026-07-28 16:40:50,081 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:40:50,081 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:40:50,144 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits
2026-07-28 16:40:50,145 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:40:50,145 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:40:50,172 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:40:50,187 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:40:50,198 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:40:50,211 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:40:50,227 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:40:50,228 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:40:50,230 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:40:50,231 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:40:50,231 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:40:50,232 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:40:50,233 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:40:50,234 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:40:50,235 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:40:50,236 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:40:50,237 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:40:50,238 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:40:50,239 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:40:50,240 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:40:50,241 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:40:50,242 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:40:50,244 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:40:50,245 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:40:50,246 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:40:50,247 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:40:50,247 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:40:50,248 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:40:50,404 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00002_mirifushort_uncal.fits'),).
2026-07-28 16:40:50,423 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:40:50,450 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:40:50,453 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:40:50,453 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:40:50,454 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:40:50,454 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:40:50,455 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:40:50,455 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:40:50,456 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:40:50,456 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:40:50,457 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:40:50,457 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:40:50,888 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:50,889 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:40:50,889 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:40:50,891 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:40:51,044 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:51,047 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:40:51,079 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:51,133 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:40:51,287 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:51,288 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:51,440 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:51,445 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:40:51,446 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:40:51,481 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:51,482 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:51,495 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:51,503 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:40:51,865 - stcal.saturation.saturation - INFO - Detected 1638 saturated pixels
2026-07-28 16:40:51,899 - stcal.saturation.saturation - INFO - Detected 6 A/D floor pixels
2026-07-28 16:40:51,913 - stpipe.step - INFO - Step saturation done
2026-07-28 16:40:52,066 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:52,067 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:52,219 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:52,220 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:52,371 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:52,374 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:40:52,527 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:52,530 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:40:52,613 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:52,614 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:52,626 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:52,663 - stpipe.step - INFO - Step reset done
2026-07-28 16:40:52,816 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:52,819 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:40:52,857 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:52,858 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:52,872 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:53,111 - stpipe.step - INFO - Step linearity done
2026-07-28 16:40:53,263 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:53,266 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:40:53,279 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:40:53,280 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:40:53,282 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:40:53,288 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:40:53,340 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:40:53,343 - stpipe.step - INFO - Step rscd done
2026-07-28 16:40:53,495 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:53,498 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:40:54,266 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:40:54,307 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:40:54,308 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:40:54,309 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:40:54,938 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:40:55,092 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:55,092 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:55,249 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:55,250 - stpipe.step - INFO - Step skipped.
2026-07-28 16:40:55,403 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:40:55,404 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:40:55,405 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:40:55,408 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:40:55,410 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:40:55,508 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:40:55,509 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:40:57,192 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:41:03,890 - stcal.jump.jump - INFO - Total showers= 1
2026-07-28 16:41:03,891 - stcal.jump.jump - INFO - Total elapsed time = 8.38133 sec
2026-07-28 16:41:03,911 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.506637
2026-07-28 16:41:03,914 - stpipe.step - INFO - Step jump done
2026-07-28 16:41:04,071 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:41:04,072 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:04,229 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:41:04,230 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:04,386 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:41:04,387 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:04,542 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:41:04,548 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:41:04,548 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:41:04,574 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:41:04,575 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:41:04,663 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:41:04,671 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:41:04,672 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:41:07,431 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.75762939453125
2026-07-28 16:41:07,593 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:41:07,753 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:41:07,757 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:41:07,770 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:41:07,771 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:41:07,927 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:41:07,952 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:41:07,953 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:41:07,956 - stpipe.step - INFO - Step xply done
2026-07-28 16:41:07,960 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:41:08,117 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:41:08,120 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:41:08,134 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:41:08,134 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:41:08,292 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2026-07-28 16:41:08,316 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:41:08,320 - stpipe.step - INFO - Step xply done
2026-07-28 16:41:08,323 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:41:08,388 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rateints.fits
2026-07-28 16:41:08,389 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:41:08,390 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:41:08,454 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits
2026-07-28 16:41:08,455 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:41:08,455 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:41:08,483 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:41:08,499 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:41:08,510 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:41:08,524 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:41:08,541 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:41:08,542 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:41:08,543 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:41:08,544 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:41:08,545 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:41:08,546 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:41:08,547 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:41:08,548 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:41:08,549 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:41:08,550 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:41:08,551 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:41:08,552 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:41:08,553 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:41:08,553 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:41:08,555 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:41:08,556 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:41:08,558 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:41:08,559 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:41:08,560 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:41:08,561 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:41:08,562 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:41:08,563 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:41:08,719 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00003_mirifulong_uncal.fits'),).
2026-07-28 16:41:08,739 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:41:08,766 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00003_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:41:08,769 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:41:08,769 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2026-07-28 16:41:08,770 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2026-07-28 16:41:08,771 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:41:08,771 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:41:08,772 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:41:08,773 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:41:08,773 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:41:08,774 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:41:08,774 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:41:09,223 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:09,224 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:41:09,225 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:41:09,227 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:41:09,385 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:09,387 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:41:09,420 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:09,476 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:41:09,633 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:09,634 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:09,792 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:09,796 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:41:09,797 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:41:09,833 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:09,834 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:09,848 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:09,856 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:41:10,262 - stcal.saturation.saturation - INFO - Detected 358 saturated pixels
2026-07-28 16:41:10,298 - stcal.saturation.saturation - INFO - Detected 26 A/D floor pixels
2026-07-28 16:41:10,314 - stpipe.step - INFO - Step saturation done
2026-07-28 16:41:10,475 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:10,476 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:10,636 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:10,637 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:10,796 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:10,798 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:41:10,959 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:10,962 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:41:11,047 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:11,048 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:11,061 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:11,099 - stpipe.step - INFO - Step reset done
2026-07-28 16:41:11,259 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:11,262 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2026-07-28 16:41:11,301 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:11,302 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:11,316 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:11,569 - stpipe.step - INFO - Step linearity done
2026-07-28 16:41:11,727 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:11,730 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:41:11,744 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:41:11,745 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:41:11,747 - jwst.rscd.rscd_sub - INFO - There are 19 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:41:11,753 - jwst.rscd.rscd_sub - INFO - Flagged 19 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:41:11,806 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 19
2026-07-28 16:41:11,809 - stpipe.step - INFO - Step rscd done
2026-07-28 16:41:11,969 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:11,972 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:41:12,760 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:12,802 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:41:12,803 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:41:12,803 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:41:13,494 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:41:13,649 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:13,650 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:13,806 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:13,807 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:13,963 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:13,963 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:41:13,964 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:41:13,967 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:41:13,969 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:41:14,062 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:41:14,063 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:41:15,751 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:41:23,726 - stcal.jump.jump - INFO - Total showers= 5
2026-07-28 16:41:23,727 - stcal.jump.jump - INFO - Total elapsed time = 9.66421 sec
2026-07-28 16:41:23,746 - jwst.jump.jump_step - INFO - The execution time in seconds: 9.782962
2026-07-28 16:41:23,750 - stpipe.step - INFO - Step jump done
2026-07-28 16:41:23,906 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:23,907 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:24,064 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:24,065 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:24,222 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:24,223 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:24,380 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:24,386 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:41:24,386 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:41:24,414 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:41:24,414 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:41:24,488 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:41:24,497 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:41:24,497 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:41:27,423 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.9238698482513428
2026-07-28 16:41:27,579 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:41:27,739 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:27,742 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:41:27,758 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:41:27,759 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:41:27,915 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:27,940 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:41:27,940 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:41:27,944 - stpipe.step - INFO - Step xply done
2026-07-28 16:41:27,947 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:41:28,103 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:28,106 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:41:28,121 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:41:28,121 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:41:28,276 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2026-07-28 16:41:28,301 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:41:28,304 - stpipe.step - INFO - Step xply done
2026-07-28 16:41:28,308 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:41:28,375 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rateints.fits
2026-07-28 16:41:28,376 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:41:28,377 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:41:28,440 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits
2026-07-28 16:41:28,440 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:41:28,441 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:41:28,466 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:41:28,482 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:41:28,492 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:41:28,506 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:41:28,523 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:41:28,524 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:41:28,525 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:41:28,527 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:41:28,528 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:41:28,529 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:41:28,530 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:41:28,532 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:41:28,533 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:41:28,533 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:41:28,535 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:41:28,535 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:41:28,536 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:41:28,537 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:41:28,539 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:41:28,539 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:41:28,541 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:41:28,542 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:41:28,543 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:41:28,544 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:41:28,544 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:41:28,546 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:41:28,704 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00003_mirifushort_uncal.fits'),).
2026-07-28 16:41:28,723 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:41:28,750 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00003_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:41:28,752 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:41:28,753 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:41:28,754 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:41:28,754 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:41:28,755 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:41:28,756 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:41:28,756 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:41:28,757 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:41:28,757 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:41:28,758 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:41:29,197 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:29,198 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:41:29,199 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:41:29,200 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:41:29,356 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:29,359 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:41:29,392 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:29,447 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:41:29,602 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:29,602 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:29,759 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:29,764 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:41:29,764 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:41:29,801 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:29,802 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:29,815 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:29,823 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:41:30,212 - stcal.saturation.saturation - INFO - Detected 1594 saturated pixels
2026-07-28 16:41:30,247 - stcal.saturation.saturation - INFO - Detected 8 A/D floor pixels
2026-07-28 16:41:30,260 - stpipe.step - INFO - Step saturation done
2026-07-28 16:41:30,415 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:30,416 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:30,572 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:30,574 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:30,731 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:30,734 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:41:30,890 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:30,893 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:41:30,976 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:30,977 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:30,991 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:31,028 - stpipe.step - INFO - Step reset done
2026-07-28 16:41:31,185 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:31,188 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:41:31,227 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:31,227 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:31,240 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:31,489 - stpipe.step - INFO - Step linearity done
2026-07-28 16:41:31,645 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:31,648 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:41:31,662 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:41:31,662 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:41:31,665 - jwst.rscd.rscd_sub - INFO - There are 53 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:41:31,670 - jwst.rscd.rscd_sub - INFO - Flagged 53 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:41:31,723 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 53
2026-07-28 16:41:31,727 - stpipe.step - INFO - Step rscd done
2026-07-28 16:41:31,883 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:31,886 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:41:32,664 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:32,706 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:41:32,707 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:41:32,707 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:41:33,318 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:41:33,474 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:33,475 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:33,632 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:33,632 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:33,790 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:33,790 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:41:33,791 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:41:33,794 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:41:33,796 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:41:33,897 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:41:33,897 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:41:35,629 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:41:42,609 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:41:42,609 - stcal.jump.jump - INFO - Total elapsed time = 8.71218 sec
2026-07-28 16:41:42,630 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.839678
2026-07-28 16:41:42,634 - stpipe.step - INFO - Step jump done
2026-07-28 16:41:42,788 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:42,789 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:42,948 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:42,949 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:43,107 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:43,107 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:43,266 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:43,271 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:41:43,272 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:41:43,298 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:41:43,299 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:41:43,384 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:41:43,385 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:41:43,386 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:41:46,274 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.886765480041504
2026-07-28 16:41:46,435 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:41:46,594 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:46,598 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:41:46,611 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:41:46,611 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:41:46,768 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:46,793 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:41:46,793 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:41:46,797 - stpipe.step - INFO - Step xply done
2026-07-28 16:41:46,801 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:41:46,960 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:46,963 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:41:46,976 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:41:46,977 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:41:47,138 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2026-07-28 16:41:47,162 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:41:47,166 - stpipe.step - INFO - Step xply done
2026-07-28 16:41:47,169 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:41:47,236 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rateints.fits
2026-07-28 16:41:47,237 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:41:47,238 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:41:47,301 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits
2026-07-28 16:41:47,302 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:41:47,303 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:41:47,331 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:41:47,347 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:41:47,357 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:41:47,371 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:41:47,388 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:41:47,389 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:41:47,390 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:41:47,391 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:41:47,392 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:41:47,393 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:41:47,394 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:41:47,395 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:41:47,396 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:41:47,397 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:41:47,398 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:41:47,398 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:41:47,399 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:41:47,401 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:41:47,402 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:41:47,403 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:41:47,404 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:41:47,406 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:41:47,407 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:41:47,408 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:41:47,409 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:41:47,410 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:41:47,567 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00004_mirifulong_uncal.fits'),).
2026-07-28 16:41:47,587 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:41:47,614 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00004_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:41:47,617 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:41:47,618 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2026-07-28 16:41:47,619 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2026-07-28 16:41:47,619 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:41:47,620 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:41:47,620 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:41:47,621 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:41:47,621 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:41:47,622 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:41:47,623 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:41:48,070 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:48,071 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:41:48,072 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:41:48,074 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:41:48,229 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:48,232 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:41:48,264 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:48,319 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:41:48,475 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:48,476 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:48,633 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:48,636 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:41:48,637 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:41:48,672 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:48,673 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:48,687 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:48,695 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:41:49,081 - stcal.saturation.saturation - INFO - Detected 359 saturated pixels
2026-07-28 16:41:49,115 - stcal.saturation.saturation - INFO - Detected 21 A/D floor pixels
2026-07-28 16:41:49,128 - stpipe.step - INFO - Step saturation done
2026-07-28 16:41:49,284 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:49,285 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:49,439 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:49,440 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:49,597 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:49,600 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:41:49,756 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:49,758 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:41:49,843 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:49,844 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:49,857 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:49,894 - stpipe.step - INFO - Step reset done
2026-07-28 16:41:50,051 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:50,054 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2026-07-28 16:41:50,093 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:50,094 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:50,107 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:50,357 - stpipe.step - INFO - Step linearity done
2026-07-28 16:41:50,513 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:50,516 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:41:50,529 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:41:50,530 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:41:50,532 - jwst.rscd.rscd_sub - INFO - There are 22 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:41:50,538 - jwst.rscd.rscd_sub - INFO - Flagged 22 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:41:50,591 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 22
2026-07-28 16:41:50,594 - stpipe.step - INFO - Step rscd done
2026-07-28 16:41:50,750 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:50,753 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:41:51,527 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:41:51,569 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:41:51,570 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:41:51,571 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:41:52,289 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:41:52,444 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:52,445 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:52,602 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:52,602 - stpipe.step - INFO - Step skipped.
2026-07-28 16:41:52,758 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:41:52,759 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:41:52,760 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:41:52,762 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:41:52,765 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:41:52,862 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:41:52,863 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:41:54,588 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:42:02,767 - stcal.jump.jump - INFO - Total showers= 4
2026-07-28 16:42:02,768 - stcal.jump.jump - INFO - Total elapsed time = 9.90457 sec
2026-07-28 16:42:02,788 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.029475
2026-07-28 16:42:02,792 - stpipe.step - INFO - Step jump done
2026-07-28 16:42:02,948 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:42:02,949 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:03,106 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:42:03,107 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:03,263 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:42:03,264 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:03,422 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:42:03,428 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:42:03,428 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:42:03,455 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:42:03,456 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:42:03,531 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:42:03,535 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:42:03,536 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:42:06,558 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.02057147026062
2026-07-28 16:42:06,715 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:42:06,873 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:42:06,876 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:42:06,891 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:42:06,892 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:42:07,051 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:42:07,075 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:42:07,076 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:42:07,079 - stpipe.step - INFO - Step xply done
2026-07-28 16:42:07,083 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:42:07,250 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:42:07,254 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:42:07,271 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:42:07,272 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:42:07,432 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2026-07-28 16:42:07,456 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:42:07,459 - stpipe.step - INFO - Step xply done
2026-07-28 16:42:07,463 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:42:07,530 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rateints.fits
2026-07-28 16:42:07,531 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:42:07,531 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:42:07,594 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits
2026-07-28 16:42:07,595 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:42:07,596 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:42:07,621 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:42:07,636 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:42:07,647 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:42:07,661 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:42:07,677 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:42:07,678 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:42:07,679 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:42:07,680 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:42:07,681 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:42:07,681 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:42:07,682 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:42:07,684 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:42:07,685 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:42:07,686 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:42:07,687 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:42:07,687 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:42:07,689 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:42:07,690 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:42:07,691 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:42:07,692 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:42:07,694 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:42:07,695 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:42:07,696 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:42:07,697 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:42:07,699 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:42:07,699 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:42:07,859 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00004_mirifushort_uncal.fits'),).
2026-07-28 16:42:07,879 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:42:07,906 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00004_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:42:07,909 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:42:07,910 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:42:07,910 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:42:07,911 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:42:07,911 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:42:07,912 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:42:07,913 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:42:07,913 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:42:07,914 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:42:07,914 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:42:08,354 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:08,355 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:42:08,356 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:42:08,358 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:42:08,513 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:08,515 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:42:08,547 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:08,600 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:42:08,757 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:08,758 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:08,916 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:08,919 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:42:08,920 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:42:08,956 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:08,956 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:08,969 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:08,977 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:42:09,345 - stcal.saturation.saturation - INFO - Detected 1515 saturated pixels
2026-07-28 16:42:09,379 - stcal.saturation.saturation - INFO - Detected 10 A/D floor pixels
2026-07-28 16:42:09,393 - stpipe.step - INFO - Step saturation done
2026-07-28 16:42:09,550 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:09,551 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:09,708 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:09,709 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:09,865 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:09,868 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:42:10,023 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:10,026 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:42:10,111 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:10,112 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:10,126 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:10,163 - stpipe.step - INFO - Step reset done
2026-07-28 16:42:10,320 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:10,323 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:42:10,360 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:10,361 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:10,373 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:10,618 - stpipe.step - INFO - Step linearity done
2026-07-28 16:42:10,775 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:10,779 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:42:10,793 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:42:10,793 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:42:10,796 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:42:10,801 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:42:10,854 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:42:10,858 - stpipe.step - INFO - Step rscd done
2026-07-28 16:42:11,016 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:11,019 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:42:11,813 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:11,856 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:42:11,857 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:42:11,858 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:42:12,472 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:42:12,629 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:12,629 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:12,787 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:12,788 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:12,946 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:12,948 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:42:12,949 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:42:12,952 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:42:12,955 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:42:13,056 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:42:13,057 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:42:14,816 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:42:21,561 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:42:21,562 - stcal.jump.jump - INFO - Total elapsed time = 8.50477 sec
2026-07-28 16:42:21,581 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.633039
2026-07-28 16:42:21,585 - stpipe.step - INFO - Step jump done
2026-07-28 16:42:21,740 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:21,741 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:21,898 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:21,899 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:22,056 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:22,057 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:22,214 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:22,220 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:42:22,220 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:42:22,245 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:42:22,246 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:42:22,321 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:42:22,329 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:42:22,330 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:42:25,076 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.7439005374908447
2026-07-28 16:42:25,234 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:42:25,393 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:25,397 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:42:25,410 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:42:25,410 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:42:25,563 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:25,587 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:42:25,588 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:42:25,591 - stpipe.step - INFO - Step xply done
2026-07-28 16:42:25,594 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:42:25,748 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:25,751 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:42:25,764 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:42:25,765 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:42:25,917 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2026-07-28 16:42:25,941 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:42:25,945 - stpipe.step - INFO - Step xply done
2026-07-28 16:42:25,948 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:42:26,015 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rateints.fits
2026-07-28 16:42:26,015 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:42:26,016 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:42:26,079 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits
2026-07-28 16:42:26,080 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:42:26,080 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:42:26,106 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:42:26,122 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:42:26,132 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:42:26,146 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:42:26,163 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:42:26,163 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:42:26,165 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:42:26,166 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:42:26,167 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:42:26,167 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:42:26,168 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:42:26,169 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:42:26,170 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:42:26,171 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:42:26,171 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:42:26,172 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:42:26,173 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:42:26,174 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:42:26,175 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:42:26,176 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:42:26,177 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:42:26,178 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:42:26,179 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:42:26,180 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:42:26,181 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:42:26,182 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:42:26,339 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00001_mirifulong_uncal.fits'),).
2026-07-28 16:42:26,359 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:42:26,387 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:42:26,390 - CRDS - INFO - Syncing 2 files
2026-07-28 16:42:26,390 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits 4.2 M bytes (1 / 2 files) (0 / 25.4 M bytes)
2026-07-28 16:42:27,304 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits 21.2 M bytes (2 / 2 files) (4.2 M / 25.4 M bytes)
2026-07-28 16:42:28,612 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:42:28,613 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:42:28,614 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2026-07-28 16:42:28,615 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:42:28,615 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:42:28,616 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:42:28,616 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:42:28,617 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:42:28,617 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:42:28,618 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:42:29,064 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:29,065 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:42:29,065 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:42:29,067 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:42:29,223 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:29,226 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:42:29,258 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:29,314 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:42:29,470 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:29,471 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:29,629 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:29,634 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:42:29,634 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:42:29,671 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:29,672 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:29,685 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:29,693 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:42:30,047 - stcal.saturation.saturation - INFO - Detected 352 saturated pixels
2026-07-28 16:42:30,081 - stcal.saturation.saturation - INFO - Detected 26 A/D floor pixels
2026-07-28 16:42:30,095 - stpipe.step - INFO - Step saturation done
2026-07-28 16:42:30,250 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:30,250 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:30,403 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:30,404 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:30,558 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:30,560 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:42:30,712 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:30,715 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:42:30,799 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:30,799 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:30,812 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:30,849 - stpipe.step - INFO - Step reset done
2026-07-28 16:42:31,005 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:31,008 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2026-07-28 16:42:31,046 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:31,047 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:31,060 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:31,299 - stpipe.step - INFO - Step linearity done
2026-07-28 16:42:31,456 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:31,459 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:42:31,473 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:42:31,473 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:42:31,476 - jwst.rscd.rscd_sub - INFO - There are 20 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:42:31,481 - jwst.rscd.rscd_sub - INFO - Flagged 20 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:42:31,534 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 20
2026-07-28 16:42:31,537 - stpipe.step - INFO - Step rscd done
2026-07-28 16:42:31,693 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:31,696 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:42:32,469 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:32,511 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:42:32,512 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:42:32,512 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:42:33,216 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:42:33,371 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:33,372 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:33,527 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:33,528 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:33,682 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:33,682 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:42:33,683 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:42:33,686 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:42:33,689 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:42:33,788 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:42:33,789 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:42:35,534 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:42:43,502 - stcal.jump.jump - INFO - Total showers= 2
2026-07-28 16:42:43,503 - stcal.jump.jump - INFO - Total elapsed time = 9.714 sec
2026-07-28 16:42:43,523 - jwst.jump.jump_step - INFO - The execution time in seconds: 9.841075
2026-07-28 16:42:43,527 - stpipe.step - INFO - Step jump done
2026-07-28 16:42:43,681 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:43,681 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:43,837 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:43,838 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:43,996 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:43,997 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:44,157 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:44,163 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:42:44,164 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:42:44,189 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:42:44,190 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:42:44,276 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:42:44,284 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:42:44,285 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:42:47,209 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.9225082397460938
2026-07-28 16:42:47,370 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:42:47,531 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:47,534 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:42:47,547 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:42:47,548 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:42:47,706 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:47,731 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:42:47,731 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:42:47,735 - stpipe.step - INFO - Step xply done
2026-07-28 16:42:47,738 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:42:47,896 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:47,899 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:42:47,913 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:42:47,913 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:42:48,068 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2026-07-28 16:42:48,092 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:42:48,096 - stpipe.step - INFO - Step xply done
2026-07-28 16:42:48,100 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:42:48,165 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rateints.fits
2026-07-28 16:42:48,166 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:42:48,166 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:42:48,230 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits
2026-07-28 16:42:48,231 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:42:48,231 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:42:48,258 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:42:48,274 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:42:48,284 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:42:48,298 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:42:48,314 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:42:48,315 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:42:48,316 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:42:48,317 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:42:48,318 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:42:48,319 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:42:48,320 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:42:48,321 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:42:48,321 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:42:48,322 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:42:48,323 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:42:48,323 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:42:48,324 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:42:48,325 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:42:48,326 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:42:48,327 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:42:48,328 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:42:48,329 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:42:48,330 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:42:48,331 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:42:48,332 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:42:48,333 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:42:48,490 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00001_mirifushort_uncal.fits'),).
2026-07-28 16:42:48,509 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:42:48,536 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:42:48,539 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:42:48,540 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:42:48,540 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:42:48,541 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:42:48,542 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:42:48,542 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:42:48,543 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:42:48,543 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:42:48,544 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:42:48,544 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:42:48,993 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:48,993 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:42:48,994 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:42:48,996 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:42:49,154 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:49,157 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:42:49,189 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:49,244 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:42:49,402 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:49,403 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:49,563 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:49,567 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:42:49,567 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:42:49,604 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:49,605 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:49,618 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:49,626 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:42:50,011 - stcal.saturation.saturation - INFO - Detected 1584 saturated pixels
2026-07-28 16:42:50,046 - stcal.saturation.saturation - INFO - Detected 7 A/D floor pixels
2026-07-28 16:42:50,060 - stpipe.step - INFO - Step saturation done
2026-07-28 16:42:50,216 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:50,218 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:50,377 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:50,378 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:50,538 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:50,541 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:42:50,700 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:50,703 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:42:50,788 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:50,789 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:50,803 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:50,840 - stpipe.step - INFO - Step reset done
2026-07-28 16:42:50,999 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:51,002 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:42:51,041 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:51,042 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:51,055 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:51,311 - stpipe.step - INFO - Step linearity done
2026-07-28 16:42:51,469 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:51,472 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:42:51,486 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:42:51,487 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:42:51,489 - jwst.rscd.rscd_sub - INFO - There are 42 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:42:51,495 - jwst.rscd.rscd_sub - INFO - Flagged 42 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:42:51,548 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 42
2026-07-28 16:42:51,551 - stpipe.step - INFO - Step rscd done
2026-07-28 16:42:51,709 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:51,713 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:42:52,489 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:42:52,532 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:42:52,533 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:42:52,533 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:42:53,171 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:42:53,329 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:53,330 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:53,488 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:53,489 - stpipe.step - INFO - Step skipped.
2026-07-28 16:42:53,647 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:42:53,648 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:42:53,649 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:42:53,652 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:42:53,654 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:42:53,756 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:42:53,756 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:42:55,523 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:43:02,664 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:43:02,665 - stcal.jump.jump - INFO - Total elapsed time = 8.90852 sec
2026-07-28 16:43:02,684 - jwst.jump.jump_step - INFO - The execution time in seconds: 9.036187
2026-07-28 16:43:02,688 - stpipe.step - INFO - Step jump done
2026-07-28 16:43:02,850 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:43:02,851 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:03,015 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:43:03,016 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:03,181 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:43:03,181 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:03,346 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:43:03,352 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:43:03,352 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:43:03,379 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:43:03,379 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:43:03,460 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:43:03,465 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:43:03,466 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:43:06,322 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.8541719913482666
2026-07-28 16:43:06,481 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:43:06,645 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:43:06,648 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:43:06,661 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:43:06,661 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:43:06,820 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:43:06,844 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:43:06,845 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:43:06,848 - stpipe.step - INFO - Step xply done
2026-07-28 16:43:06,852 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:43:07,012 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:43:07,015 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:43:07,028 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:43:07,029 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:43:07,189 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2026-07-28 16:43:07,213 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:43:07,217 - stpipe.step - INFO - Step xply done
2026-07-28 16:43:07,220 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:43:07,288 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rateints.fits
2026-07-28 16:43:07,289 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:43:07,290 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:43:07,353 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits
2026-07-28 16:43:07,353 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:43:07,354 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:43:07,380 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:43:07,395 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:43:07,406 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:43:07,420 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:43:07,436 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:43:07,437 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:43:07,439 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:43:07,440 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:43:07,441 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:43:07,441 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:43:07,443 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:43:07,444 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:43:07,445 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:43:07,445 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:43:07,446 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:43:07,447 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:43:07,448 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:43:07,449 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:43:07,450 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:43:07,451 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:43:07,452 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:43:07,453 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:43:07,455 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:43:07,456 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:43:07,456 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:43:07,457 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:43:07,617 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00002_mirifulong_uncal.fits'),).
2026-07-28 16:43:07,636 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:43:07,663 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:43:07,666 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:43:07,666 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:43:07,667 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2026-07-28 16:43:07,667 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:43:07,668 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:43:07,668 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:43:07,669 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:43:07,669 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:43:07,670 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:43:07,670 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:43:08,113 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:08,114 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:43:08,115 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:43:08,117 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:43:08,275 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:08,278 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:43:08,310 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:08,365 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:43:08,522 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:08,523 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:08,682 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:08,686 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:43:08,687 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:43:08,723 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:08,723 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:08,736 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:08,745 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:43:09,121 - stcal.saturation.saturation - INFO - Detected 343 saturated pixels
2026-07-28 16:43:09,156 - stcal.saturation.saturation - INFO - Detected 25 A/D floor pixels
2026-07-28 16:43:09,170 - stpipe.step - INFO - Step saturation done
2026-07-28 16:43:09,330 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:09,331 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:09,493 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:09,494 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:09,657 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:09,659 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:43:09,819 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:09,822 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:43:09,908 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:09,909 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:09,922 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:09,960 - stpipe.step - INFO - Step reset done
2026-07-28 16:43:10,121 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:10,124 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2026-07-28 16:43:10,163 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:10,164 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:10,178 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:10,433 - stpipe.step - INFO - Step linearity done
2026-07-28 16:43:10,595 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:10,598 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:43:10,612 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:43:10,613 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:43:10,615 - jwst.rscd.rscd_sub - INFO - There are 19 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:43:10,621 - jwst.rscd.rscd_sub - INFO - Flagged 19 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:43:10,675 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 19
2026-07-28 16:43:10,679 - stpipe.step - INFO - Step rscd done
2026-07-28 16:43:10,842 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:10,845 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:43:11,646 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:11,695 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:43:11,696 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:43:11,696 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:43:12,396 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:43:12,557 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:12,558 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:12,721 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:12,722 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:12,886 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:12,886 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:43:12,887 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:43:12,890 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:43:12,893 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:43:12,996 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:43:12,997 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:43:14,757 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:43:23,029 - stcal.jump.jump - INFO - Total showers= 4
2026-07-28 16:43:23,030 - stcal.jump.jump - INFO - Total elapsed time = 10.0328 sec
2026-07-28 16:43:23,050 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.163447
2026-07-28 16:43:23,054 - stpipe.step - INFO - Step jump done
2026-07-28 16:43:23,217 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:23,217 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:23,382 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:23,383 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:23,548 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:23,549 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:23,713 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:23,719 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:43:23,720 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:43:23,745 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:43:23,746 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:43:23,831 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:43:23,836 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:43:23,837 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:43:26,882 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.042971134185791
2026-07-28 16:43:27,046 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:43:27,215 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:27,218 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:43:27,232 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:43:27,233 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:43:27,395 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:27,420 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:43:27,421 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:43:27,424 - stpipe.step - INFO - Step xply done
2026-07-28 16:43:27,428 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:43:27,594 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:27,597 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:43:27,611 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:43:27,611 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:43:27,775 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2026-07-28 16:43:27,800 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:43:27,804 - stpipe.step - INFO - Step xply done
2026-07-28 16:43:27,807 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:43:27,875 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rateints.fits
2026-07-28 16:43:27,876 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:43:27,876 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:43:27,942 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits
2026-07-28 16:43:27,943 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:43:27,943 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:43:27,972 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:43:27,988 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:43:27,999 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:43:28,014 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:43:28,031 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:43:28,032 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:43:28,034 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:43:28,035 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:43:28,036 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:43:28,036 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:43:28,037 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:43:28,038 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:43:28,039 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:43:28,040 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:43:28,041 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:43:28,042 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:43:28,043 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:43:28,045 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:43:28,046 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:43:28,047 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:43:28,049 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:43:28,049 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:43:28,051 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:43:28,052 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:43:28,053 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:43:28,053 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:43:28,218 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00002_mirifushort_uncal.fits'),).
2026-07-28 16:43:28,243 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:43:28,276 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:43:28,279 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:43:28,280 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:43:28,280 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:43:28,281 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:43:28,281 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:43:28,282 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:43:28,283 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:43:28,283 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:43:28,284 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:43:28,284 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:43:28,772 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:28,773 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:43:28,774 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:43:28,776 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:43:28,941 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:28,944 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:43:28,977 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:29,038 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:43:29,207 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:29,208 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:29,373 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:29,377 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:43:29,378 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:43:29,415 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:29,416 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:29,429 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:29,438 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:43:29,854 - stcal.saturation.saturation - INFO - Detected 1534 saturated pixels
2026-07-28 16:43:29,890 - stcal.saturation.saturation - INFO - Detected 7 A/D floor pixels
2026-07-28 16:43:29,904 - stpipe.step - INFO - Step saturation done
2026-07-28 16:43:30,068 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:30,069 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:30,234 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:30,235 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:30,400 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:30,403 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:43:30,566 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:30,569 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:43:30,656 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:30,657 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:30,672 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:30,711 - stpipe.step - INFO - Step reset done
2026-07-28 16:43:30,875 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:30,878 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:43:30,918 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:30,919 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:30,932 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:31,196 - stpipe.step - INFO - Step linearity done
2026-07-28 16:43:31,361 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:31,363 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:43:31,378 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:43:31,378 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:43:31,381 - jwst.rscd.rscd_sub - INFO - There are 44 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:43:31,386 - jwst.rscd.rscd_sub - INFO - Flagged 44 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:43:31,440 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 44
2026-07-28 16:43:31,443 - stpipe.step - INFO - Step rscd done
2026-07-28 16:43:31,605 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:31,608 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:43:32,424 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:32,473 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:43:32,474 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:43:32,474 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:43:33,111 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:43:33,274 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:33,275 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:33,440 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:33,441 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:33,606 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:33,607 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:43:33,608 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:43:33,611 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:43:33,614 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:43:33,717 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:43:33,718 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:43:35,501 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:43:42,578 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:43:42,579 - stcal.jump.jump - INFO - Total elapsed time = 8.86052 sec
2026-07-28 16:43:42,598 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.990746
2026-07-28 16:43:42,602 - stpipe.step - INFO - Step jump done
2026-07-28 16:43:42,762 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:42,762 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:42,926 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:42,927 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:43,090 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:43,091 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:43,253 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:43,259 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:43:43,259 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:43:43,285 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:43:43,286 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:43:43,361 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:43:43,369 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:43:43,370 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:43:46,091 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.718669891357422
2026-07-28 16:43:46,251 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:43:46,415 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:46,418 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:43:46,432 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:43:46,432 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:43:46,592 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:46,617 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:43:46,618 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:43:46,621 - stpipe.step - INFO - Step xply done
2026-07-28 16:43:46,624 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:43:46,786 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:46,789 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:43:46,803 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:43:46,803 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:43:46,966 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2026-07-28 16:43:46,990 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:43:46,994 - stpipe.step - INFO - Step xply done
2026-07-28 16:43:46,997 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:43:47,064 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rateints.fits
2026-07-28 16:43:47,065 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:43:47,066 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:43:47,130 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits
2026-07-28 16:43:47,131 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:43:47,131 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:43:47,159 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:43:47,175 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:43:47,186 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:43:47,201 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:43:47,228 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:43:47,229 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:43:47,231 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:43:47,233 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:43:47,234 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:43:47,235 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:43:47,237 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:43:47,240 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:43:47,241 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:43:47,242 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:43:47,243 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:43:47,244 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:43:47,246 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:43:47,247 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:43:47,248 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:43:47,249 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:43:47,250 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:43:47,251 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:43:47,252 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:43:47,253 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:43:47,254 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:43:47,255 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:43:47,422 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00003_mirifulong_uncal.fits'),).
2026-07-28 16:43:47,442 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:43:47,469 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00003_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:43:47,472 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:43:47,473 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:43:47,474 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2026-07-28 16:43:47,474 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:43:47,475 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:43:47,475 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:43:47,476 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:43:47,477 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:43:47,477 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:43:47,478 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:43:47,944 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:47,945 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:43:47,946 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:43:47,948 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:43:48,111 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:48,114 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:43:48,147 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:48,202 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:43:48,364 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:48,365 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:48,529 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:48,533 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:43:48,534 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:43:48,571 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:48,571 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:48,584 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:48,592 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:43:48,986 - stcal.saturation.saturation - INFO - Detected 347 saturated pixels
2026-07-28 16:43:49,021 - stcal.saturation.saturation - INFO - Detected 21 A/D floor pixels
2026-07-28 16:43:49,035 - stpipe.step - INFO - Step saturation done
2026-07-28 16:43:49,200 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:49,201 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:49,364 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:49,365 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:49,529 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:49,532 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:43:49,696 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:49,698 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:43:49,784 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:49,785 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:49,798 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:49,836 - stpipe.step - INFO - Step reset done
2026-07-28 16:43:49,999 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:50,002 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2026-07-28 16:43:50,041 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:50,041 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:50,054 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:50,317 - stpipe.step - INFO - Step linearity done
2026-07-28 16:43:50,480 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:50,483 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:43:50,497 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:43:50,498 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:43:50,500 - jwst.rscd.rscd_sub - INFO - There are 23 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:43:50,506 - jwst.rscd.rscd_sub - INFO - Flagged 23 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:43:50,560 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 23
2026-07-28 16:43:50,563 - stpipe.step - INFO - Step rscd done
2026-07-28 16:43:50,722 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:50,726 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:43:51,519 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:43:51,566 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:43:51,567 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:43:51,568 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:43:52,296 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:43:52,459 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:52,460 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:52,623 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:52,624 - stpipe.step - INFO - Step skipped.
2026-07-28 16:43:52,789 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:43:52,790 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:43:52,792 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:43:52,795 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:43:52,798 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:43:52,902 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:43:52,903 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:43:54,701 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:44:03,166 - stcal.jump.jump - INFO - Total showers= 8
2026-07-28 16:44:03,167 - stcal.jump.jump - INFO - Total elapsed time = 10.264 sec
2026-07-28 16:44:03,186 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.395906
2026-07-28 16:44:03,190 - stpipe.step - INFO - Step jump done
2026-07-28 16:44:03,356 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:44:03,356 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:03,525 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:44:03,526 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:03,688 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:44:03,689 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:03,852 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:44:03,857 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:44:03,858 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:44:03,884 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:44:03,885 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:44:03,960 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:44:03,961 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:44:03,962 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:44:07,028 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.0641539096832275
2026-07-28 16:44:07,187 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:44:07,348 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:44:07,351 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:44:07,364 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:44:07,365 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:44:07,525 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:44:07,549 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:44:07,550 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:44:07,553 - stpipe.step - INFO - Step xply done
2026-07-28 16:44:07,556 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:44:07,714 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:44:07,717 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:44:07,731 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:44:07,731 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:44:07,891 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2026-07-28 16:44:07,915 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:44:07,919 - stpipe.step - INFO - Step xply done
2026-07-28 16:44:07,922 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:44:07,993 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rateints.fits
2026-07-28 16:44:07,994 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:44:07,994 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:44:08,058 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits
2026-07-28 16:44:08,059 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:44:08,059 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:44:08,087 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:44:08,102 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:44:08,114 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:44:08,128 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:44:08,144 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:44:08,146 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:44:08,147 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:44:08,148 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:44:08,149 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:44:08,150 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:44:08,151 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:44:08,153 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:44:08,153 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:44:08,154 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:44:08,155 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:44:08,156 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:44:08,157 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:44:08,158 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:44:08,159 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:44:08,160 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:44:08,162 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:44:08,163 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:44:08,164 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:44:08,164 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:44:08,165 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:44:08,167 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:44:08,328 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00003_mirifushort_uncal.fits'),).
2026-07-28 16:44:08,348 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:44:08,376 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00003_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:44:08,379 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:44:08,379 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:44:08,380 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:44:08,380 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:44:08,381 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:44:08,381 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:44:08,382 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:44:08,382 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:44:08,383 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:44:08,383 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:44:08,836 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:08,837 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:44:08,837 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:44:08,840 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:44:09,002 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:09,005 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:44:09,038 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:09,094 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:44:09,256 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:09,257 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:09,420 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:09,424 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:44:09,424 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:44:09,461 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:09,461 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:09,475 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:09,483 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:44:09,904 - stcal.saturation.saturation - INFO - Detected 1466 saturated pixels
2026-07-28 16:44:09,940 - stcal.saturation.saturation - INFO - Detected 6 A/D floor pixels
2026-07-28 16:44:09,954 - stpipe.step - INFO - Step saturation done
2026-07-28 16:44:10,117 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:10,118 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:10,282 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:10,283 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:10,444 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:10,447 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:44:10,608 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:10,611 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:44:10,699 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:10,700 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:10,713 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:10,751 - stpipe.step - INFO - Step reset done
2026-07-28 16:44:10,915 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:10,918 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:44:10,957 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:10,958 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:10,971 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:11,232 - stpipe.step - INFO - Step linearity done
2026-07-28 16:44:11,394 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:11,397 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:44:11,411 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:44:11,411 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:44:11,414 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:44:11,421 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:44:11,475 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:44:11,478 - stpipe.step - INFO - Step rscd done
2026-07-28 16:44:11,644 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:11,647 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:44:12,442 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:12,490 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:44:12,491 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:44:12,491 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:44:13,117 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:44:13,282 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:13,283 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:13,449 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:13,450 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:13,615 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:13,616 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:44:13,616 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:44:13,619 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:44:13,622 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:44:13,723 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:44:13,724 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:44:15,536 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:44:22,612 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:44:22,613 - stcal.jump.jump - INFO - Total elapsed time = 8.88935 sec
2026-07-28 16:44:22,632 - jwst.jump.jump_step - INFO - The execution time in seconds: 9.016269
2026-07-28 16:44:22,636 - stpipe.step - INFO - Step jump done
2026-07-28 16:44:22,798 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:22,799 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:22,965 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:22,966 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:23,133 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:23,134 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:23,299 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:23,305 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:44:23,306 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:44:23,332 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:44:23,332 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:44:23,406 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:44:23,414 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:44:23,415 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:44:26,157 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.7400927543640137
2026-07-28 16:44:26,318 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:44:26,484 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:26,487 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:44:26,501 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:44:26,501 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:44:26,662 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:26,687 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:44:26,687 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:44:26,691 - stpipe.step - INFO - Step xply done
2026-07-28 16:44:26,694 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:44:26,858 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:26,861 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:44:26,875 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:44:26,875 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:44:27,037 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2026-07-28 16:44:27,062 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:44:27,065 - stpipe.step - INFO - Step xply done
2026-07-28 16:44:27,069 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:44:27,135 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rateints.fits
2026-07-28 16:44:27,135 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:44:27,136 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:44:27,200 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits
2026-07-28 16:44:27,200 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:44:27,201 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:44:27,232 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:44:27,249 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:44:27,261 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:44:27,276 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:44:27,293 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:44:27,294 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:44:27,295 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:44:27,296 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:44:27,297 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:44:27,298 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:44:27,299 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:44:27,300 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:44:27,301 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:44:27,302 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:44:27,303 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:44:27,304 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:44:27,304 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:44:27,306 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:44:27,307 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:44:27,307 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:44:27,309 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:44:27,310 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:44:27,311 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:44:27,313 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:44:27,314 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:44:27,315 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:44:27,481 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00004_mirifulong_uncal.fits'),).
2026-07-28 16:44:27,501 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:44:27,528 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00004_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:44:27,531 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:44:27,531 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:44:27,532 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2026-07-28 16:44:27,532 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:44:27,533 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:44:27,534 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:44:27,534 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:44:27,535 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:44:27,535 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:44:27,536 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:44:27,989 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:27,990 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:44:27,991 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:44:27,993 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:44:28,153 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:28,155 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:44:28,188 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:28,243 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:44:28,409 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:28,409 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:28,573 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:28,577 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:44:28,577 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:44:28,613 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:28,614 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:28,627 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:28,635 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:44:29,026 - stcal.saturation.saturation - INFO - Detected 352 saturated pixels
2026-07-28 16:44:29,060 - stcal.saturation.saturation - INFO - Detected 26 A/D floor pixels
2026-07-28 16:44:29,074 - stpipe.step - INFO - Step saturation done
2026-07-28 16:44:29,237 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:29,238 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:29,401 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:29,402 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:29,566 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:29,569 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:44:29,731 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:29,735 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:44:29,827 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:29,828 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:29,842 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:29,880 - stpipe.step - INFO - Step reset done
2026-07-28 16:44:30,041 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:30,044 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2026-07-28 16:44:30,084 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:30,085 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:30,098 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:30,352 - stpipe.step - INFO - Step linearity done
2026-07-28 16:44:30,513 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:30,516 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:44:30,530 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:44:30,531 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:44:30,534 - jwst.rscd.rscd_sub - INFO - There are 17 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:44:30,539 - jwst.rscd.rscd_sub - INFO - Flagged 17 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:44:30,592 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 17
2026-07-28 16:44:30,595 - stpipe.step - INFO - Step rscd done
2026-07-28 16:44:30,756 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:30,759 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:44:31,554 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:31,597 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:44:31,598 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:44:31,598 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:44:32,315 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:44:32,477 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:32,478 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:32,642 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:32,643 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:32,805 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:32,806 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:44:32,806 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:44:32,809 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:44:32,812 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:44:32,911 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:44:32,911 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:44:34,699 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:44:43,112 - stcal.jump.jump - INFO - Total showers= 1
2026-07-28 16:44:43,113 - stcal.jump.jump - INFO - Total elapsed time = 10.2017 sec
2026-07-28 16:44:43,133 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.326886
2026-07-28 16:44:43,136 - stpipe.step - INFO - Step jump done
2026-07-28 16:44:43,299 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:43,300 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:43,465 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:43,465 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:43,628 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:43,628 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:43,791 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:43,796 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:44:43,797 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:44:43,823 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:44:43,823 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:44:43,897 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:44:43,905 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:44:43,906 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:44:46,828 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.920077085494995
2026-07-28 16:44:46,991 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:44:47,156 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:47,160 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:44:47,173 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:44:47,174 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:44:47,340 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:47,365 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:44:47,366 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:44:47,369 - stpipe.step - INFO - Step xply done
2026-07-28 16:44:47,373 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:44:47,538 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:47,541 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:44:47,555 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:44:47,556 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:44:47,722 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2026-07-28 16:44:47,747 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:44:47,751 - stpipe.step - INFO - Step xply done
2026-07-28 16:44:47,754 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:44:47,822 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rateints.fits
2026-07-28 16:44:47,823 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:44:47,823 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:44:47,888 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits
2026-07-28 16:44:47,889 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:44:47,890 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:44:47,918 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:44:47,934 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:44:47,945 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:44:47,960 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:44:47,977 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:44:47,978 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:44:47,979 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:44:47,980 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:44:47,981 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:44:47,982 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:44:47,983 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:44:47,984 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:44:47,985 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:44:47,986 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:44:47,987 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:44:47,987 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:44:47,988 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:44:47,990 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:44:47,990 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:44:47,991 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:44:47,994 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:44:47,995 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:44:47,997 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:44:47,998 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:44:47,999 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:44:48,000 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:44:48,173 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00004_mirifushort_uncal.fits'),).
2026-07-28 16:44:48,193 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:44:48,219 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00004_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:44:48,223 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:44:48,223 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:44:48,224 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:44:48,225 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:44:48,225 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:44:48,226 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:44:48,226 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:44:48,227 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:44:48,228 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:44:48,228 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:44:48,681 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:48,682 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:44:48,683 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:44:48,685 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:44:48,850 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:48,853 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:44:48,885 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:48,940 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:44:49,105 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:49,106 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:49,270 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:49,274 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:44:49,275 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:44:49,312 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:49,312 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:49,325 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:49,333 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:44:49,747 - stcal.saturation.saturation - INFO - Detected 1451 saturated pixels
2026-07-28 16:44:49,782 - stcal.saturation.saturation - INFO - Detected 8 A/D floor pixels
2026-07-28 16:44:49,796 - stpipe.step - INFO - Step saturation done
2026-07-28 16:44:49,962 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:49,963 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:50,129 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:50,130 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:50,296 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:50,300 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:44:50,463 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:50,466 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:44:50,555 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:50,556 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:50,573 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:50,613 - stpipe.step - INFO - Step reset done
2026-07-28 16:44:50,782 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:50,786 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:44:50,827 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:50,828 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:50,842 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:51,104 - stpipe.step - INFO - Step linearity done
2026-07-28 16:44:51,266 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:51,269 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:44:51,283 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:44:51,284 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:44:51,286 - jwst.rscd.rscd_sub - INFO - There are 38 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:44:51,292 - jwst.rscd.rscd_sub - INFO - Flagged 38 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:44:51,347 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 38
2026-07-28 16:44:51,350 - stpipe.step - INFO - Step rscd done
2026-07-28 16:44:51,515 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:51,518 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:44:52,340 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:44:52,385 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:44:52,385 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:44:52,386 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:44:53,013 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:44:53,174 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:53,175 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:53,343 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:53,344 - stpipe.step - INFO - Step skipped.
2026-07-28 16:44:53,507 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:44:53,508 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:44:53,508 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:44:53,512 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:44:53,514 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:44:53,615 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:44:53,616 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:44:55,385 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:45:02,466 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:45:02,467 - stcal.jump.jump - INFO - Total elapsed time = 8.85086 sec
2026-07-28 16:45:02,486 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.978530
2026-07-28 16:45:02,490 - stpipe.step - INFO - Step jump done
2026-07-28 16:45:02,652 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:45:02,653 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:02,820 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:45:02,821 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:02,987 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:45:02,988 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:03,154 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:45:03,159 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:45:03,160 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:45:03,186 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:45:03,187 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:45:03,262 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:45:03,271 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:45:03,272 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:45:06,045 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.771122694015503
2026-07-28 16:45:06,206 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:45:06,369 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:45:06,372 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:45:06,386 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:45:06,387 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:45:06,551 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:45:06,576 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:45:06,577 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:45:06,580 - stpipe.step - INFO - Step xply done
2026-07-28 16:45:06,584 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:45:06,750 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:45:06,753 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:45:06,767 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:45:06,768 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:45:06,928 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2026-07-28 16:45:06,953 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:45:06,957 - stpipe.step - INFO - Step xply done
2026-07-28 16:45:06,960 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:45:07,026 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rateints.fits
2026-07-28 16:45:07,027 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:45:07,027 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:45:07,090 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits
2026-07-28 16:45:07,091 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:45:07,091 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:45:07,118 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:45:07,133 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:45:07,144 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:45:07,158 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:45:07,174 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:45:07,175 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:45:07,176 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:45:07,177 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:45:07,178 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:45:07,179 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:45:07,180 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:45:07,181 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:45:07,182 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:45:07,182 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:45:07,183 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:45:07,184 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:45:07,185 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:45:07,186 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:45:07,187 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:45:07,188 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:45:07,189 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:45:07,190 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:45:07,191 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:45:07,192 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:45:07,193 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:45:07,194 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:45:07,352 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00001_mirifulong_uncal.fits'),).
2026-07-28 16:45:07,375 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:45:07,402 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:45:07,406 - CRDS - INFO - Syncing 1 files
2026-07-28 16:45:07,407 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits 21.2 M bytes (1 / 1 files) (0 / 21.2 M bytes)
2026-07-28 16:45:08,749 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:45:08,750 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:45:08,751 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2026-07-28 16:45:08,752 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:45:08,752 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:45:08,753 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:45:08,753 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:45:08,754 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:45:08,754 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:45:08,755 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:45:09,208 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:09,209 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:45:09,210 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:45:09,212 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:45:09,371 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:09,374 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:45:09,407 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:09,462 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:45:09,625 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:09,626 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:09,789 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:09,793 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:45:09,793 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:45:09,830 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:09,831 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:09,844 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:09,852 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:45:10,246 - stcal.saturation.saturation - INFO - Detected 316 saturated pixels
2026-07-28 16:45:10,281 - stcal.saturation.saturation - INFO - Detected 28 A/D floor pixels
2026-07-28 16:45:10,295 - stpipe.step - INFO - Step saturation done
2026-07-28 16:45:10,457 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:10,457 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:10,621 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:10,622 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:10,784 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:10,787 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:45:10,945 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:10,948 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:45:11,034 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:11,035 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:11,048 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:11,087 - stpipe.step - INFO - Step reset done
2026-07-28 16:45:11,252 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:11,255 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2026-07-28 16:45:11,295 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:11,296 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:11,309 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:11,577 - stpipe.step - INFO - Step linearity done
2026-07-28 16:45:11,742 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:11,745 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:45:11,759 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:45:11,760 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:45:11,762 - jwst.rscd.rscd_sub - INFO - There are 22 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:45:11,769 - jwst.rscd.rscd_sub - INFO - Flagged 22 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:45:11,825 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 22
2026-07-28 16:45:11,829 - stpipe.step - INFO - Step rscd done
2026-07-28 16:45:11,992 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:11,995 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:45:12,793 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:12,841 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:45:12,841 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:45:12,842 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:45:13,564 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:45:13,728 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:13,728 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:13,892 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:13,893 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:14,059 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:14,060 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:45:14,061 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:45:14,063 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:45:14,066 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:45:14,169 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:45:14,170 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:45:15,932 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:45:24,479 - stcal.jump.jump - INFO - Total showers= 7
2026-07-28 16:45:24,480 - stcal.jump.jump - INFO - Total elapsed time = 10.3096 sec
2026-07-28 16:45:24,499 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.439359
2026-07-28 16:45:24,503 - stpipe.step - INFO - Step jump done
2026-07-28 16:45:24,666 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:24,667 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:24,827 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:24,828 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:24,989 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:24,990 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:25,151 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:25,157 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:45:25,157 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:45:25,183 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:45:25,183 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:45:25,258 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:45:25,263 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:45:25,264 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:45:28,268 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.002317428588867
2026-07-28 16:45:28,430 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:45:28,593 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:28,596 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:45:28,610 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:45:28,610 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:45:28,772 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:28,796 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:45:28,797 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:45:28,801 - stpipe.step - INFO - Step xply done
2026-07-28 16:45:28,804 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:45:28,965 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:28,968 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:45:28,982 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:45:28,983 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:45:29,144 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2026-07-28 16:45:29,168 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:45:29,172 - stpipe.step - INFO - Step xply done
2026-07-28 16:45:29,175 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:45:29,242 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rateints.fits
2026-07-28 16:45:29,243 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:45:29,244 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:45:29,308 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits
2026-07-28 16:45:29,308 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:45:29,309 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:45:29,336 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:45:29,352 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:45:29,363 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:45:29,377 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:45:29,394 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:45:29,395 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:45:29,396 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:45:29,397 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:45:29,398 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:45:29,399 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:45:29,400 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:45:29,401 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:45:29,401 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:45:29,402 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:45:29,403 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:45:29,404 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:45:29,405 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:45:29,406 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:45:29,407 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:45:29,407 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:45:29,409 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:45:29,410 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:45:29,411 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:45:29,412 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:45:29,413 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:45:29,414 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:45:29,577 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00001_mirifushort_uncal.fits'),).
2026-07-28 16:45:29,597 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:45:29,624 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:45:29,628 - CRDS - INFO - Syncing 1 files
2026-07-28 16:45:29,628 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits 8.5 M bytes (1 / 1 files) (0 / 8.5 M bytes)
2026-07-28 16:45:30,665 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:45:30,666 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2026-07-28 16:45:30,667 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:45:30,668 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:45:30,668 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:45:30,669 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:45:30,669 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:45:30,670 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:45:30,671 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:45:30,671 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:45:31,117 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:31,118 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:45:31,119 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:45:31,121 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:45:31,281 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:31,283 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:45:31,316 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:31,369 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:45:31,526 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:31,527 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:31,689 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:31,693 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:45:31,694 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:45:31,731 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:31,732 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:31,745 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:31,753 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:45:32,156 - stcal.saturation.saturation - INFO - Detected 1585 saturated pixels
2026-07-28 16:45:32,191 - stcal.saturation.saturation - INFO - Detected 9 A/D floor pixels
2026-07-28 16:45:32,205 - stpipe.step - INFO - Step saturation done
2026-07-28 16:45:32,366 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:32,366 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:32,529 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:32,531 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:32,693 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:32,696 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:45:32,860 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:32,864 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:45:32,947 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:32,948 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:32,961 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:32,998 - stpipe.step - INFO - Step reset done
2026-07-28 16:45:33,158 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:33,161 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:45:33,199 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:33,200 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:33,213 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:33,462 - stpipe.step - INFO - Step linearity done
2026-07-28 16:45:33,620 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:33,623 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:45:33,637 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:45:33,638 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:45:33,640 - jwst.rscd.rscd_sub - INFO - There are 42 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:45:33,646 - jwst.rscd.rscd_sub - INFO - Flagged 42 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:45:33,699 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 42
2026-07-28 16:45:33,703 - stpipe.step - INFO - Step rscd done
2026-07-28 16:45:33,861 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:33,864 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:45:34,636 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:34,679 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:45:34,680 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:45:34,681 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:45:35,310 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:45:35,470 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:35,470 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:35,633 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:35,634 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:35,796 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:35,796 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:45:35,797 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:45:35,800 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:45:35,803 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:45:35,895 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:45:35,896 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:45:37,631 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:45:44,582 - stcal.jump.jump - INFO - Total showers= 2
2026-07-28 16:45:44,583 - stcal.jump.jump - INFO - Total elapsed time = 8.6876 sec
2026-07-28 16:45:44,603 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.806277
2026-07-28 16:45:44,606 - stpipe.step - INFO - Step jump done
2026-07-28 16:45:44,763 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:44,764 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:44,926 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:44,927 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:45,088 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:45,089 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:45,252 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:45,257 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:45:45,258 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:45:45,286 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:45:45,287 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:45:45,369 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:45:45,373 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:45:45,374 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:45:48,176 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.8003740310668945
2026-07-28 16:45:48,338 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:45:48,501 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:48,505 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:45:48,521 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:45:48,521 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:45:48,679 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:48,704 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:45:48,704 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:45:48,708 - stpipe.step - INFO - Step xply done
2026-07-28 16:45:48,711 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:45:48,868 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:48,871 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:45:48,887 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:45:48,887 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:45:49,044 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2026-07-28 16:45:49,068 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:45:49,072 - stpipe.step - INFO - Step xply done
2026-07-28 16:45:49,075 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:45:49,140 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rateints.fits
2026-07-28 16:45:49,141 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:45:49,142 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:45:49,204 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits
2026-07-28 16:45:49,205 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:45:49,206 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:45:49,234 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:45:49,249 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:45:49,260 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:45:49,273 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:45:49,290 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:45:49,291 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:45:49,292 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:45:49,293 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:45:49,294 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:45:49,294 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:45:49,295 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:45:49,296 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:45:49,297 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:45:49,299 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:45:49,300 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:45:49,301 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:45:49,302 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:45:49,303 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:45:49,305 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:45:49,305 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:45:49,307 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:45:49,308 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:45:49,309 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:45:49,310 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:45:49,311 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:45:49,312 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:45:49,472 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00002_mirifulong_uncal.fits'),).
2026-07-28 16:45:49,491 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:45:49,518 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:45:49,521 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:45:49,522 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:45:49,522 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2026-07-28 16:45:49,523 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:45:49,524 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:45:49,524 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:45:49,525 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:45:49,526 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:45:49,526 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:45:49,526 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:45:49,973 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:49,974 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:45:49,975 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:45:49,977 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:45:50,135 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:50,138 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:45:50,170 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:50,225 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:45:50,385 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:50,386 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:50,545 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:50,549 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:45:50,550 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:45:50,585 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:50,586 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:50,599 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:50,608 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:45:50,977 - stcal.saturation.saturation - INFO - Detected 315 saturated pixels
2026-07-28 16:45:51,011 - stcal.saturation.saturation - INFO - Detected 23 A/D floor pixels
2026-07-28 16:45:51,025 - stpipe.step - INFO - Step saturation done
2026-07-28 16:45:51,186 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:51,187 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:51,348 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:51,349 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:51,512 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:51,515 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:45:51,676 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:51,679 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:45:51,763 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:51,764 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:51,777 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:51,814 - stpipe.step - INFO - Step reset done
2026-07-28 16:45:51,977 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:51,980 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2026-07-28 16:45:52,022 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:52,023 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:52,038 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:52,312 - stpipe.step - INFO - Step linearity done
2026-07-28 16:45:52,485 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:52,489 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:45:52,503 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:45:52,504 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:45:52,507 - jwst.rscd.rscd_sub - INFO - There are 19 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:45:52,512 - jwst.rscd.rscd_sub - INFO - Flagged 19 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:45:52,565 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 19
2026-07-28 16:45:52,569 - stpipe.step - INFO - Step rscd done
2026-07-28 16:45:52,729 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:52,732 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:45:53,516 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:45:53,564 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:45:53,565 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:45:53,565 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:45:54,263 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:45:54,422 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:54,423 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:54,583 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:54,583 - stpipe.step - INFO - Step skipped.
2026-07-28 16:45:54,746 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:45:54,746 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:45:54,747 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:45:54,750 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:45:54,752 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:45:54,851 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:45:54,852 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:45:56,575 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:46:04,950 - stcal.jump.jump - INFO - Total showers= 5
2026-07-28 16:46:04,950 - stcal.jump.jump - INFO - Total elapsed time = 10.0984 sec
2026-07-28 16:46:04,969 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.223186
2026-07-28 16:46:04,973 - stpipe.step - INFO - Step jump done
2026-07-28 16:46:05,132 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:46:05,133 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:05,294 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:46:05,294 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:05,455 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:46:05,456 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:05,620 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:46:05,625 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:46:05,625 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:46:05,651 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:46:05,652 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:46:05,726 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:46:05,727 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:46:05,728 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:46:08,763 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.0332555770874023
2026-07-28 16:46:08,923 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:46:09,087 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:46:09,090 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:46:09,104 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:46:09,105 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:46:09,267 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:46:09,292 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:46:09,293 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:46:09,296 - stpipe.step - INFO - Step xply done
2026-07-28 16:46:09,300 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:46:09,462 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:46:09,466 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:46:09,488 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:46:09,488 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:46:09,677 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2026-07-28 16:46:09,701 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:46:09,705 - stpipe.step - INFO - Step xply done
2026-07-28 16:46:09,709 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:46:09,775 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rateints.fits
2026-07-28 16:46:09,776 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:46:09,777 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:46:09,841 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits
2026-07-28 16:46:09,841 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:46:09,842 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:46:09,869 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:46:09,885 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:46:09,896 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:46:09,910 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:46:09,927 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:46:09,928 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:46:09,929 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:46:09,930 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:46:09,931 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:46:09,932 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:46:09,933 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:46:09,934 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:46:09,935 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:46:09,936 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:46:09,936 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:46:09,937 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:46:09,939 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:46:09,940 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:46:09,941 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:46:09,942 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:46:09,944 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:46:09,945 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:46:09,946 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:46:09,947 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:46:09,948 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:46:09,949 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:46:10,112 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00002_mirifushort_uncal.fits'),).
2026-07-28 16:46:10,132 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:46:10,159 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:46:10,162 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:46:10,162 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2026-07-28 16:46:10,163 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:46:10,163 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:46:10,164 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:46:10,164 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:46:10,165 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:46:10,166 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:46:10,166 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:46:10,167 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:46:10,616 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:10,618 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:46:10,618 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:46:10,620 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:46:10,781 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:10,783 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:46:10,816 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:10,871 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:46:11,032 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:11,033 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:11,198 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:11,202 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:46:11,202 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:46:11,239 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:11,240 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:11,253 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:11,261 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:46:11,664 - stcal.saturation.saturation - INFO - Detected 1516 saturated pixels
2026-07-28 16:46:11,700 - stcal.saturation.saturation - INFO - Detected 7 A/D floor pixels
2026-07-28 16:46:11,714 - stpipe.step - INFO - Step saturation done
2026-07-28 16:46:11,875 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:11,875 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:12,037 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:12,038 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:12,201 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:12,204 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:46:12,365 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:12,368 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:46:12,454 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:12,455 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:12,468 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:12,506 - stpipe.step - INFO - Step reset done
2026-07-28 16:46:12,668 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:12,671 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:46:12,709 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:12,710 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:12,723 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:12,979 - stpipe.step - INFO - Step linearity done
2026-07-28 16:46:13,142 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:13,145 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:46:13,159 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:46:13,160 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:46:13,162 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:46:13,168 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:46:13,222 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:46:13,225 - stpipe.step - INFO - Step rscd done
2026-07-28 16:46:13,387 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:13,390 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:46:14,186 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:14,231 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:46:14,232 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:46:14,233 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:46:14,876 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:46:15,037 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:15,038 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:15,200 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:15,201 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:15,365 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:15,366 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:46:15,366 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:46:15,369 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:46:15,372 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:46:15,467 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:46:15,468 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:46:17,214 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:46:24,097 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:46:24,097 - stcal.jump.jump - INFO - Total elapsed time = 8.62971 sec
2026-07-28 16:46:24,117 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.750675
2026-07-28 16:46:24,120 - stpipe.step - INFO - Step jump done
2026-07-28 16:46:24,278 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:24,279 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:24,439 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:24,440 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:24,600 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:24,601 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:24,765 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:24,770 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:46:24,771 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:46:24,799 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:46:24,800 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:46:24,887 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:46:24,895 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:46:24,896 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:46:27,623 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.726393222808838
2026-07-28 16:46:27,782 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:46:27,945 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:27,949 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:46:27,964 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:46:27,964 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:46:28,123 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:28,147 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:46:28,148 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:46:28,151 - stpipe.step - INFO - Step xply done
2026-07-28 16:46:28,154 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:46:28,312 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:28,315 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:46:28,330 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:46:28,331 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:46:28,488 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2026-07-28 16:46:28,513 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:46:28,516 - stpipe.step - INFO - Step xply done
2026-07-28 16:46:28,520 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:46:28,586 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rateints.fits
2026-07-28 16:46:28,587 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:46:28,587 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:46:28,650 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits
2026-07-28 16:46:28,651 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:46:28,652 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:46:28,679 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:46:28,695 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:46:28,705 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:46:28,719 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:46:28,736 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:46:28,737 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:46:28,738 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:46:28,739 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:46:28,740 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:46:28,741 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:46:28,742 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:46:28,743 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:46:28,744 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:46:28,745 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:46:28,746 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:46:28,746 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:46:28,747 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:46:28,748 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:46:28,749 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:46:28,750 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:46:28,752 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:46:28,752 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:46:28,753 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:46:28,754 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:46:28,755 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:46:28,757 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:46:28,920 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00003_mirifulong_uncal.fits'),).
2026-07-28 16:46:28,939 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:46:28,966 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00003_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:46:28,969 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:46:28,970 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:46:28,971 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2026-07-28 16:46:28,971 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:46:28,972 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:46:28,972 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:46:28,973 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:46:28,973 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:46:28,974 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:46:28,974 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:46:29,445 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:29,446 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:46:29,446 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:46:29,448 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:46:29,609 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:29,611 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:46:29,644 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:29,699 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:46:29,861 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:29,862 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:30,025 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:30,029 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:46:30,030 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:46:30,065 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:30,066 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:30,079 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:30,087 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:46:30,456 - stcal.saturation.saturation - INFO - Detected 317 saturated pixels
2026-07-28 16:46:30,491 - stcal.saturation.saturation - INFO - Detected 22 A/D floor pixels
2026-07-28 16:46:30,505 - stpipe.step - INFO - Step saturation done
2026-07-28 16:46:30,664 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:30,665 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:30,828 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:30,828 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:30,989 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:30,992 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:46:31,150 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:31,153 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:46:31,238 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:31,238 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:31,252 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:31,290 - stpipe.step - INFO - Step reset done
2026-07-28 16:46:31,450 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:31,454 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2026-07-28 16:46:31,491 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:31,492 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:31,505 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:31,753 - stpipe.step - INFO - Step linearity done
2026-07-28 16:46:31,914 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:31,917 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:46:31,931 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:46:31,932 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:46:31,934 - jwst.rscd.rscd_sub - INFO - There are 23 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:46:31,940 - jwst.rscd.rscd_sub - INFO - Flagged 23 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:46:31,993 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 23
2026-07-28 16:46:31,996 - stpipe.step - INFO - Step rscd done
2026-07-28 16:46:32,157 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:32,161 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:46:32,942 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:32,985 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:46:32,986 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:46:32,987 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:46:33,691 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:46:33,852 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:33,852 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:34,013 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:34,014 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:34,177 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:34,178 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:46:34,179 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:46:34,182 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:46:34,185 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:46:34,285 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:46:34,286 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:46:36,042 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:46:44,523 - stcal.jump.jump - INFO - Total showers= 9
2026-07-28 16:46:44,524 - stcal.jump.jump - INFO - Total elapsed time = 10.2384 sec
2026-07-28 16:46:44,543 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.365124
2026-07-28 16:46:44,547 - stpipe.step - INFO - Step jump done
2026-07-28 16:46:44,707 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:44,708 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:44,871 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:44,872 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:45,034 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:45,035 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:45,200 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:45,205 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:46:45,205 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:46:45,231 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:46:45,231 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:46:45,305 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:46:45,310 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:46:45,311 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:46:48,288 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.975120782852173
2026-07-28 16:46:48,449 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:46:48,614 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:48,617 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:46:48,632 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:46:48,632 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:46:48,810 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:48,835 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:46:48,835 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:46:48,839 - stpipe.step - INFO - Step xply done
2026-07-28 16:46:48,842 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:46:49,006 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:49,009 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:46:49,023 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:46:49,024 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:46:49,186 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2026-07-28 16:46:49,211 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:46:49,215 - stpipe.step - INFO - Step xply done
2026-07-28 16:46:49,218 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:46:49,283 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rateints.fits
2026-07-28 16:46:49,284 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:46:49,285 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:46:49,349 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits
2026-07-28 16:46:49,349 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:46:49,350 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:46:49,377 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:46:49,393 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:46:49,403 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:46:49,418 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:46:49,435 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:46:49,436 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:46:49,438 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:46:49,439 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:46:49,440 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:46:49,441 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:46:49,441 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:46:49,442 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:46:49,443 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:46:49,444 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:46:49,445 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:46:49,446 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:46:49,447 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:46:49,448 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:46:49,449 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:46:49,450 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:46:49,452 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:46:49,453 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:46:49,454 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:46:49,455 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:46:49,456 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:46:49,456 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:46:49,619 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00003_mirifushort_uncal.fits'),).
2026-07-28 16:46:49,639 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:46:49,666 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00003_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:46:49,669 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:46:49,670 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2026-07-28 16:46:49,671 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:46:49,671 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:46:49,672 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:46:49,672 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:46:49,673 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:46:49,674 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:46:49,674 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:46:49,675 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:46:50,132 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:50,133 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:46:50,133 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:46:50,136 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:46:50,297 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:50,301 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:46:50,333 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:50,388 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:46:50,550 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:50,551 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:50,713 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:50,718 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:46:50,718 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:46:50,755 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:50,756 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:50,769 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:50,777 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:46:51,145 - stcal.saturation.saturation - INFO - Detected 1446 saturated pixels
2026-07-28 16:46:51,180 - stcal.saturation.saturation - INFO - Detected 9 A/D floor pixels
2026-07-28 16:46:51,194 - stpipe.step - INFO - Step saturation done
2026-07-28 16:46:51,359 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:51,360 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:51,524 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:51,525 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:51,686 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:51,689 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:46:51,852 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:51,854 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:46:51,938 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:51,939 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:51,951 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:51,989 - stpipe.step - INFO - Step reset done
2026-07-28 16:46:52,148 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:52,151 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:46:52,190 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:52,191 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:52,203 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:52,450 - stpipe.step - INFO - Step linearity done
2026-07-28 16:46:52,612 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:52,615 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:46:52,630 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:46:52,630 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:46:52,633 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:46:52,639 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:46:52,692 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:46:52,696 - stpipe.step - INFO - Step rscd done
2026-07-28 16:46:52,857 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:52,860 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:46:53,630 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:46:53,672 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:46:53,673 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:46:53,674 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:46:54,294 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:46:54,454 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:54,455 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:54,618 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:54,619 - stpipe.step - INFO - Step skipped.
2026-07-28 16:46:54,783 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:46:54,784 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:46:54,784 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:46:54,787 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:46:54,790 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:46:54,884 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:46:54,885 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:46:56,677 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:47:03,457 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:47:03,457 - stcal.jump.jump - INFO - Total elapsed time = 8.57255 sec
2026-07-28 16:47:03,477 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.693109
2026-07-28 16:47:03,481 - stpipe.step - INFO - Step jump done
2026-07-28 16:47:03,639 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:47:03,640 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:03,813 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:47:03,814 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:03,977 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:47:03,977 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:04,137 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:47:04,142 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:47:04,143 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:47:04,170 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:47:04,171 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:47:04,253 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:47:04,261 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:47:04,262 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:47:06,963 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.699816942214966
2026-07-28 16:47:07,125 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:47:07,290 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:47:07,293 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:47:07,309 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:47:07,310 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:47:07,471 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:47:07,496 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:47:07,497 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:47:07,500 - stpipe.step - INFO - Step xply done
2026-07-28 16:47:07,504 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:47:07,664 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:47:07,667 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:47:07,682 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:47:07,683 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:47:07,845 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2026-07-28 16:47:07,870 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:47:07,873 - stpipe.step - INFO - Step xply done
2026-07-28 16:47:07,878 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:47:07,944 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rateints.fits
2026-07-28 16:47:07,945 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:47:07,946 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:47:08,011 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits
2026-07-28 16:47:08,012 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:47:08,012 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:47:08,040 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:47:08,055 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:47:08,066 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:47:08,081 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:47:08,098 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:47:08,099 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:47:08,100 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:47:08,101 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:47:08,102 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:47:08,103 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:47:08,103 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:47:08,105 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:47:08,106 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:47:08,107 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:47:08,108 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:47:08,109 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:47:08,110 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:47:08,111 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:47:08,112 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:47:08,113 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:47:08,115 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:47:08,115 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:47:08,117 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:47:08,118 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:47:08,118 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:47:08,119 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:47:08,282 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00004_mirifulong_uncal.fits'),).
2026-07-28 16:47:08,301 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:47:08,327 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00004_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:47:08,330 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:47:08,331 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:47:08,331 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2026-07-28 16:47:08,332 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:47:08,333 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:47:08,333 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:47:08,334 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:47:08,334 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:47:08,335 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:47:08,336 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:47:08,789 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:08,790 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:47:08,791 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:47:08,793 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:47:08,954 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:08,956 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:47:08,988 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:09,042 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:47:09,204 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:09,205 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:09,366 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:09,370 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:47:09,370 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:47:09,407 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:09,408 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:09,420 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:09,429 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:47:09,808 - stcal.saturation.saturation - INFO - Detected 315 saturated pixels
2026-07-28 16:47:09,843 - stcal.saturation.saturation - INFO - Detected 28 A/D floor pixels
2026-07-28 16:47:09,857 - stpipe.step - INFO - Step saturation done
2026-07-28 16:47:10,015 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:10,018 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:10,179 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:10,180 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:10,345 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:10,347 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:47:10,510 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:10,513 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:47:10,596 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:10,597 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:10,610 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:10,647 - stpipe.step - INFO - Step reset done
2026-07-28 16:47:10,807 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:10,810 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2026-07-28 16:47:10,847 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:10,848 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:10,861 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:11,109 - stpipe.step - INFO - Step linearity done
2026-07-28 16:47:11,266 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:11,270 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:47:11,283 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:47:11,284 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:47:11,286 - jwst.rscd.rscd_sub - INFO - There are 16 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:47:11,292 - jwst.rscd.rscd_sub - INFO - Flagged 16 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:47:11,347 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 16
2026-07-28 16:47:11,350 - stpipe.step - INFO - Step rscd done
2026-07-28 16:47:11,513 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:11,516 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:47:12,299 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:12,342 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:47:12,343 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:47:12,344 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:47:13,077 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:47:13,246 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:13,247 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:13,406 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:13,406 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:13,568 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:13,568 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:47:13,569 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:47:13,572 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:47:13,575 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:47:13,676 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:47:13,677 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:47:15,387 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:47:23,519 - stcal.jump.jump - INFO - Total showers= 8
2026-07-28 16:47:23,519 - stcal.jump.jump - INFO - Total elapsed time = 9.84253 sec
2026-07-28 16:47:23,539 - jwst.jump.jump_step - INFO - The execution time in seconds: 9.970207
2026-07-28 16:47:23,542 - stpipe.step - INFO - Step jump done
2026-07-28 16:47:23,701 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:23,702 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:23,867 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:23,867 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:24,030 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:24,031 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:24,191 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:24,197 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:47:24,197 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:47:24,223 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:47:24,224 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:47:24,296 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:47:24,304 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:47:24,305 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:47:27,171 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.8642144203186035
2026-07-28 16:47:27,330 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:47:27,494 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:27,497 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:47:27,510 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:47:27,511 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:47:27,670 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:27,694 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:47:27,695 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:47:27,698 - stpipe.step - INFO - Step xply done
2026-07-28 16:47:27,701 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:47:27,860 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:27,863 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:47:27,876 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:47:27,877 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:47:28,039 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2026-07-28 16:47:28,064 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:47:28,067 - stpipe.step - INFO - Step xply done
2026-07-28 16:47:28,071 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:47:28,136 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rateints.fits
2026-07-28 16:47:28,137 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:47:28,138 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:47:28,207 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits
2026-07-28 16:47:28,208 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:47:28,208 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:47:28,235 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:47:28,251 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:47:28,262 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:47:28,276 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:47:28,292 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:47:28,293 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:47:28,295 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:47:28,296 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:47:28,297 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:47:28,298 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:47:28,299 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:47:28,300 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:47:28,301 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:47:28,302 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:47:28,303 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:47:28,304 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:47:28,305 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:47:28,306 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:47:28,307 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:47:28,308 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:47:28,309 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:47:28,310 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:47:28,311 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:47:28,312 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:47:28,313 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:47:28,314 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:47:28,484 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00004_mirifushort_uncal.fits'),).
2026-07-28 16:47:28,506 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:47:28,534 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00004_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:47:28,538 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:47:28,538 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2026-07-28 16:47:28,539 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:47:28,540 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:47:28,540 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:47:28,541 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:47:28,542 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:47:28,542 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:47:28,543 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:47:28,543 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:47:28,990 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:28,991 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:47:28,992 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:47:28,994 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:47:29,154 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:29,157 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:47:29,190 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:29,244 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:47:29,402 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:29,403 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:29,561 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:29,565 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:47:29,566 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:47:29,603 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:29,604 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:29,617 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:29,625 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:47:30,022 - stcal.saturation.saturation - INFO - Detected 1408 saturated pixels
2026-07-28 16:47:30,057 - stcal.saturation.saturation - INFO - Detected 5 A/D floor pixels
2026-07-28 16:47:30,071 - stpipe.step - INFO - Step saturation done
2026-07-28 16:47:30,232 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:30,233 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:30,394 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:30,395 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:30,555 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:30,558 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:47:30,716 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:30,719 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:47:30,804 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:30,805 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:30,818 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:30,856 - stpipe.step - INFO - Step reset done
2026-07-28 16:47:31,019 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:31,022 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:47:31,094 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:31,095 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:31,108 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:31,356 - stpipe.step - INFO - Step linearity done
2026-07-28 16:47:31,517 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:31,520 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:47:31,533 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:47:31,534 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:47:31,536 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:47:31,542 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:47:31,595 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:47:31,598 - stpipe.step - INFO - Step rscd done
2026-07-28 16:47:31,761 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:31,765 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:47:32,562 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:32,604 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:47:32,605 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:47:32,605 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:47:33,276 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:47:33,436 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:33,437 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:33,601 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:33,601 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:33,763 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:33,763 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:47:33,764 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:47:33,767 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:47:33,770 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:47:33,869 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:47:33,870 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:47:35,607 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:47:42,463 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:47:42,464 - stcal.jump.jump - INFO - Total elapsed time = 8.59445 sec
2026-07-28 16:47:42,483 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.719578
2026-07-28 16:47:42,487 - stpipe.step - INFO - Step jump done
2026-07-28 16:47:42,644 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:42,645 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:42,803 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:42,804 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:42,965 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:42,966 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:43,128 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:43,133 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:47:43,134 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:47:43,162 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:47:43,162 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:47:43,247 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:47:43,255 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:47:43,256 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:47:45,980 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.7217628955841064
2026-07-28 16:47:46,138 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:47:46,303 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:46,306 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:47:46,321 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:47:46,322 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:47:46,481 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:46,505 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:47:46,506 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:47:46,509 - stpipe.step - INFO - Step xply done
2026-07-28 16:47:46,512 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:47:46,671 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:46,674 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:47:46,690 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:47:46,690 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:47:46,851 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2026-07-28 16:47:46,876 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:47:46,879 - stpipe.step - INFO - Step xply done
2026-07-28 16:47:46,883 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:47:46,948 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rateints.fits
2026-07-28 16:47:46,948 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:47:46,949 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:47:47,012 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits
2026-07-28 16:47:47,013 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:47:47,014 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
Calibrating Background Files#
Look for input background files and run calwebb_detector1 pipeline using the call method.
# Now let's look for input files of the form *uncal.fits from the background
# observations
sstring = os.path.join(uncal_bgdir, 'jw*mirifu*uncal.fits')
uncal_files = np.array(sorted(glob.glob(sstring)))
# Check that these are the band/channel to use
uncal_files = select_ch_band_files(uncal_files, use_ch, use_band)
print('Found ' + str(len(uncal_files)) + ' background input files')
Found 12 background input files
# Run the pipeline on these input files by a simple loop over files using
# our custom parameter dictionary
if dodet1bg:
for file in uncal_files:
Detector1Pipeline.call(file, steps=det1dict, save_results=True, output_dir=det1_bgdir)
else:
print('Skipping Detector1 processing for BG data')
2026-07-28 16:47:47,050 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:47:47,066 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:47:47,077 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:47:47,091 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:47:47,108 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:47:47,109 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:47:47,110 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:47:47,111 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:47:47,112 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:47:47,113 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:47:47,114 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:47:47,115 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:47:47,116 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:47:47,117 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:47:47,117 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:47:47,118 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:47:47,119 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:47:47,120 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:47:47,121 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:47:47,122 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:47:47,123 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:47:47,124 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:47:47,125 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:47:47,126 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:47:47,127 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:47:47,128 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:47:47,289 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00001_mirifulong_uncal.fits'),).
2026-07-28 16:47:47,308 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:47:47,335 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:47:47,339 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:47:47,339 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2026-07-28 16:47:47,340 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2026-07-28 16:47:47,341 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:47:47,341 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:47:47,342 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:47:47,342 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:47:47,343 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:47:47,343 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:47:47,344 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:47:47,789 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:47,790 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:47:47,791 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:47:47,793 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:47:47,952 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:47,955 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:47:47,987 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:48,041 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:47:48,199 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:48,200 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:48,358 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:48,363 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:47:48,363 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:47:48,399 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:48,400 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:48,412 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:48,420 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:47:48,769 - stcal.saturation.saturation - INFO - Detected 326 saturated pixels
2026-07-28 16:47:48,803 - stcal.saturation.saturation - INFO - Detected 26 A/D floor pixels
2026-07-28 16:47:48,816 - stpipe.step - INFO - Step saturation done
2026-07-28 16:47:48,976 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:48,977 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:49,140 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:49,141 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:49,303 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:49,306 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:47:49,465 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:49,468 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:47:49,552 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:49,553 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:49,566 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:49,603 - stpipe.step - INFO - Step reset done
2026-07-28 16:47:49,764 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:49,767 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2026-07-28 16:47:49,805 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:49,806 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:49,818 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:50,062 - stpipe.step - INFO - Step linearity done
2026-07-28 16:47:50,225 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:50,228 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:47:50,243 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:47:50,244 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:47:50,247 - jwst.rscd.rscd_sub - INFO - There are 26 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:47:50,252 - jwst.rscd.rscd_sub - INFO - Flagged 26 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:47:50,306 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 26
2026-07-28 16:47:50,309 - stpipe.step - INFO - Step rscd done
2026-07-28 16:47:50,469 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:50,472 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:47:51,248 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:47:51,291 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:47:51,292 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:47:51,292 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:47:52,025 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:47:52,188 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:52,189 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:52,352 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:52,354 - stpipe.step - INFO - Step skipped.
2026-07-28 16:47:52,517 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:47:52,518 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:47:52,519 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:47:52,521 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:47:52,524 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:47:52,618 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:47:52,619 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:47:54,384 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:48:02,717 - stcal.jump.jump - INFO - Total showers= 11
2026-07-28 16:48:02,717 - stcal.jump.jump - INFO - Total elapsed time = 10.0987 sec
2026-07-28 16:48:02,736 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.218316
2026-07-28 16:48:02,740 - stpipe.step - INFO - Step jump done
2026-07-28 16:48:02,900 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:48:02,901 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:03,065 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:48:03,066 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:03,229 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:48:03,230 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:03,392 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:48:03,398 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:48:03,399 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:48:03,427 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:48:03,428 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:48:03,511 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:48:03,512 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:48:03,513 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:48:06,574 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.05997896194458
2026-07-28 16:48:06,734 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:48:06,899 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:48:06,902 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:48:06,917 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:48:06,918 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:48:07,080 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:48:07,105 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:48:07,106 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:48:07,110 - stpipe.step - INFO - Step xply done
2026-07-28 16:48:07,113 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:48:07,273 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:48:07,277 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:48:07,292 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:48:07,293 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:48:07,453 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2026-07-28 16:48:07,477 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:48:07,481 - stpipe.step - INFO - Step xply done
2026-07-28 16:48:07,484 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:48:07,551 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rateints.fits
2026-07-28 16:48:07,551 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:48:07,552 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:48:07,615 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits
2026-07-28 16:48:07,616 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:48:07,616 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:48:07,644 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:48:07,659 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:48:07,670 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:48:07,684 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:48:07,701 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:48:07,702 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:48:07,703 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:48:07,704 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:48:07,705 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:48:07,706 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:48:07,707 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:48:07,708 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:48:07,709 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:48:07,710 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:48:07,711 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:48:07,712 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:48:07,713 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:48:07,714 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:48:07,715 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:48:07,716 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:48:07,717 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:48:07,718 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:48:07,719 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:48:07,720 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:48:07,721 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:48:07,722 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:48:07,883 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00001_mirifushort_uncal.fits'),).
2026-07-28 16:48:07,903 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:48:07,930 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:48:07,933 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:48:07,934 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:48:07,934 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:48:07,935 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:48:07,936 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:48:07,936 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:48:07,937 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:48:07,937 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:48:07,938 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:48:07,938 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:48:08,382 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:08,383 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:48:08,383 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:48:08,385 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:48:08,543 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:08,545 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:48:08,578 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:08,633 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:48:08,793 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:08,794 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:08,957 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:08,961 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:48:08,962 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:48:08,999 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:09,000 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:09,013 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:09,021 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:48:09,411 - stcal.saturation.saturation - INFO - Detected 1697 saturated pixels
2026-07-28 16:48:09,446 - stcal.saturation.saturation - INFO - Detected 9 A/D floor pixels
2026-07-28 16:48:09,461 - stpipe.step - INFO - Step saturation done
2026-07-28 16:48:09,624 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:09,624 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:09,790 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:09,791 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:09,959 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:09,962 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:48:10,124 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:10,127 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:48:10,214 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:10,215 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:10,228 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:10,266 - stpipe.step - INFO - Step reset done
2026-07-28 16:48:10,428 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:10,431 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:48:10,469 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:10,469 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:10,483 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:10,729 - stpipe.step - INFO - Step linearity done
2026-07-28 16:48:10,891 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:10,894 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:48:10,908 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:48:10,909 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:48:10,911 - jwst.rscd.rscd_sub - INFO - There are 38 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:48:10,917 - jwst.rscd.rscd_sub - INFO - Flagged 38 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:48:10,970 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 38
2026-07-28 16:48:10,974 - stpipe.step - INFO - Step rscd done
2026-07-28 16:48:11,135 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:11,138 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:48:11,931 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:11,977 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:48:11,978 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:48:11,978 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:48:12,612 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:48:12,771 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:12,772 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:12,933 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:12,934 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:13,097 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:13,098 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:48:13,098 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:48:13,102 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:48:13,104 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:48:13,204 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:48:13,205 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:48:14,958 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:48:21,991 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:48:21,991 - stcal.jump.jump - INFO - Total elapsed time = 8.78628 sec
2026-07-28 16:48:22,011 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.913299
2026-07-28 16:48:22,015 - stpipe.step - INFO - Step jump done
2026-07-28 16:48:22,173 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:22,174 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:22,336 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:22,337 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:22,500 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:22,500 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:22,663 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:22,668 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:48:22,669 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:48:22,694 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:48:22,694 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:48:22,769 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:48:22,774 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:48:22,775 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:48:25,581 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.8037772178649902
2026-07-28 16:48:25,745 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:48:25,915 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:25,919 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:48:25,932 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:48:25,933 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:48:26,097 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:26,122 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:48:26,123 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:48:26,126 - stpipe.step - INFO - Step xply done
2026-07-28 16:48:26,129 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:48:26,293 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:26,296 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:48:26,310 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:48:26,311 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:48:26,473 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2026-07-28 16:48:26,498 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:48:26,502 - stpipe.step - INFO - Step xply done
2026-07-28 16:48:26,505 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:48:26,572 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rateints.fits
2026-07-28 16:48:26,573 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:48:26,573 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:48:26,637 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits
2026-07-28 16:48:26,638 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:48:26,639 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:48:26,666 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:48:26,681 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:48:26,693 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:48:26,707 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:48:26,724 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:48:26,725 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:48:26,726 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:48:26,727 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:48:26,728 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:48:26,729 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:48:26,730 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:48:26,731 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:48:26,732 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:48:26,733 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:48:26,733 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:48:26,734 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:48:26,735 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:48:26,736 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:48:26,737 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:48:26,738 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:48:26,740 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:48:26,741 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:48:26,742 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:48:26,743 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:48:26,743 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:48:26,744 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:48:26,909 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00002_mirifulong_uncal.fits'),).
2026-07-28 16:48:26,928 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:48:26,956 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:48:26,961 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:48:26,962 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2026-07-28 16:48:26,962 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2026-07-28 16:48:26,963 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:48:26,964 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:48:26,964 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:48:26,965 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:48:26,965 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:48:26,966 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:48:26,967 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:48:27,420 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:27,421 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:48:27,421 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:48:27,424 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:48:27,590 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:27,593 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:48:27,627 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:27,684 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:48:27,848 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:27,849 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:28,011 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:28,016 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:48:28,016 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:48:28,053 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:28,054 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:28,068 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:28,076 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:48:28,445 - stcal.saturation.saturation - INFO - Detected 316 saturated pixels
2026-07-28 16:48:28,480 - stcal.saturation.saturation - INFO - Detected 27 A/D floor pixels
2026-07-28 16:48:28,494 - stpipe.step - INFO - Step saturation done
2026-07-28 16:48:28,654 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:28,655 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:28,817 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:28,818 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:28,980 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:28,983 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:48:29,148 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:29,151 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:48:29,235 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:29,235 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:29,249 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:29,286 - stpipe.step - INFO - Step reset done
2026-07-28 16:48:29,446 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:29,449 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2026-07-28 16:48:29,487 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:29,488 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:29,500 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:29,751 - stpipe.step - INFO - Step linearity done
2026-07-28 16:48:29,913 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:29,916 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:48:29,930 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:48:29,930 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:48:29,932 - jwst.rscd.rscd_sub - INFO - There are 23 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:48:29,938 - jwst.rscd.rscd_sub - INFO - Flagged 23 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:48:29,991 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 23
2026-07-28 16:48:29,994 - stpipe.step - INFO - Step rscd done
2026-07-28 16:48:30,155 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:30,158 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:48:30,950 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:30,993 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:48:30,994 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:48:30,994 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:48:31,693 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:48:31,855 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:31,855 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:32,021 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:32,022 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:32,186 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:32,187 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:48:32,188 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:48:32,190 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:48:32,193 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:48:32,290 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:48:32,290 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:48:34,020 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:48:42,444 - stcal.jump.jump - INFO - Total showers= 3
2026-07-28 16:48:42,444 - stcal.jump.jump - INFO - Total elapsed time = 10.154 sec
2026-07-28 16:48:42,464 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.276820
2026-07-28 16:48:42,468 - stpipe.step - INFO - Step jump done
2026-07-28 16:48:42,628 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:42,629 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:42,792 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:42,793 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:42,957 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:42,958 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:43,120 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:43,125 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:48:43,126 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:48:43,154 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:48:43,154 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:48:43,229 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:48:43,230 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:48:43,230 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:48:46,300 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.068696975708008
2026-07-28 16:48:46,460 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:48:46,624 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:46,627 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:48:46,643 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:48:46,643 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:48:46,806 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:46,830 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:48:46,831 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:48:46,834 - stpipe.step - INFO - Step xply done
2026-07-28 16:48:46,837 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:48:47,002 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:47,005 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2026-07-28 16:48:47,021 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:48:47,021 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:48:47,184 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2026-07-28 16:48:47,209 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:48:47,212 - stpipe.step - INFO - Step xply done
2026-07-28 16:48:47,216 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:48:47,284 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rateints.fits
2026-07-28 16:48:47,284 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:48:47,285 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:48:47,348 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits
2026-07-28 16:48:47,349 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:48:47,349 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:48:47,376 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:48:47,391 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:48:47,401 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:48:47,415 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:48:47,432 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:48:47,433 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:48:47,434 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:48:47,435 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:48:47,436 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:48:47,437 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:48:47,437 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:48:47,438 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:48:47,439 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:48:47,440 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:48:47,441 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:48:47,442 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:48:47,443 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:48:47,444 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:48:47,445 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:48:47,446 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:48:47,448 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:48:47,449 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:48:47,450 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:48:47,451 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:48:47,451 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:48:47,453 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:48:47,615 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00002_mirifushort_uncal.fits'),).
2026-07-28 16:48:47,634 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:48:47,661 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:48:47,664 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:48:47,664 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:48:47,665 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:48:47,666 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:48:47,666 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:48:47,667 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:48:47,667 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:48:47,668 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:48:47,668 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:48:47,669 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:48:48,114 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:48,114 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:48:48,115 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:48:48,117 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:48:48,277 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:48,279 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:48:48,311 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:48,366 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:48:48,525 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:48,526 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:48,687 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:48,691 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:48:48,692 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:48:48,728 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:48,729 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:48,742 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:48,750 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:48:49,109 - stcal.saturation.saturation - INFO - Detected 1608 saturated pixels
2026-07-28 16:48:49,143 - stcal.saturation.saturation - INFO - Detected 10 A/D floor pixels
2026-07-28 16:48:49,157 - stpipe.step - INFO - Step saturation done
2026-07-28 16:48:49,316 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:49,317 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:49,478 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:49,479 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:49,639 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:49,642 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:48:49,802 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:49,805 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:48:49,890 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:49,890 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:49,903 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:49,941 - stpipe.step - INFO - Step reset done
2026-07-28 16:48:50,101 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:50,104 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:48:50,142 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:50,142 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:50,155 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:50,402 - stpipe.step - INFO - Step linearity done
2026-07-28 16:48:50,562 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:50,565 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:48:50,579 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:48:50,580 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:48:50,582 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:48:50,588 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:48:50,640 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:48:50,643 - stpipe.step - INFO - Step rscd done
2026-07-28 16:48:50,803 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:50,806 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:48:51,568 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:48:51,610 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:48:51,610 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:48:51,611 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:48:52,236 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:48:52,397 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:52,398 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:52,557 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:52,558 - stpipe.step - INFO - Step skipped.
2026-07-28 16:48:52,719 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:48:52,719 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:48:52,720 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:48:52,723 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:48:52,725 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:48:52,823 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:48:52,823 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:48:54,557 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:49:01,520 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:49:01,521 - stcal.jump.jump - INFO - Total elapsed time = 8.69728 sec
2026-07-28 16:49:01,540 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.820424
2026-07-28 16:49:01,543 - stpipe.step - INFO - Step jump done
2026-07-28 16:49:01,705 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:49:01,706 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:01,870 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:49:01,871 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:02,032 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:49:02,033 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:02,194 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:49:02,199 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:49:02,200 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:49:02,225 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:49:02,226 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:49:02,303 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:49:02,311 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:49:02,312 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:49:05,013 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.6991970539093018
2026-07-28 16:49:05,171 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:49:05,332 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:49:05,336 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:49:05,349 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:49:05,349 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:49:05,507 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:49:05,531 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:49:05,531 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:49:05,535 - stpipe.step - INFO - Step xply done
2026-07-28 16:49:05,538 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:49:05,697 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:49:05,700 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:49:05,713 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:49:05,714 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:49:05,869 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2026-07-28 16:49:05,894 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:49:05,898 - stpipe.step - INFO - Step xply done
2026-07-28 16:49:05,901 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:49:05,966 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rateints.fits
2026-07-28 16:49:05,966 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:49:05,967 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:49:06,029 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits
2026-07-28 16:49:06,030 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:49:06,031 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:49:06,058 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:49:06,073 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:49:06,083 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:49:06,097 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:49:06,113 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:49:06,114 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:49:06,115 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:49:06,116 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:49:06,117 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:49:06,118 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:49:06,119 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:49:06,120 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:49:06,121 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:49:06,121 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:49:06,122 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:49:06,123 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:49:06,124 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:49:06,125 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:49:06,126 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:49:06,127 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:49:06,128 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:49:06,129 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:49:06,130 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:49:06,131 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:49:06,132 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:49:06,133 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:49:06,291 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00001_mirifulong_uncal.fits'),).
2026-07-28 16:49:06,311 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:49:06,337 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:49:06,340 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:49:06,341 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:49:06,342 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2026-07-28 16:49:06,342 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:49:06,343 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:49:06,343 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:49:06,344 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:49:06,345 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:49:06,345 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:49:06,345 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:49:06,797 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:06,798 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:49:06,798 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:49:06,800 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:49:06,957 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:06,960 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:49:06,991 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:07,045 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:49:07,202 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:07,203 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:07,362 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:07,366 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:49:07,367 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:49:07,402 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:07,403 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:07,415 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:07,423 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:49:07,750 - stcal.saturation.saturation - INFO - Detected 329 saturated pixels
2026-07-28 16:49:07,782 - stcal.saturation.saturation - INFO - Detected 25 A/D floor pixels
2026-07-28 16:49:07,795 - stpipe.step - INFO - Step saturation done
2026-07-28 16:49:07,955 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:07,956 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:08,115 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:08,116 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:08,271 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:08,273 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:49:08,424 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:08,427 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:49:08,508 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:08,509 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:08,521 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:08,558 - stpipe.step - INFO - Step reset done
2026-07-28 16:49:08,713 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:08,716 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2026-07-28 16:49:08,753 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:08,754 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:08,766 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:09,001 - stpipe.step - INFO - Step linearity done
2026-07-28 16:49:09,159 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:09,162 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:49:09,176 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:49:09,177 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:49:09,179 - jwst.rscd.rscd_sub - INFO - There are 22 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:49:09,185 - jwst.rscd.rscd_sub - INFO - Flagged 22 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:49:09,237 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 22
2026-07-28 16:49:09,240 - stpipe.step - INFO - Step rscd done
2026-07-28 16:49:09,395 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:09,398 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:49:10,166 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:10,209 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:49:10,210 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:49:10,210 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:49:10,898 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:49:11,058 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:11,058 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:11,223 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:11,223 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:11,384 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:11,385 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:49:11,385 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:49:11,388 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:49:11,391 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:49:11,491 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:49:11,492 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:49:13,224 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:49:21,598 - stcal.jump.jump - INFO - Total showers= 1
2026-07-28 16:49:21,599 - stcal.jump.jump - INFO - Total elapsed time = 10.1069 sec
2026-07-28 16:49:21,618 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.233228
2026-07-28 16:49:21,622 - stpipe.step - INFO - Step jump done
2026-07-28 16:49:21,786 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:21,787 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:21,951 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:21,952 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:22,114 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:22,115 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:22,278 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:22,284 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:49:22,284 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:49:22,310 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:49:22,311 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:49:22,386 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:49:22,387 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 0
2026-07-28 16:49:22,388 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:49:25,424 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 3.033581256866455
2026-07-28 16:49:25,583 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:49:25,749 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:25,752 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:49:25,766 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:49:25,767 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:49:25,926 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:25,951 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:49:25,952 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:49:25,955 - stpipe.step - INFO - Step xply done
2026-07-28 16:49:25,959 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:49:26,119 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:26,122 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:49:26,136 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:49:26,136 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:49:26,299 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2026-07-28 16:49:26,323 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:49:26,327 - stpipe.step - INFO - Step xply done
2026-07-28 16:49:26,330 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:49:26,397 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rateints.fits
2026-07-28 16:49:26,398 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:49:26,398 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:49:26,462 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits
2026-07-28 16:49:26,463 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:49:26,463 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:49:26,489 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:49:26,504 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:49:26,515 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:49:26,528 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:49:26,545 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:49:26,546 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:49:26,546 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:49:26,547 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:49:26,548 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:49:26,549 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:49:26,550 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:49:26,551 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:49:26,552 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:49:26,553 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:49:26,554 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:49:26,554 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:49:26,555 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:49:26,556 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:49:26,557 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:49:26,558 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:49:26,560 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:49:26,561 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:49:26,563 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:49:26,563 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:49:26,564 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:49:26,566 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:49:26,736 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00001_mirifushort_uncal.fits'),).
2026-07-28 16:49:26,756 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:49:26,782 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:49:26,785 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:49:26,786 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:49:26,786 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:49:26,787 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:49:26,787 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:49:26,788 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:49:26,788 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:49:26,789 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:49:26,789 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:49:26,790 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:49:27,238 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:27,238 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:49:27,239 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:49:27,241 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:49:27,401 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:27,404 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:49:27,437 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:27,492 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:49:27,653 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:27,654 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:27,816 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:27,820 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:49:27,821 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:49:27,857 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:27,858 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:27,871 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:27,880 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:49:28,274 - stcal.saturation.saturation - INFO - Detected 1607 saturated pixels
2026-07-28 16:49:28,310 - stcal.saturation.saturation - INFO - Detected 2 A/D floor pixels
2026-07-28 16:49:28,324 - stpipe.step - INFO - Step saturation done
2026-07-28 16:49:28,483 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:28,484 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:28,643 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:28,644 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:28,803 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:28,806 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:49:28,970 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:28,973 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:49:29,060 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:29,061 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:29,074 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:29,113 - stpipe.step - INFO - Step reset done
2026-07-28 16:49:29,278 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:29,281 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:49:29,320 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:29,321 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:29,334 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:29,589 - stpipe.step - INFO - Step linearity done
2026-07-28 16:49:29,751 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:29,754 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:49:29,768 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:49:29,768 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:49:29,771 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:49:29,776 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:49:29,830 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:49:29,833 - stpipe.step - INFO - Step rscd done
2026-07-28 16:49:29,996 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:29,999 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:49:30,788 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:30,830 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:49:30,831 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:49:30,832 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:49:31,443 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:49:31,605 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:31,606 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:31,768 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:31,769 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:31,932 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:31,933 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:49:31,934 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:49:31,937 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:49:31,939 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:49:32,038 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:49:32,039 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:49:33,770 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:49:40,780 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:49:40,781 - stcal.jump.jump - INFO - Total elapsed time = 8.74255 sec
2026-07-28 16:49:40,800 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.867231
2026-07-28 16:49:40,804 - stpipe.step - INFO - Step jump done
2026-07-28 16:49:40,968 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:40,969 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:41,133 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:41,134 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:41,296 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:41,297 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:41,458 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:41,464 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:49:41,464 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:49:41,489 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:49:41,490 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:49:41,564 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:49:41,569 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:49:41,570 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:49:44,379 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.806670904159546
2026-07-28 16:49:44,540 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:49:44,708 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:44,711 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:49:44,724 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:49:44,725 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:49:44,887 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:44,912 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:49:44,913 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:49:44,916 - stpipe.step - INFO - Step xply done
2026-07-28 16:49:44,919 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:49:45,081 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:45,084 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:49:45,097 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:49:45,097 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:49:45,257 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2026-07-28 16:49:45,282 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:49:45,285 - stpipe.step - INFO - Step xply done
2026-07-28 16:49:45,289 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:49:45,354 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rateints.fits
2026-07-28 16:49:45,355 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:49:45,356 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:49:45,419 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits
2026-07-28 16:49:45,420 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:49:45,420 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:49:45,449 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:49:45,464 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:49:45,475 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:49:45,489 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:49:45,505 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:49:45,506 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:49:45,507 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:49:45,508 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:49:45,509 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:49:45,510 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:49:45,511 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:49:45,512 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:49:45,512 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:49:45,513 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:49:45,514 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:49:45,515 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:49:45,516 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:49:45,517 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:49:45,519 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:49:45,520 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:49:45,521 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:49:45,522 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:49:45,523 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:49:45,524 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:49:45,526 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:49:45,526 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:49:45,689 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00002_mirifulong_uncal.fits'),).
2026-07-28 16:49:45,709 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:49:45,736 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:49:45,740 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:49:45,740 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:49:45,741 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2026-07-28 16:49:45,742 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:49:45,742 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:49:45,743 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:49:45,743 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:49:45,744 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:49:45,745 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:49:45,745 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:49:46,184 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:46,185 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:49:46,185 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:49:46,187 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:49:46,347 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:46,350 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:49:46,381 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:46,435 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:49:46,596 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:46,597 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:46,757 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:46,761 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:49:46,762 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:49:46,797 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:46,798 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:46,810 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:46,818 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:49:47,165 - stcal.saturation.saturation - INFO - Detected 319 saturated pixels
2026-07-28 16:49:47,199 - stcal.saturation.saturation - INFO - Detected 25 A/D floor pixels
2026-07-28 16:49:47,212 - stpipe.step - INFO - Step saturation done
2026-07-28 16:49:47,371 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:47,372 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:47,532 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:47,533 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:47,694 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:47,697 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:49:47,855 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:47,858 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:49:47,940 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:47,941 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:47,954 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:47,990 - stpipe.step - INFO - Step reset done
2026-07-28 16:49:48,151 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:48,153 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2026-07-28 16:49:48,191 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:48,192 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:48,204 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:48,445 - stpipe.step - INFO - Step linearity done
2026-07-28 16:49:48,605 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:48,608 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:49:48,622 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:49:48,623 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:49:48,625 - jwst.rscd.rscd_sub - INFO - There are 22 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:49:48,631 - jwst.rscd.rscd_sub - INFO - Flagged 22 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:49:48,684 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 22
2026-07-28 16:49:48,688 - stpipe.step - INFO - Step rscd done
2026-07-28 16:49:48,849 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:48,852 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:49:49,639 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:49:49,683 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:49:49,684 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:49:49,685 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:49:50,442 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:49:50,606 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:50,607 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:50,774 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:50,775 - stpipe.step - INFO - Step skipped.
2026-07-28 16:49:50,940 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:49:50,941 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:49:50,941 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:49:50,944 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:49:50,947 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:49:51,049 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:49:51,050 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:49:52,807 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:50:00,866 - stcal.jump.jump - INFO - Total showers= 7
2026-07-28 16:50:00,867 - stcal.jump.jump - INFO - Total elapsed time = 9.81759 sec
2026-07-28 16:50:00,888 - jwst.jump.jump_step - INFO - The execution time in seconds: 9.946769
2026-07-28 16:50:00,891 - stpipe.step - INFO - Step jump done
2026-07-28 16:50:01,054 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:50:01,055 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:01,219 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:50:01,219 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:01,386 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:50:01,387 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:01,554 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:50:01,559 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:50:01,560 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:50:01,586 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:50:01,587 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:50:01,674 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:50:01,678 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:50:01,679 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:50:04,670 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.988792657852173
2026-07-28 16:50:04,831 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:50:04,993 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:50:04,997 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:50:05,010 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:50:05,011 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:50:05,173 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:50:05,197 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:50:05,198 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:50:05,201 - stpipe.step - INFO - Step xply done
2026-07-28 16:50:05,204 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:50:05,367 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:50:05,371 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:50:05,385 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:50:05,386 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:50:05,545 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2026-07-28 16:50:05,570 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:50:05,573 - stpipe.step - INFO - Step xply done
2026-07-28 16:50:05,577 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:50:05,645 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rateints.fits
2026-07-28 16:50:05,646 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:50:05,647 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:50:05,709 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits
2026-07-28 16:50:05,710 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:50:05,711 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:50:05,739 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:50:05,754 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:50:05,765 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:50:05,779 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:50:05,796 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:50:05,797 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:50:05,798 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:50:05,799 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:50:05,800 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:50:05,801 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:50:05,802 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:50:05,803 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:50:05,804 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:50:05,805 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:50:05,807 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:50:05,808 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:50:05,808 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:50:05,809 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:50:05,810 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:50:05,811 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:50:05,813 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:50:05,814 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:50:05,815 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:50:05,816 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:50:05,818 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:50:05,818 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:50:05,982 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00002_mirifushort_uncal.fits'),).
2026-07-28 16:50:06,001 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:50:06,028 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:50:06,031 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:50:06,032 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2026-07-28 16:50:06,033 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:50:06,034 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:50:06,034 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:50:06,035 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:50:06,035 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:50:06,036 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:50:06,036 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:50:06,037 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:50:06,486 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:06,487 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:50:06,488 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:50:06,490 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:50:06,649 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:06,652 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:50:06,684 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:06,739 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:50:06,899 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:06,900 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:07,062 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:07,066 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:50:07,067 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:50:07,103 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:07,104 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:07,117 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:07,125 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:50:07,517 - stcal.saturation.saturation - INFO - Detected 1472 saturated pixels
2026-07-28 16:50:07,552 - stcal.saturation.saturation - INFO - Detected 9 A/D floor pixels
2026-07-28 16:50:07,566 - stpipe.step - INFO - Step saturation done
2026-07-28 16:50:07,726 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:07,727 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:07,891 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:07,892 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:08,056 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:08,059 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:50:08,221 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:08,224 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:50:08,310 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:08,312 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:08,325 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:08,364 - stpipe.step - INFO - Step reset done
2026-07-28 16:50:08,527 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:08,529 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:50:08,568 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:08,569 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:08,582 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:08,831 - stpipe.step - INFO - Step linearity done
2026-07-28 16:50:08,995 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:08,998 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:50:09,013 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:50:09,013 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:50:09,016 - jwst.rscd.rscd_sub - INFO - There are 32 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:50:09,021 - jwst.rscd.rscd_sub - INFO - Flagged 32 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:50:09,076 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 32
2026-07-28 16:50:09,079 - stpipe.step - INFO - Step rscd done
2026-07-28 16:50:09,245 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:09,248 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:50:10,039 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:10,079 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:50:10,080 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:50:10,081 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:50:10,704 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:50:10,865 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:10,866 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:11,029 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:11,029 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:11,191 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:11,192 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:50:11,193 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:50:11,196 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:50:11,198 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:50:11,297 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:50:11,298 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:50:13,048 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:50:20,017 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:50:20,018 - stcal.jump.jump - INFO - Total elapsed time = 8.71979 sec
2026-07-28 16:50:20,037 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.844754
2026-07-28 16:50:20,041 - stpipe.step - INFO - Step jump done
2026-07-28 16:50:20,200 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:20,201 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:20,364 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:20,365 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:20,526 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:20,527 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:20,687 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:20,693 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:50:20,693 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:50:20,719 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:50:20,720 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:50:20,796 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:50:20,805 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:50:20,806 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:50:23,551 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.7431206703186035
2026-07-28 16:50:23,712 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:50:23,878 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:23,882 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:50:23,895 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:50:23,896 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:50:24,060 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:24,086 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:50:24,087 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:50:24,091 - stpipe.step - INFO - Step xply done
2026-07-28 16:50:24,095 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:50:24,262 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:24,265 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2026-07-28 16:50:24,279 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:50:24,279 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:50:24,441 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2026-07-28 16:50:24,466 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:50:24,470 - stpipe.step - INFO - Step xply done
2026-07-28 16:50:24,474 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:50:24,540 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rateints.fits
2026-07-28 16:50:24,540 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:50:24,541 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:50:24,605 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits
2026-07-28 16:50:24,605 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:50:24,606 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:50:24,633 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:50:24,649 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:50:24,660 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:50:24,674 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:50:24,690 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:50:24,691 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:50:24,693 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:50:24,694 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:50:24,694 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:50:24,695 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:50:24,696 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:50:24,697 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:50:24,698 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:50:24,699 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:50:24,700 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:50:24,700 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:50:24,701 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:50:24,702 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:50:24,703 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:50:24,704 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:50:24,706 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:50:24,707 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:50:24,708 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:50:24,709 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:50:24,709 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:50:24,710 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:50:24,872 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00001_mirifulong_uncal.fits'),).
2026-07-28 16:50:24,892 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:50:24,919 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:50:24,922 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:50:24,923 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:50:24,924 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2026-07-28 16:50:24,924 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:50:24,925 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:50:24,926 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:50:24,926 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:50:24,927 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:50:24,927 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:50:24,928 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:50:25,368 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:25,369 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:50:25,369 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:50:25,371 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:50:25,528 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:25,531 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:50:25,563 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:25,618 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:50:25,777 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:25,778 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:25,938 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:25,942 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:50:25,943 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:50:25,979 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:25,980 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:25,993 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:26,001 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:50:26,360 - stcal.saturation.saturation - INFO - Detected 320 saturated pixels
2026-07-28 16:50:26,394 - stcal.saturation.saturation - INFO - Detected 25 A/D floor pixels
2026-07-28 16:50:26,408 - stpipe.step - INFO - Step saturation done
2026-07-28 16:50:26,566 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:26,567 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:26,727 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:26,728 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:26,889 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:26,892 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:50:27,053 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:27,056 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:50:27,140 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:27,141 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:27,154 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:27,191 - stpipe.step - INFO - Step reset done
2026-07-28 16:50:27,355 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:27,358 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2026-07-28 16:50:27,397 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:27,398 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:27,410 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:27,655 - stpipe.step - INFO - Step linearity done
2026-07-28 16:50:27,818 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:27,821 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:50:27,835 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:50:27,836 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:50:27,838 - jwst.rscd.rscd_sub - INFO - There are 23 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:50:27,843 - jwst.rscd.rscd_sub - INFO - Flagged 23 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:50:27,896 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 23
2026-07-28 16:50:27,899 - stpipe.step - INFO - Step rscd done
2026-07-28 16:50:28,062 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:28,065 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:50:28,844 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:28,890 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:50:28,891 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:50:28,892 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:50:29,596 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:50:29,759 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:29,760 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:29,923 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:29,924 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:30,087 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:30,088 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:50:30,088 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:50:30,091 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:50:30,094 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:50:30,194 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:50:30,195 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:50:31,941 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:50:40,242 - stcal.jump.jump - INFO - Total showers= 5
2026-07-28 16:50:40,243 - stcal.jump.jump - INFO - Total elapsed time = 10.0485 sec
2026-07-28 16:50:40,263 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.174815
2026-07-28 16:50:40,266 - stpipe.step - INFO - Step jump done
2026-07-28 16:50:40,429 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:40,430 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:40,596 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:40,597 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:40,764 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:40,765 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:40,931 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:40,937 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:50:40,938 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:50:40,964 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:50:40,965 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:50:41,040 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:50:41,045 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:50:41,046 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:50:43,974 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.926159143447876
2026-07-28 16:50:44,132 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:50:44,293 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:44,296 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:50:44,309 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:50:44,310 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:50:44,469 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:44,493 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:50:44,494 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:50:44,498 - stpipe.step - INFO - Step xply done
2026-07-28 16:50:44,501 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:50:44,660 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:44,663 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:50:44,676 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:50:44,677 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:50:44,836 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2026-07-28 16:50:44,861 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:50:44,864 - stpipe.step - INFO - Step xply done
2026-07-28 16:50:44,868 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:50:44,936 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rateints.fits
2026-07-28 16:50:44,937 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:50:44,937 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:50:45,001 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits
2026-07-28 16:50:45,002 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:50:45,002 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:50:45,028 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:50:45,044 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:50:45,055 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:50:45,069 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:50:45,086 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:50:45,087 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:50:45,088 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:50:45,089 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:50:45,090 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:50:45,091 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:50:45,092 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:50:45,093 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:50:45,094 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:50:45,094 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:50:45,095 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:50:45,096 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:50:45,098 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:50:45,099 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:50:45,100 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:50:45,101 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:50:45,102 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:50:45,103 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:50:45,104 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:50:45,106 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:50:45,106 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:50:45,107 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:50:45,268 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00001_mirifushort_uncal.fits'),).
2026-07-28 16:50:45,288 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:50:45,315 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:50:45,318 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:50:45,319 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2026-07-28 16:50:45,319 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:50:45,320 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:50:45,321 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:50:45,321 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:50:45,322 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:50:45,322 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:50:45,323 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:50:45,323 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:50:45,766 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:45,766 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:50:45,767 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:50:45,769 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:50:45,928 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:45,931 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:50:45,963 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:46,018 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:50:46,178 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:46,179 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:46,342 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:46,346 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:50:46,347 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:50:46,383 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:46,384 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:46,397 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:46,405 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:50:46,797 - stcal.saturation.saturation - INFO - Detected 1606 saturated pixels
2026-07-28 16:50:46,831 - stcal.saturation.saturation - INFO - Detected 4 A/D floor pixels
2026-07-28 16:50:46,845 - stpipe.step - INFO - Step saturation done
2026-07-28 16:50:47,004 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:47,005 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:47,166 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:47,167 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:47,329 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:47,332 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:50:47,492 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:47,496 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:50:47,583 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:47,584 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:47,597 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:47,635 - stpipe.step - INFO - Step reset done
2026-07-28 16:50:47,797 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:47,799 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:50:47,838 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:47,839 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:47,852 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:48,098 - stpipe.step - INFO - Step linearity done
2026-07-28 16:50:48,263 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:48,266 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:50:48,280 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:50:48,281 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:50:48,283 - jwst.rscd.rscd_sub - INFO - There are 45 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:50:48,288 - jwst.rscd.rscd_sub - INFO - Flagged 45 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:50:48,340 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 45
2026-07-28 16:50:48,343 - stpipe.step - INFO - Step rscd done
2026-07-28 16:50:48,501 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:48,505 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:50:49,264 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:50:49,308 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:50:49,309 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:50:49,310 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:50:49,923 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:50:50,081 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:50,082 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:50,243 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:50,244 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:50,406 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:50,407 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:50:50,407 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:50:50,410 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:50:50,413 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:50:50,503 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:50:50,504 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:50:52,279 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:50:59,273 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:50:59,274 - stcal.jump.jump - INFO - Total elapsed time = 8.76939 sec
2026-07-28 16:50:59,293 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.886339
2026-07-28 16:50:59,297 - stpipe.step - INFO - Step jump done
2026-07-28 16:50:59,460 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:59,461 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:59,627 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:59,628 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:59,794 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:59,795 - stpipe.step - INFO - Step skipped.
2026-07-28 16:50:59,959 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:50:59,964 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:50:59,964 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:50:59,993 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:50:59,993 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:51:00,077 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:51:00,082 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:51:00,083 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:51:02,868 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.783299446105957
2026-07-28 16:51:03,028 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:51:03,196 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:51:03,199 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:51:03,215 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:51:03,216 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:51:03,379 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:51:03,404 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:51:03,404 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:51:03,407 - stpipe.step - INFO - Step xply done
2026-07-28 16:51:03,411 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:51:03,570 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:51:03,573 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:51:03,589 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:51:03,590 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:51:03,750 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2026-07-28 16:51:03,775 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:51:03,778 - stpipe.step - INFO - Step xply done
2026-07-28 16:51:03,781 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:51:03,847 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rateints.fits
2026-07-28 16:51:03,848 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:51:03,849 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:51:03,914 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits
2026-07-28 16:51:03,915 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:51:03,916 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:51:03,944 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:51:03,959 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:51:03,970 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:51:03,984 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:51:04,001 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:51:04,002 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:51:04,003 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:51:04,004 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:51:04,005 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:51:04,005 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:51:04,006 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:51:04,007 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:51:04,008 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:51:04,009 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:51:04,010 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:51:04,010 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:51:04,011 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:51:04,012 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:51:04,013 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:51:04,014 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:51:04,016 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:51:04,017 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:51:04,018 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:51:04,019 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:51:04,019 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:51:04,021 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:51:04,182 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00002_mirifulong_uncal.fits'),).
2026-07-28 16:51:04,201 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:51:04,228 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:51:04,231 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits'.
2026-07-28 16:51:04,232 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2026-07-28 16:51:04,232 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2026-07-28 16:51:04,233 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2026-07-28 16:51:04,233 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits'.
2026-07-28 16:51:04,234 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2026-07-28 16:51:04,235 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits'.
2026-07-28 16:51:04,236 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2026-07-28 16:51:04,236 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:51:04,237 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:51:04,685 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:04,686 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:51:04,686 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:51:04,688 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:51:04,850 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:04,852 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2026-07-28 16:51:04,886 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:04,940 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:51:05,101 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:05,102 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:05,264 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:05,269 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2026-07-28 16:51:05,269 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:51:05,305 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:05,306 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:05,319 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:05,327 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:51:05,700 - stcal.saturation.saturation - INFO - Detected 319 saturated pixels
2026-07-28 16:51:05,734 - stcal.saturation.saturation - INFO - Detected 26 A/D floor pixels
2026-07-28 16:51:05,747 - stpipe.step - INFO - Step saturation done
2026-07-28 16:51:05,906 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:05,906 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:06,066 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:06,067 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:06,226 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:06,229 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:51:06,389 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:06,393 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2026-07-28 16:51:06,475 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:06,476 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:06,488 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:06,525 - stpipe.step - INFO - Step reset done
2026-07-28 16:51:06,687 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:06,690 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2026-07-28 16:51:06,729 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:06,730 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:06,744 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:07,003 - stpipe.step - INFO - Step linearity done
2026-07-28 16:51:07,173 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:07,176 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0024.fits
2026-07-28 16:51:07,190 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:51:07,190 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:51:07,193 - jwst.rscd.rscd_sub - INFO - There are 22 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:51:07,199 - jwst.rscd.rscd_sub - INFO - Flagged 22 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:51:07,254 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 22
2026-07-28 16:51:07,258 - stpipe.step - INFO - Step rscd done
2026-07-28 16:51:07,422 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:07,425 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0114.fits
2026-07-28 16:51:08,262 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:08,310 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:51:08,311 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:51:08,312 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:51:09,038 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:51:09,210 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:09,211 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:09,378 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:09,379 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:09,545 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:09,545 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:51:09,546 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:51:09,549 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:51:09,551 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:51:09,658 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:51:09,659 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:51:11,400 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:51:19,809 - stcal.jump.jump - INFO - Total showers= 5
2026-07-28 16:51:19,810 - stcal.jump.jump - INFO - Total elapsed time = 10.1514 sec
2026-07-28 16:51:19,829 - jwst.jump.jump_step - INFO - The execution time in seconds: 10.284152
2026-07-28 16:51:19,833 - stpipe.step - INFO - Step jump done
2026-07-28 16:51:20,001 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:20,002 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:20,173 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:20,173 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:20,343 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:20,344 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:20,516 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:20,521 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0090.fits
2026-07-28 16:51:20,522 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:51:20,548 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:51:20,549 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:51:20,626 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:51:20,631 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2026-07-28 16:51:20,632 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:51:23,603 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.9690864086151123
2026-07-28 16:51:23,762 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:51:23,926 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:23,929 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:51:23,942 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:51:23,943 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:51:24,106 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:24,131 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:51:24,132 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:51:24,135 - stpipe.step - INFO - Step xply done
2026-07-28 16:51:24,138 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:51:24,303 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:24,306 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2026-07-28 16:51:24,319 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:51:24,320 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:51:24,484 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2026-07-28 16:51:24,509 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:51:24,512 - stpipe.step - INFO - Step xply done
2026-07-28 16:51:24,516 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:51:24,584 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rateints.fits
2026-07-28 16:51:24,585 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:51:24,586 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:51:24,649 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits
2026-07-28 16:51:24,650 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:51:24,651 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
2026-07-28 16:51:24,677 - stpipe.step - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2026-07-28 16:51:24,692 - stpipe.step - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2026-07-28 16:51:24,703 - stpipe.step - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2026-07-28 16:51:24,718 - stpipe.pipeline - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2026-07-28 16:51:24,735 - stpipe.step - INFO - Detector1Pipeline instance created.
2026-07-28 16:51:24,736 - stpipe.step - INFO - GroupScaleStep instance created.
2026-07-28 16:51:24,736 - stpipe.step - INFO - DQInitStep instance created.
2026-07-28 16:51:24,737 - stpipe.step - INFO - EmiCorrStep instance created.
2026-07-28 16:51:24,738 - stpipe.step - INFO - SaturationStep instance created.
2026-07-28 16:51:24,739 - stpipe.step - INFO - IPCStep instance created.
2026-07-28 16:51:24,740 - stpipe.step - INFO - SuperBiasStep instance created.
2026-07-28 16:51:24,741 - stpipe.step - INFO - RefPixStep instance created.
2026-07-28 16:51:24,742 - stpipe.step - INFO - RscdStep instance created.
2026-07-28 16:51:24,743 - stpipe.step - INFO - FirstFrameStep instance created.
2026-07-28 16:51:24,743 - stpipe.step - INFO - LastFrameStep instance created.
2026-07-28 16:51:24,744 - stpipe.step - INFO - LinearityStep instance created.
2026-07-28 16:51:24,745 - stpipe.step - INFO - DarkCurrentStep instance created.
2026-07-28 16:51:24,746 - stpipe.step - INFO - ResetStep instance created.
2026-07-28 16:51:24,747 - stpipe.step - INFO - PersistenceStep instance created.
2026-07-28 16:51:24,749 - stpipe.step - INFO - ChargeMigrationStep instance created.
2026-07-28 16:51:24,750 - stpipe.step - INFO - JumpStep instance created.
2026-07-28 16:51:24,752 - stpipe.step - INFO - PictureFrameStep instance created.
2026-07-28 16:51:24,753 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:51:24,754 - stpipe.step - INFO - RampFitStep instance created.
2026-07-28 16:51:24,754 - stpipe.step - INFO - GainScaleStep instance created.
2026-07-28 16:51:24,755 - stpipe.step - INFO - XplyStep instance created.
2026-07-28 16:51:24,920 - stpipe.step - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00002_mirifushort_uncal.fits'),).
2026-07-28 16:51:24,939 - stpipe.step - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage1
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
user_supplied_dq: None
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: joint
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
odd_even_columns: True
use_side_ref_pixels: True
side_smoothing_length: 11
side_gain: 1.0
odd_even_rows: True
ovr_corr_mitigation_ftr: 3.0
preserve_irs2_refpix: False
irs2_mean_subtraction: False
refpix_algorithm: median
sigreject: 4.0
gaussmooth: 1.0
halfwidth: 30
siglimit: 3.0
rscd:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
firstframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: True
lastframe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
linearity:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_current:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dark_output: None
average_dark_current: 1.0
reset:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
persistence:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_persistence: None
persistence_time: None
dn_threshold: None
persistence_array_file: None
persistence_dnu: False
charge_migration:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
signal_threshold: 25000.0
jump:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
rejection_threshold: 4.0
three_group_rejection_threshold: 100
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000.0
min_jump_to_flag_neighbors: 10.0
after_jump_flag_dn1: 0.0
after_jump_flag_time1: 0.0
after_jump_flag_dn2: 0.0
after_jump_flag_time2: 0.0
expand_large_events: False
min_sat_area: 1.0
min_jump_area: 5.0
expand_factor: 2.0
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 1.2
extend_min_area: 90
extend_inner_radius: 1.0
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 15.0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
picture_frame:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
mask_science_regions: True
n_sigma: 2.0
save_mask: False
save_correction: False
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks:
- !!python/name:__main__.XplyStep ''
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 16:51:24,967 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias']
2026-07-28 16:51:24,970 - stpipe.pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits'.
2026-07-28 16:51:24,970 - stpipe.pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2026-07-28 16:51:24,971 - stpipe.pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2026-07-28 16:51:24,971 - stpipe.pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2026-07-28 16:51:24,972 - stpipe.pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits'.
2026-07-28 16:51:24,972 - stpipe.pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2026-07-28 16:51:24,973 - stpipe.pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits'.
2026-07-28 16:51:24,974 - stpipe.pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2026-07-28 16:51:24,974 - stpipe.pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2026-07-28 16:51:24,975 - jwst.pipeline.calwebb_detector1 - INFO - Starting calwebb_detector1 ...
2026-07-28 16:51:25,421 - stpipe.step - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:25,422 - jwst.group_scale.group_scale_step - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2026-07-28 16:51:25,422 - jwst.group_scale.group_scale_step - INFO - Step will be skipped
2026-07-28 16:51:25,424 - stpipe.step - INFO - Step group_scale done
2026-07-28 16:51:25,594 - stpipe.step - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:25,597 - jwst.dq_init.dq_init_step - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2026-07-28 16:51:25,630 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:25,685 - stpipe.step - INFO - Step dq_init done
2026-07-28 16:51:25,848 - stpipe.step - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:25,848 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:26,011 - stpipe.step - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:26,015 - jwst.saturation.saturation_step - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2026-07-28 16:51:26,016 - jwst.saturation.saturation_step - INFO - Using SUPERBIAS reference file N/A
2026-07-28 16:51:26,053 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:26,053 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:26,067 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:26,075 - jwst.saturation.saturation - INFO - Using read_pattern with nframes 1
2026-07-28 16:51:26,481 - stcal.saturation.saturation - INFO - Detected 1489 saturated pixels
2026-07-28 16:51:26,516 - stcal.saturation.saturation - INFO - Detected 3 A/D floor pixels
2026-07-28 16:51:26,530 - stpipe.step - INFO - Step saturation done
2026-07-28 16:51:26,696 - stpipe.step - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:26,697 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:26,864 - stpipe.step - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:26,865 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:27,026 - stpipe.step - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:27,029 - stpipe.step - INFO - Step lastframe done
2026-07-28 16:51:27,189 - stpipe.step - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:27,192 - jwst.reset.reset_step - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2026-07-28 16:51:27,279 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:27,280 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:27,294 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:27,332 - stpipe.step - INFO - Step reset done
2026-07-28 16:51:27,492 - stpipe.step - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:27,496 - jwst.linearity.linearity_step - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2026-07-28 16:51:27,535 - stdatamodels.dynamicdq - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:27,536 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:27,549 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:27,803 - stpipe.step - INFO - Step linearity done
2026-07-28 16:51:27,964 - stpipe.step - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:27,967 - jwst.rscd.rscd_step - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0025.fits
2026-07-28 16:51:27,981 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 1 to flag: 2
2026-07-28 16:51:27,981 - jwst.rscd.rscd_sub - INFO - # groups from RSCD reference file for int 2 and higher to flag: 2
2026-07-28 16:51:27,984 - jwst.rscd.rscd_sub - INFO - There are 41 saturated pixels that require the number of rscd groups flagged to be lowered
2026-07-28 16:51:27,989 - jwst.rscd.rscd_sub - INFO - Flagged 41 pixels as FLUX_ESTIMATED due to RSCD back-off.
2026-07-28 16:51:28,042 - jwst.rscd.rscd_sub - INFO - Number of usable bright pixels with rscd flag groups not set to DO_NOT_USE: 41
2026-07-28 16:51:28,045 - stpipe.step - INFO - Step rscd done
2026-07-28 16:51:28,207 - stpipe.step - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:28,210 - jwst.dark_current.dark_current_step - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0112.fits
2026-07-28 16:51:28,989 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:51:29,033 - jwst.dark_current.dark_current_step - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2026-07-28 16:51:29,034 - stcal.dark_current.dark_sub - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2026-07-28 16:51:29,035 - stcal.dark_current.dark_sub - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2026-07-28 16:51:29,666 - stpipe.step - INFO - Step dark_current done
2026-07-28 16:51:29,828 - stpipe.step - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:29,829 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:29,992 - stpipe.step - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:29,993 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:30,158 - stpipe.step - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:30,159 - jwst.jump.jump_step - INFO - CR rejection threshold = 4 sigma
2026-07-28 16:51:30,160 - jwst.jump.jump_step - INFO - Maximum cores to use = half
2026-07-28 16:51:30,163 - jwst.jump.jump_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:51:30,165 - jwst.jump.jump_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:51:30,259 - stcal.jump.jump - INFO - Executing two-point difference method
2026-07-28 16:51:30,260 - stcal.jump.jump - INFO - Creating 2 processes for jump detection
2026-07-28 16:51:32,005 - stcal.jump.jump - INFO - Flagging Showers
2026-07-28 16:51:38,774 - stcal.jump.jump - INFO - Total showers= 0
2026-07-28 16:51:38,775 - stcal.jump.jump - INFO - Total elapsed time = 8.5146 sec
2026-07-28 16:51:38,794 - jwst.jump.jump_step - INFO - The execution time in seconds: 8.634647
2026-07-28 16:51:38,797 - stpipe.step - INFO - Step jump done
2026-07-28 16:51:38,958 - stpipe.step - INFO - Step picture_frame running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:38,959 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:39,121 - stpipe.step - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:39,122 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:39,285 - stpipe.step - INFO - Step persistence running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:39,286 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:39,449 - stpipe.step - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:39,455 - jwst.ramp_fitting.ramp_fit_step - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0088.fits
2026-07-28 16:51:39,455 - jwst.ramp_fitting.ramp_fit_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:51:39,483 - jwst.ramp_fitting.ramp_fit_step - INFO - Using algorithm = OLS_C
2026-07-28 16:51:39,484 - jwst.ramp_fitting.ramp_fit_step - INFO - Using weighting = optimal
2026-07-28 16:51:39,569 - stcal.ramp_fitting.ols_fit - INFO - Number of multiprocessing slices: 1
2026-07-28 16:51:39,577 - stcal.ramp_fitting.ols_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 2
2026-07-28 16:51:39,578 - stcal.ramp_fitting.ols_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2026-07-28 16:51:42,262 - stcal.ramp_fitting.ols_fit - INFO - Ramp Fitting C Time: 2.6833088397979736
2026-07-28 16:51:42,422 - stpipe.step - INFO - Step ramp_fit done
2026-07-28 16:51:42,585 - stpipe.step - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:42,589 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:51:42,604 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:51:42,605 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:51:42,764 - stpipe.step - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:42,789 - py.warnings - WARNING - /tmp/ipykernel_3064/3735983842.py:14: DeprecationWarning: The Step.log attribute is deprecated and will be removed in a future release. Please use a local logger, retrieved via logging.getLogger.
self.log.info('Multiplied everything by one in custom step!')
2026-07-28 16:51:42,790 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:51:42,793 - stpipe.step - INFO - Step xply done
2026-07-28 16:51:42,796 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:51:42,958 - stpipe.step - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:42,961 - jwst.gain_scale.gain_scale_step - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2026-07-28 16:51:42,977 - jwst.gain_scale.gain_scale_step - INFO - GAINFACT not found in gain reference file
2026-07-28 16:51:42,978 - jwst.gain_scale.gain_scale_step - INFO - Step will be skipped
2026-07-28 16:51:43,138 - stpipe.step - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2026-07-28 16:51:43,163 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2026-07-28 16:51:43,167 - stpipe.step - INFO - Step xply done
2026-07-28 16:51:43,170 - stpipe.step - INFO - Step gain_scale done
2026-07-28 16:51:43,236 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rateints.fits
2026-07-28 16:51:43,237 - jwst.pipeline.calwebb_detector1 - INFO - ... ending calwebb_detector1
2026-07-28 16:51:43,238 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:51:43,300 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits
2026-07-28 16:51:43,301 - stpipe.step - INFO - Step Detector1Pipeline done
2026-07-28 16:51:43,302 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime so far: {time1 - time0:0.4f} seconds")
Runtime so far: 1051.6012 seconds
6.-Spec2 Pipeline#
In this section we process our countrate (slope) image products from Stage 1 (calwebb_detector1) through the Spec2 (calwebb_spec2) pipeline in order to produce Stage 2 data products (i.e., calibrated slope images and quick-look data cubes and 1d spectra). These data products have units of MJy/sr (or Jy for extracted point-source spectra).
See https://jwst-docs.stsci.edu/jwst-science-calibration-pipeline/stages-of-jwst-data-processing/calwebb_spec2
If pixel-based background subtraction was chosen above, this will be
applied during this stage.
To override certain steps and reference files use the examples below.
time_spec2 = time.perf_counter()
# Set up a dictionary to define how the Spec2 pipeline should be configured.
# Boilerplate dictionary setup
spec2dict = defaultdict(dict)
# Overrides for whether or not certain steps should be skipped (example)
#spec2dict['straylight']['skip'] = True
# Pixel-based background usage was set up above, propagate that here
if (pixel_bg is True):
spec2dict['bkg_subtract']['skip'] = False
else:
spec2dict['bkg_subtract']['skip'] = True
# Overrides for various reference files
# Files should be in the base local directory or provide full path
#spec2dict['assign_wcs']['override_distortion'] = 'myfile.asdf' # Spatial distortion (ASDF file)
#spec2dict['assign_wcs']['override_regions'] = 'myfile.asdf' # IFU slice regions on detector (ASDF file)
#spec2dict['assign_wcs']['override_specwcs'] = 'myfile.asdf' # Spectral distortion (ASDF file)
#spec2dict['assign_wcs']['override_wavelengthrange'] = 'myfile.asdf' # Wavelength channel mapping (ASDF file)
#spec2dict['flat_field']['override_flat'] = 'myfile.fits' # Pixel flatfield
#spec2dict['straylight']['override_mrsxartcorr'] = 'myfile.fits' # Cross-artifact model parameters
#spec2dict['fringe']['override_fringe'] = 'myfile.fits' # Static fringe-flat
#spec2dict['photom']['override_photom'] = 'myfile.fits' # Photometric calibration array
#spec2dict['cube_build']['override_cubepar'] = 'myfile.fits' # Cube-building parameters
#spec2dict['extract_1d']['override_extract1d'] = 'myfile.asdf' # Spectral extraction parameters (ASDF file)
#spec2dict['extract_1d']['override_apcorr'] = 'myfile.asdf' # Aperture correction parameters (ASDF file)
# Turn on residual cosmic-ray shower correction (off by default)
# (see https://jwst-docs.stsci.edu/known-issues-with-jwst-data/shower-and-snowball-artifacts)
#spec2dict['straylight']['clean_showers'] = True
# Turn on 2d residual fringe correction (off by default)
# This can sometimes improve residual fringing in science results, but takes
# a long time to run and often does not work as well as 1d residual fringe
# correction (in calwebb_spec3)
#spec2dict['residual_fringe']['skip'] = False
# Turn on bad pixel self-calibration, where all exposures on a given detector are used to find and
# flag bad pixels that may have been missed by the bad pixel mask.
# This step is experimental, and works best when dedicated background observations are included
#spec2dict['badpix_selfcal']['skip'] = False
#spec2dict['badpix_selfcal']['flagfrac_upper']=0.005 # Fraction of pixels to flag (dial as desired; 1.0 would be 100% of pixels)
Define a function to create association files for Stage 2. This will enable use of the pixel-based background subtraction, if chosen above. This requires one input SCI file, but can have multiple input background files.
Note that the background will not be applied properly to all files if more than *one* SCI file is included in the association.
def writel2asn(onescifile, bgfiles, selfcalfiles, asnfile, prodname):
# Define the basic association of science files
asn = afl.asn_from_list([onescifile], rule=DMSLevel2bBase, product_name=prodname) # Wrap in array since input was single exposure
#Channel/band configuration for this sci file
with fits.open(onescifile) as hdu:
hdu.verify()
hdr = hdu[0].header
this_channel, this_band = hdr['CHANNEL'], hdr['BAND']
# If backgrounds were provided, find which are appropriate to this
# channel/band and add to association
for file in bgfiles:
with fits.open(file) as hdu:
hdu.verify()
if ((hdu[0].header['CHANNEL'] == this_channel) & (hdu[0].header['BAND'] == this_band)):
asn['products'][0]['members'].append({'expname': file, 'exptype': 'background'})
# If provided with a list of files to use for bad pixel self-calibration, find which
# are appropriate to this detector and add to association
for file in selfcalfiles:
with fits.open(file) as hdu:
hdu.verify()
if (hdu[0].header['CHANNEL'] == this_channel):
asn['products'][0]['members'].append({'expname': file, 'exptype': 'selfcal'})
# Write the association to a json file
_, serialized = asn.dump()
with open(asnfile, 'w') as outfile:
outfile.write(serialized)
Find and sort all of the input files, ensuring use of absolute paths
sstring = os.path.join(det1_dir, 'jw*mirifu*rate.fits') # Use files from the detector1 output folder
ratefiles = sorted(glob.glob(sstring))
for ii in range(0, len(ratefiles)):
ratefiles[ii] = os.path.abspath(ratefiles[ii])
ratefiles = np.array(ratefiles)
# Check that these are the band/channel to use
ratefiles = select_ch_band_files(ratefiles, use_ch, use_band)
# Background Files
sstring = os.path.join(det1_bgdir, 'jw*mirifu*rate.fits')
bgfiles = sorted(glob.glob(sstring))
for ii in range(0, len(bgfiles)):
bgfiles[ii] = os.path.abspath(bgfiles[ii])
bgfiles = np.array(bgfiles)
# Check that these are the band/channel to use
bgfiles = select_ch_band_files(bgfiles, use_ch, use_band)
# Define any files to use for self-calibration (if step enabled)
# Typically this is all science and background exposures
selfcalfiles = ratefiles.copy()
selfcalfiles = np.append(selfcalfiles, bgfiles)
print('Found ' + str(len(ratefiles)) + ' science files')
print('Found ' + str(len(bgfiles)) + ' background files')
print('Found ' + str(len(selfcalfiles)) + ' potential selfcal files')
Found 24 science files
Found 12 background files
Found 36 potential selfcal files
Step through each of the science files, using relevant associated backgrounds in calwebb_spec2 processing.
The background files are used in this step to perform pixel-based background subtraction (if desired), otherwise background subtraction is done later with Spec3 files.
# To save runtime, make a new version of our spec2 parameter dictionary
# that turns off creation of quicklook cubes and 1d spectra for science
# data
spec2dict_sci = copy.deepcopy(spec2dict)
spec2dict_sci['cube_build']['skip'] = True
spec2dict_sci['extract_1d']['skip'] = True
if dospec2:
for file in ratefiles:
asnfile = os.path.join(sci_dir, 'l2asn.json')
writel2asn(file, bgfiles, selfcalfiles, asnfile, 'Level2')
Spec2Pipeline.call(asnfile, steps=spec2dict_sci, save_results=True, output_dir=spec2_dir)
else:
print('Skipping Spec2 processing for SCI data')
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:51:43,770 - CRDS - INFO - Syncing 1 files
2026-07-28 16:51:43,771 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf 965 bytes (1 / 1 files) (0 / 965 bytes)
2026-07-28 16:51:43,991 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:51:44,000 - CRDS - INFO - Syncing 1 files
2026-07-28 16:51:44,001 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf 987 bytes (1 / 1 files) (0 / 987 bytes)
2026-07-28 16:51:44,199 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:51:44,209 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:51:44,218 - CRDS - INFO - Syncing 1 files
2026-07-28 16:51:44,219 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf 1.0 K bytes (1 / 1 files) (0 / 1.0 K bytes)
2026-07-28 16:51:44,420 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:51:44,430 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:51:44,438 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:51:44,447 - CRDS - INFO - Syncing 1 files
2026-07-28 16:51:44,447 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf 2.1 K bytes (1 / 1 files) (0 / 2.1 K bytes)
2026-07-28 16:51:44,668 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:51:44,692 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:51:44,693 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:51:44,694 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:51:44,695 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:51:44,696 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:51:44,697 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:51:44,698 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:51:44,699 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:51:44,703 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:51:44,705 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:51:44,705 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:51:44,706 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:51:44,707 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:51:44,708 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:51:44,709 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:51:44,711 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:51:44,712 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:51:44,713 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:51:44,714 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:51:44,715 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:51:44,716 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:51:44,716 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:51:44,718 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:51:44,718 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:51:44,719 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:51:44,720 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:51:44,721 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:51:44,722 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:51:44,723 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:51:44,724 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:51:44,726 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:51:44,728 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:51:44,890 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:51:44,922 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:51:44,985 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:51:44,989 - CRDS - INFO - Syncing 8 files
2026-07-28 16:51:44,989 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf 125.0 K bytes (1 / 8 files) (0 / 106.3 M bytes)
2026-07-28 16:51:45,345 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits 21.2 M bytes (2 / 8 files) (125.0 K / 106.3 M bytes)
2026-07-28 16:51:46,764 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits 12.7 M bytes (3 / 8 files) (21.3 M / 106.3 M bytes)
2026-07-28 16:51:47,816 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits 383.0 K bytes (4 / 8 files) (34.0 M / 106.3 M bytes)
2026-07-28 16:51:48,290 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits 33.9 M bytes (5 / 8 files) (34.4 M / 106.3 M bytes)
2026-07-28 16:51:49,840 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf 38.0 M bytes (6 / 8 files) (68.2 M / 106.3 M bytes)
2026-07-28 16:51:51,323 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf 40.4 K bytes (7 / 8 files) (106.3 M / 106.3 M bytes)
2026-07-28 16:51:51,593 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf 3.7 K bytes (8 / 8 files) (106.3 M / 106.3 M bytes)
2026-07-28 16:51:51,792 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:51:51,793 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:51:51,793 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:51:51,794 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:51:51,794 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:51:51,795 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:51:51,795 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:51:51,796 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf'.
2026-07-28 16:51:51,796 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:51:51,797 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:51:51,797 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2026-07-28 16:51:51,798 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:51:51,798 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:51:51,799 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2026-07-28 16:51:51,800 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:51:51,800 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:51:51,801 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:51:51,801 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:51:51,802 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:51:51,802 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:51:51,803 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:51:51,803 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:51:51,804 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits'.
2026-07-28 16:51:51,804 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf'.
2026-07-28 16:51:51,805 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:51:51,805 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf'.
2026-07-28 16:51:51,806 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:51:51,806 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:51:51,807 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:51:51,814 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong
2026-07-28 16:51:51,815 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits ...
2026-07-28 16:51:52,031 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:51:52,703 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.00000873758768
2026-07-28 16:51:53,850 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:51:54,539 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.081822880 -70.085618819 81.089625616 -70.085618819 81.089625616 -70.082957758 81.081822880 -70.082957758
2026-07-28 16:51:54,540 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:51:54,544 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:51:54,733 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits']).
2026-07-28 16:51:54,735 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:54,915 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:51:54,916 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:55,096 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:51:55,096 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:55,275 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>, []).
2026-07-28 16:51:55,276 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:55,455 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', []).
2026-07-28 16:51:55,456 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:55,634 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', []).
2026-07-28 16:51:55,635 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:55,811 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits']).
2026-07-28 16:51:55,812 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:55,991 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:51:55,991 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:51:55,992 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:51:55,993 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:51:55,996 - stpipe.step - INFO - Step srctype done
2026-07-28 16:51:56,169 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:51:56,170 - stpipe.step - INFO - Step skipped.
2026-07-28 16:51:56,346 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:51:56,400 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:51:56,551 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:52:17,715 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:52:38,548 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03631567023694515 DN/s
2026-07-28 16:52:38,548 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:52:38,552 - stpipe.step - INFO - Step straylight done
2026-07-28 16:52:38,728 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:52:38,806 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:52:38,814 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2026-07-28 16:52:38,814 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:52:38,815 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:52:38,815 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:52:38,889 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:52:39,065 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:52:39,076 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2026-07-28 16:52:39,117 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:52:39,118 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:52:39,119 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:52:39,160 - stpipe.step - INFO - Step fringe done
2026-07-28 16:52:39,338 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:52:39,339 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:39,515 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:52:39,516 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:39,693 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:52:39,712 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits
2026-07-28 16:52:39,712 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:52:39,713 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:52:39,714 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 16:52:39,715 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:52:39,715 - jwst.photom.photom - INFO - band: LONG
2026-07-28 16:52:39,811 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:52:39,831 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:52:39,832 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:52:39,868 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:52:40,406 - stpipe.step - INFO - Step photom done
2026-07-28 16:52:40,583 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2026-07-28 16:52:40,584 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:41,369 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits>,).
2026-07-28 16:52:41,370 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:41,571 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits>,).
2026-07-28 16:52:41,572 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:41,774 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits>,).
2026-07-28 16:52:41,775 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:42,564 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits>,).
2026-07-28 16:52:42,565 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:42,569 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong
2026-07-28 16:52:42,570 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 16:52:42,571 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:52:42,969 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits
2026-07-28 16:52:42,970 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 16:52:42,970 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:52:43,361 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:52:43,370 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:52:43,379 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:52:43,387 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:52:43,396 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:52:43,405 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:52:43,413 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:52:43,435 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:52:43,437 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:52:43,438 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:52:43,438 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:52:43,440 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:52:43,441 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:52:43,441 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:52:43,442 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:52:43,447 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:52:43,448 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:52:43,449 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:52:43,449 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:52:43,450 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:52:43,451 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:52:43,452 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:52:43,454 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:52:43,455 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:52:43,455 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:52:43,456 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:52:43,457 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:52:43,458 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:52:43,459 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:52:43,460 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:52:43,461 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:52:43,462 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:52:43,463 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:52:43,464 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:52:43,465 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:52:43,465 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:52:43,467 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:52:43,468 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:52:43,469 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:52:43,740 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:52:43,774 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:52:43,833 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:52:43,837 - CRDS - INFO - Syncing 6 files
2026-07-28 16:52:43,837 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf 166.4 K bytes (1 / 6 files) (0 / 106.0 M bytes)
2026-07-28 16:52:44,245 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits 21.2 M bytes (2 / 6 files) (166.4 K / 106.0 M bytes)
2026-07-28 16:52:45,531 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits 12.7 M bytes (3 / 6 files) (21.3 M / 106.0 M bytes)
2026-07-28 16:52:46,650 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits 33.9 M bytes (4 / 6 files) (34.0 M / 106.0 M bytes)
2026-07-28 16:52:48,379 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 106.0 M bytes)
2026-07-28 16:52:49,947 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf 53.7 K bytes (6 / 6 files) (105.9 M / 106.0 M bytes)
2026-07-28 16:52:50,280 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:52:50,281 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:52:50,282 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:52:50,282 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:52:50,283 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:52:50,284 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:52:50,284 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:52:50,285 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf'.
2026-07-28 16:52:50,286 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:52:50,286 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:52:50,286 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2026-07-28 16:52:50,287 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:52:50,287 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:52:50,288 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2026-07-28 16:52:50,289 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:52:50,289 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:52:50,290 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:52:50,290 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:52:50,291 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:52:50,292 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:52:50,292 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:52:50,292 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:52:50,293 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits'.
2026-07-28 16:52:50,294 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf'.
2026-07-28 16:52:50,294 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:52:50,295 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf'.
2026-07-28 16:52:50,295 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:52:50,296 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:52:50,296 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:52:50,303 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort
2026-07-28 16:52:50,303 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits ...
2026-07-28 16:52:50,514 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:52:51,122 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.00000873758768
2026-07-28 16:52:52,574 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:52:53,355 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083690295 -70.085077549 81.088195633 -70.085077549 81.088195633 -70.083474314 81.083690295 -70.083474314
2026-07-28 16:52:53,356 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:52:53,360 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:52:53,619 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits']).
2026-07-28 16:52:53,622 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:53,811 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:52:53,812 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:54,001 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:52:54,002 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:54,193 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>, []).
2026-07-28 16:52:54,194 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:54,383 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', []).
2026-07-28 16:52:54,384 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:54,572 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', []).
2026-07-28 16:52:54,572 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:54,760 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits']).
2026-07-28 16:52:54,761 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:54,954 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:52:54,954 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:52:54,955 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:52:54,956 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:52:54,958 - stpipe.step - INFO - Step srctype done
2026-07-28 16:52:55,152 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:52:55,153 - stpipe.step - INFO - Step skipped.
2026-07-28 16:52:55,349 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:52:55,354 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:52:55,501 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:53:17,456 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:53:38,376 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.01862138039133427 DN/s
2026-07-28 16:53:38,377 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:53:38,381 - stpipe.step - INFO - Step straylight done
2026-07-28 16:53:38,571 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:53:38,632 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:53:38,639 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2026-07-28 16:53:38,640 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:53:38,640 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:53:38,641 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:53:38,711 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:53:38,902 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:53:38,907 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2026-07-28 16:53:38,946 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:53:38,947 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:53:38,948 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:53:38,988 - stpipe.step - INFO - Step fringe done
2026-07-28 16:53:39,179 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:53:39,180 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:39,374 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:53:39,374 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:39,565 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:53:39,574 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits
2026-07-28 16:53:39,574 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:53:39,575 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:53:39,575 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 16:53:39,576 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:53:39,577 - jwst.photom.photom - INFO - band: LONG
2026-07-28 16:53:39,664 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:53:39,685 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:53:39,686 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:53:39,723 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:53:40,293 - stpipe.step - INFO - Step photom done
2026-07-28 16:53:40,487 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2026-07-28 16:53:40,487 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:41,516 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits>,).
2026-07-28 16:53:41,517 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:41,744 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits>,).
2026-07-28 16:53:41,745 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:41,973 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits>,).
2026-07-28 16:53:41,974 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:43,005 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits>,).
2026-07-28 16:53:43,006 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:43,010 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort
2026-07-28 16:53:43,011 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 16:53:43,012 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:53:43,470 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits
2026-07-28 16:53:43,471 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 16:53:43,472 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:53:43,864 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:53:43,873 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:53:43,882 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:53:43,890 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:53:43,899 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:53:43,909 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:53:43,917 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:53:43,940 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:53:43,941 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:53:43,943 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:53:43,944 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:53:43,945 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:53:43,946 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:53:43,947 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:53:43,948 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:53:43,953 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:53:43,954 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:53:43,955 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:53:43,956 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:53:43,957 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:53:43,958 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:53:43,959 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:53:43,960 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:53:43,961 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:53:43,962 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:53:43,963 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:53:43,964 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:53:43,965 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:53:43,966 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:53:43,967 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:53:43,968 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:53:43,969 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:53:43,970 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:53:43,971 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:53:43,972 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:53:43,972 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:53:43,973 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:53:43,975 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:53:43,976 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:53:44,355 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:53:44,389 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:53:44,448 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:53:44,451 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:53:44,452 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:53:44,452 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:53:44,453 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:53:44,453 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:53:44,454 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:53:44,454 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:53:44,455 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf'.
2026-07-28 16:53:44,456 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:53:44,456 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:53:44,457 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2026-07-28 16:53:44,457 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:53:44,457 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:53:44,458 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2026-07-28 16:53:44,459 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:53:44,459 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:53:44,460 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:53:44,460 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:53:44,461 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:53:44,461 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:53:44,462 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:53:44,462 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:53:44,463 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits'.
2026-07-28 16:53:44,463 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf'.
2026-07-28 16:53:44,464 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:53:44,464 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf'.
2026-07-28 16:53:44,465 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:53:44,465 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:53:44,466 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:53:44,472 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong
2026-07-28 16:53:44,473 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits ...
2026-07-28 16:53:44,682 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:53:45,153 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 16:53:46,341 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:53:47,021 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.082556597 -70.084786022 81.090359058 -70.084786022 81.090359058 -70.082124945 81.082556597 -70.082124945
2026-07-28 16:53:47,022 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:53:47,026 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:53:47,227 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits']).
2026-07-28 16:53:47,229 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:47,417 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:53:47,418 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:47,607 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:53:47,608 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:47,796 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>, []).
2026-07-28 16:53:47,797 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:47,985 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', []).
2026-07-28 16:53:47,985 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:48,175 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', []).
2026-07-28 16:53:48,176 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:48,364 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits']).
2026-07-28 16:53:48,365 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:48,552 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:53:48,553 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:53:48,554 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:53:48,554 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:53:48,557 - stpipe.step - INFO - Step srctype done
2026-07-28 16:53:48,742 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:53:48,743 - stpipe.step - INFO - Step skipped.
2026-07-28 16:53:48,932 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:53:48,936 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:53:49,082 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:54:10,275 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:54:31,193 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.04294331930577755 DN/s
2026-07-28 16:54:31,194 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:54:31,198 - stpipe.step - INFO - Step straylight done
2026-07-28 16:54:31,384 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:54:31,443 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:54:31,451 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2026-07-28 16:54:31,451 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:54:31,452 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:54:31,453 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:54:31,522 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:54:31,708 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:54:31,712 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2026-07-28 16:54:31,753 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:54:31,753 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:54:31,754 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:54:31,796 - stpipe.step - INFO - Step fringe done
2026-07-28 16:54:31,981 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:54:31,982 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:32,168 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:54:32,169 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:32,355 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:54:32,363 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits
2026-07-28 16:54:32,364 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:54:32,364 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:54:32,365 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 16:54:32,365 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:54:32,365 - jwst.photom.photom - INFO - band: LONG
2026-07-28 16:54:32,452 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:54:32,473 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:54:32,474 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:54:32,511 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:54:33,042 - stpipe.step - INFO - Step photom done
2026-07-28 16:54:33,231 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2026-07-28 16:54:33,232 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:34,035 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits>,).
2026-07-28 16:54:34,036 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:34,247 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits>,).
2026-07-28 16:54:34,247 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:34,457 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits>,).
2026-07-28 16:54:34,458 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:35,274 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits>,).
2026-07-28 16:54:35,274 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:35,278 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong
2026-07-28 16:54:35,279 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 16:54:35,280 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:54:35,656 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits
2026-07-28 16:54:35,657 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 16:54:35,658 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:54:36,053 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:54:36,061 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:54:36,070 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:54:36,078 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:54:36,086 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:54:36,095 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:54:36,104 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:54:36,126 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:54:36,128 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:54:36,129 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:54:36,130 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:54:36,131 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:54:36,132 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:54:36,133 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:54:36,134 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:54:36,138 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:54:36,140 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:54:36,140 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:54:36,141 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:54:36,142 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:54:36,143 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:54:36,144 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:54:36,146 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:54:36,147 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:54:36,148 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:54:36,149 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:54:36,149 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:54:36,150 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:54:36,152 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:54:36,153 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:54:36,153 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:54:36,154 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:54:36,155 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:54:36,156 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:54:36,158 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:54:36,159 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:54:36,160 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:54:36,161 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:54:36,163 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:54:36,493 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:54:36,525 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:54:36,584 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:54:36,587 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:54:36,588 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:54:36,588 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:54:36,588 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:54:36,589 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:54:36,589 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:54:36,590 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:54:36,590 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf'.
2026-07-28 16:54:36,591 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:54:36,591 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:54:36,592 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2026-07-28 16:54:36,593 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:54:36,593 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:54:36,593 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2026-07-28 16:54:36,594 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:54:36,594 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:54:36,595 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:54:36,595 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:54:36,596 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:54:36,596 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:54:36,597 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:54:36,597 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:54:36,598 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits'.
2026-07-28 16:54:36,598 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf'.
2026-07-28 16:54:36,599 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:54:36,599 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf'.
2026-07-28 16:54:36,600 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:54:36,600 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:54:36,601 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:54:36,608 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort
2026-07-28 16:54:36,608 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits ...
2026-07-28 16:54:36,817 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:54:37,431 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.00000873758768
2026-07-28 16:54:38,914 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:54:39,689 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084423941 -70.084244745 81.088929130 -70.084244745 81.088929130 -70.082641503 81.084423941 -70.082641503
2026-07-28 16:54:39,691 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:54:39,694 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:54:39,974 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits']).
2026-07-28 16:54:39,976 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:40,173 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:54:40,174 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:40,374 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:54:40,376 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:40,576 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>, []).
2026-07-28 16:54:40,577 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:40,773 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', []).
2026-07-28 16:54:40,774 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:40,974 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', []).
2026-07-28 16:54:40,974 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:41,173 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits']).
2026-07-28 16:54:41,174 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:41,372 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:54:41,373 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:54:41,374 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:54:41,374 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:54:41,377 - stpipe.step - INFO - Step srctype done
2026-07-28 16:54:41,582 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:54:41,582 - stpipe.step - INFO - Step skipped.
2026-07-28 16:54:41,784 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:54:41,789 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:54:41,937 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:55:03,919 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:55:24,808 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.02334309954371149 DN/s
2026-07-28 16:55:24,809 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:55:24,813 - stpipe.step - INFO - Step straylight done
2026-07-28 16:55:25,010 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:55:25,069 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:55:25,077 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2026-07-28 16:55:25,077 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:55:25,078 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:55:25,079 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:55:25,147 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:55:25,341 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:55:25,345 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2026-07-28 16:55:25,386 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:55:25,387 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:55:25,387 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:55:25,428 - stpipe.step - INFO - Step fringe done
2026-07-28 16:55:25,623 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:55:25,624 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:25,822 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:55:25,823 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:26,022 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:55:26,030 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits
2026-07-28 16:55:26,031 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:55:26,032 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:55:26,032 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 16:55:26,033 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:55:26,033 - jwst.photom.photom - INFO - band: LONG
2026-07-28 16:55:26,121 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:55:26,142 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:55:26,143 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:55:26,180 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:55:26,745 - stpipe.step - INFO - Step photom done
2026-07-28 16:55:26,943 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2026-07-28 16:55:26,943 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:27,983 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits>,).
2026-07-28 16:55:27,984 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:28,218 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits>,).
2026-07-28 16:55:28,218 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:28,454 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits>,).
2026-07-28 16:55:28,455 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:29,506 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits>,).
2026-07-28 16:55:29,507 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:29,510 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort
2026-07-28 16:55:29,511 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 16:55:29,512 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:55:29,971 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits
2026-07-28 16:55:29,972 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 16:55:29,973 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:55:30,367 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:55:30,375 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:55:30,383 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:55:30,392 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:55:30,400 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:55:30,409 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:55:30,417 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:55:30,439 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:55:30,440 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:55:30,442 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:55:30,442 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:55:30,443 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:55:30,444 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:55:30,445 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:55:30,447 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:55:30,451 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:55:30,452 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:55:30,453 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:55:30,454 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:55:30,455 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:55:30,456 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:55:30,457 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:55:30,459 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:55:30,459 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:55:30,460 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:55:30,461 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:55:30,462 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:55:30,463 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:55:30,464 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:55:30,465 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:55:30,466 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:55:30,467 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:55:30,468 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:55:30,469 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:55:30,471 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:55:30,472 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:55:30,473 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:55:30,474 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:55:30,476 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:55:30,879 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:55:30,911 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:55:30,971 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:55:30,974 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:55:30,975 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:55:30,975 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:55:30,976 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:55:30,977 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:55:30,977 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:55:30,978 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:55:30,978 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf'.
2026-07-28 16:55:30,979 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:55:30,979 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:55:30,980 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2026-07-28 16:55:30,980 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:55:30,981 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:55:30,981 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2026-07-28 16:55:30,982 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:55:30,983 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:55:30,983 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:55:30,983 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:55:30,984 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:55:30,985 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:55:30,985 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:55:30,985 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:55:30,986 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits'.
2026-07-28 16:55:30,987 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf'.
2026-07-28 16:55:30,987 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:55:30,988 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf'.
2026-07-28 16:55:30,988 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:55:30,989 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:55:30,989 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:55:30,996 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong
2026-07-28 16:55:30,997 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits ...
2026-07-28 16:55:31,202 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:55:31,670 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.00000873758768
2026-07-28 16:55:32,846 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:55:33,510 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.081901038 -70.085479096 81.089703724 -70.085479096 81.089703724 -70.082818034 81.081901038 -70.082818034
2026-07-28 16:55:33,512 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:55:33,515 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:55:33,712 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits']).
2026-07-28 16:55:33,714 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:33,898 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:55:33,898 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:34,085 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:55:34,085 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:34,272 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>, []).
2026-07-28 16:55:34,273 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:34,459 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', []).
2026-07-28 16:55:34,460 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:34,646 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', []).
2026-07-28 16:55:34,647 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:34,831 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits']).
2026-07-28 16:55:34,832 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:35,018 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:55:35,019 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:55:35,019 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:55:35,020 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:55:35,023 - stpipe.step - INFO - Step srctype done
2026-07-28 16:55:35,208 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:55:35,209 - stpipe.step - INFO - Step skipped.
2026-07-28 16:55:35,395 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:55:35,400 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:55:35,544 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:55:56,730 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:56:17,648 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03502415120601654 DN/s
2026-07-28 16:56:17,649 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:56:17,653 - stpipe.step - INFO - Step straylight done
2026-07-28 16:56:17,844 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:56:17,905 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:56:17,912 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2026-07-28 16:56:17,913 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:56:17,914 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:56:17,914 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:56:17,985 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:56:18,175 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:56:18,179 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2026-07-28 16:56:18,220 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:56:18,221 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:56:18,222 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:56:18,264 - stpipe.step - INFO - Step fringe done
2026-07-28 16:56:18,448 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:56:18,449 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:18,635 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:56:18,636 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:18,835 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:56:18,843 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits
2026-07-28 16:56:18,844 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:56:18,844 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:56:18,845 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 16:56:18,846 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:56:18,846 - jwst.photom.photom - INFO - band: LONG
2026-07-28 16:56:18,933 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:56:18,954 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:56:18,954 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:56:18,992 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:56:19,526 - stpipe.step - INFO - Step photom done
2026-07-28 16:56:19,712 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2026-07-28 16:56:19,713 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:20,521 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits>,).
2026-07-28 16:56:20,522 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:20,739 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits>,).
2026-07-28 16:56:20,740 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:20,956 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits>,).
2026-07-28 16:56:20,956 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:21,794 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits>,).
2026-07-28 16:56:21,795 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:21,799 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong
2026-07-28 16:56:21,800 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 16:56:21,800 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:56:22,177 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits
2026-07-28 16:56:22,177 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 16:56:22,178 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:56:22,566 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:56:22,574 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:56:22,583 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:56:22,591 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:56:22,600 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:56:22,609 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:56:22,617 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:56:22,640 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:56:22,642 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:56:22,643 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:56:22,644 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:56:22,645 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:56:22,646 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:56:22,647 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:56:22,648 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:56:22,652 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:56:22,653 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:56:22,654 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:56:22,655 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:56:22,656 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:56:22,657 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:56:22,658 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:56:22,659 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:56:22,660 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:56:22,661 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:56:22,662 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:56:22,663 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:56:22,664 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:56:22,665 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:56:22,666 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:56:22,667 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:56:22,668 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:56:22,669 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:56:22,670 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:56:22,671 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:56:22,672 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:56:22,674 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:56:22,675 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:56:22,677 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:56:23,031 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:56:23,063 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:56:23,122 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:56:23,126 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:56:23,126 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:56:23,127 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:56:23,127 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:56:23,128 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:56:23,128 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:56:23,129 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:56:23,129 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf'.
2026-07-28 16:56:23,130 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:56:23,130 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:56:23,131 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2026-07-28 16:56:23,131 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:56:23,132 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:56:23,132 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2026-07-28 16:56:23,133 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:56:23,133 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:56:23,134 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:56:23,134 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:56:23,135 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:56:23,135 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:56:23,136 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:56:23,136 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:56:23,137 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits'.
2026-07-28 16:56:23,137 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf'.
2026-07-28 16:56:23,138 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:56:23,138 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf'.
2026-07-28 16:56:23,139 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:56:23,139 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:56:23,140 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:56:23,146 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort
2026-07-28 16:56:23,147 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits ...
2026-07-28 16:56:23,362 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:56:23,974 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.00000873758768
2026-07-28 16:56:25,456 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:56:26,227 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083768439 -70.084937825 81.088273750 -70.084937825 81.088273750 -70.083334589 81.083768439 -70.083334589
2026-07-28 16:56:26,228 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:56:26,232 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:56:26,500 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits']).
2026-07-28 16:56:26,502 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:26,705 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:56:26,705 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:26,903 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:56:26,904 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:27,101 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>, []).
2026-07-28 16:56:27,102 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:27,301 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', []).
2026-07-28 16:56:27,301 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:27,497 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', []).
2026-07-28 16:56:27,498 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:27,695 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits']).
2026-07-28 16:56:27,696 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:27,891 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:56:27,892 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:56:27,893 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:56:27,893 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:56:27,896 - stpipe.step - INFO - Step srctype done
2026-07-28 16:56:28,092 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:56:28,093 - stpipe.step - INFO - Step skipped.
2026-07-28 16:56:28,291 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:56:28,296 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:56:28,442 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:56:50,408 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:57:11,297 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03316158295852964 DN/s
2026-07-28 16:57:11,298 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:57:11,302 - stpipe.step - INFO - Step straylight done
2026-07-28 16:57:11,495 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:57:11,554 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:57:11,562 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2026-07-28 16:57:11,562 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:57:11,563 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:57:11,563 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:57:11,634 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:57:11,831 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:57:11,836 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2026-07-28 16:57:11,877 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:57:11,878 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:57:11,879 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:57:11,919 - stpipe.step - INFO - Step fringe done
2026-07-28 16:57:12,116 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:57:12,116 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:12,316 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:57:12,317 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:12,517 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:57:12,525 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits
2026-07-28 16:57:12,526 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:57:12,526 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:57:12,527 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 16:57:12,527 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:57:12,528 - jwst.photom.photom - INFO - band: LONG
2026-07-28 16:57:12,614 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:57:12,635 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:57:12,636 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:57:12,673 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:57:13,236 - stpipe.step - INFO - Step photom done
2026-07-28 16:57:13,437 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2026-07-28 16:57:13,438 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:14,482 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits>,).
2026-07-28 16:57:14,483 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:14,721 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits>,).
2026-07-28 16:57:14,721 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:14,959 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits>,).
2026-07-28 16:57:14,960 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:16,031 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits>,).
2026-07-28 16:57:16,032 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:16,035 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort
2026-07-28 16:57:16,036 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 16:57:16,037 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:57:16,494 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits
2026-07-28 16:57:16,495 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 16:57:16,496 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:57:16,889 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:57:16,897 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:57:16,906 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:57:16,914 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:57:16,923 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:57:16,932 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:57:16,940 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:57:16,963 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:57:16,964 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:57:16,965 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:57:16,966 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:57:16,967 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:57:16,969 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:57:16,969 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:57:16,971 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:57:16,975 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:57:16,976 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:57:16,977 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:57:16,978 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:57:16,979 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:57:16,979 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:57:16,980 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:57:16,982 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:57:16,983 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:57:16,984 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:57:16,985 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:57:16,986 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:57:16,987 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:57:16,988 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:57:16,989 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:57:16,989 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:57:16,990 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:57:16,991 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:57:16,992 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:57:16,993 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:57:16,994 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:57:16,995 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:57:16,997 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:57:16,998 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:57:17,403 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:57:17,436 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:57:17,494 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:57:17,498 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:57:17,498 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:57:17,500 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:57:17,500 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:57:17,501 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:57:17,501 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:57:17,503 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:57:17,504 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf'.
2026-07-28 16:57:17,504 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:57:17,505 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:57:17,505 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2026-07-28 16:57:17,506 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:57:17,506 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:57:17,507 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2026-07-28 16:57:17,507 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:57:17,508 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:57:17,508 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:57:17,509 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:57:17,509 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:57:17,510 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:57:17,510 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:57:17,511 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:57:17,512 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits'.
2026-07-28 16:57:17,512 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf'.
2026-07-28 16:57:17,513 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:57:17,513 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf'.
2026-07-28 16:57:17,514 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:57:17,514 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:57:17,515 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:57:17,522 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong
2026-07-28 16:57:17,522 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits ...
2026-07-28 16:57:17,733 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:57:18,202 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 16:57:19,378 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:57:20,049 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.082636066 -70.084648190 81.090438468 -70.084648190 81.090438468 -70.081987117 81.082636066 -70.081987117
2026-07-28 16:57:20,051 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:57:20,054 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:57:20,257 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits']).
2026-07-28 16:57:20,259 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:20,455 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:57:20,456 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:20,649 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:57:20,650 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:20,844 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>, []).
2026-07-28 16:57:20,844 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:21,040 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', []).
2026-07-28 16:57:21,041 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:21,231 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', []).
2026-07-28 16:57:21,232 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:21,421 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits']).
2026-07-28 16:57:21,422 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:21,610 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:57:21,611 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:57:21,612 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:57:21,612 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:57:21,615 - stpipe.step - INFO - Step srctype done
2026-07-28 16:57:21,803 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:57:21,804 - stpipe.step - INFO - Step skipped.
2026-07-28 16:57:21,995 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:57:22,001 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:57:22,145 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:57:43,352 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:58:04,301 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.04003297910094261 DN/s
2026-07-28 16:58:04,302 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:58:04,305 - stpipe.step - INFO - Step straylight done
2026-07-28 16:58:04,490 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:58:04,549 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:04,557 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2026-07-28 16:58:04,557 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:58:04,558 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:58:04,558 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:58:04,628 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:58:04,813 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:58:04,818 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2026-07-28 16:58:04,858 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:04,859 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:04,860 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:04,900 - stpipe.step - INFO - Step fringe done
2026-07-28 16:58:05,087 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:58:05,088 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:05,279 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:58:05,280 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:05,471 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:58:05,479 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits
2026-07-28 16:58:05,479 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:58:05,480 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:58:05,480 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 16:58:05,481 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:58:05,481 - jwst.photom.photom - INFO - band: LONG
2026-07-28 16:58:05,570 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:05,590 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:58:05,591 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:58:05,628 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:58:06,144 - stpipe.step - INFO - Step photom done
2026-07-28 16:58:06,333 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2026-07-28 16:58:06,333 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:07,146 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits>,).
2026-07-28 16:58:07,147 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:07,365 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits>,).
2026-07-28 16:58:07,366 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:07,584 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits>,).
2026-07-28 16:58:07,585 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:08,423 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits>,).
2026-07-28 16:58:08,424 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:08,428 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong
2026-07-28 16:58:08,429 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 16:58:08,430 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:58:08,805 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits
2026-07-28 16:58:08,806 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 16:58:08,806 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:58:09,191 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:58:09,200 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:58:09,208 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:58:09,217 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:58:09,226 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:58:09,235 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:58:09,243 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:58:09,266 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:58:09,268 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:58:09,269 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:58:09,270 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:58:09,271 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:58:09,272 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:58:09,273 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:58:09,274 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:58:09,279 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:58:09,280 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:58:09,281 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:58:09,282 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:58:09,282 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:58:09,284 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:58:09,285 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:58:09,286 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:58:09,287 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:58:09,288 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:58:09,289 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:58:09,289 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:58:09,290 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:58:09,292 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:58:09,293 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:58:09,293 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:58:09,294 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:58:09,295 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:58:09,296 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:58:09,298 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:58:09,298 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:58:09,299 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:58:09,301 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:58:09,303 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:58:09,651 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:58:09,684 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:58:09,744 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:58:09,747 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:58:09,748 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:58:09,748 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:58:09,749 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:58:09,750 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:58:09,750 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:58:09,750 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:58:09,751 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf'.
2026-07-28 16:58:09,752 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:58:09,752 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:58:09,752 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2026-07-28 16:58:09,753 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:58:09,754 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:58:09,754 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2026-07-28 16:58:09,755 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:58:09,755 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:58:09,756 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:58:09,756 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:58:09,757 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:58:09,757 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:58:09,758 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:58:09,758 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:58:09,759 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits'.
2026-07-28 16:58:09,759 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf'.
2026-07-28 16:58:09,760 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:58:09,760 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf'.
2026-07-28 16:58:09,761 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:58:09,761 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:58:09,762 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:58:09,768 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort
2026-07-28 16:58:09,769 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits ...
2026-07-28 16:58:09,975 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:10,583 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 16:58:12,058 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:58:12,848 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084503398 -70.084106914 81.089008551 -70.084106914 81.089008551 -70.082503674 81.084503398 -70.082503674
2026-07-28 16:58:12,850 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:58:12,853 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:58:13,125 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits']).
2026-07-28 16:58:13,127 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:13,324 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:13,325 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:13,524 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:13,525 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:13,720 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>, []).
2026-07-28 16:58:13,720 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:13,915 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', []).
2026-07-28 16:58:13,916 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:14,112 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', []).
2026-07-28 16:58:14,112 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:14,307 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits']).
2026-07-28 16:58:14,308 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:14,504 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:14,504 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:58:14,505 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:58:14,505 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:58:14,508 - stpipe.step - INFO - Step srctype done
2026-07-28 16:58:14,702 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:14,703 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:14,899 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:14,904 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:58:15,048 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:58:37,021 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:58:57,904 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.04123371486581802 DN/s
2026-07-28 16:58:57,905 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:58:57,909 - stpipe.step - INFO - Step straylight done
2026-07-28 16:58:58,103 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:58,162 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:58,169 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2026-07-28 16:58:58,169 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:58:58,170 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:58:58,171 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:58:58,239 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:58:58,431 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:58,436 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2026-07-28 16:58:58,477 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:58,477 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:58,478 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:58,519 - stpipe.step - INFO - Step fringe done
2026-07-28 16:58:58,714 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:58,715 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:58,914 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:58,914 - stpipe.step - INFO - Step skipped.
2026-07-28 16:58:59,113 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:58:59,121 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits
2026-07-28 16:58:59,122 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:58:59,123 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:58:59,123 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 16:58:59,124 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:58:59,124 - jwst.photom.photom - INFO - band: LONG
2026-07-28 16:58:59,212 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:58:59,234 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:58:59,235 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:58:59,273 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:58:59,844 - stpipe.step - INFO - Step photom done
2026-07-28 16:59:00,041 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2026-07-28 16:59:00,041 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:01,093 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits>,).
2026-07-28 16:59:01,094 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:01,329 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits>,).
2026-07-28 16:59:01,329 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:01,566 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits>,).
2026-07-28 16:59:01,567 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:02,621 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits>,).
2026-07-28 16:59:02,622 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:02,625 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort
2026-07-28 16:59:02,626 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 16:59:02,627 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 16:59:03,089 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits
2026-07-28 16:59:03,090 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 16:59:03,090 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 16:59:03,485 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:59:03,493 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:59:03,501 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 16:59:03,510 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 16:59:03,519 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 16:59:03,528 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 16:59:03,536 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 16:59:03,559 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 16:59:03,560 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 16:59:03,562 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 16:59:03,562 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 16:59:03,563 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 16:59:03,565 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 16:59:03,565 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 16:59:03,566 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 16:59:03,571 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 16:59:03,572 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:59:03,574 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:59:03,575 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:59:03,576 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:59:03,576 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:59:03,578 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:59:03,579 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:59:03,580 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 16:59:03,581 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 16:59:03,582 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 16:59:03,583 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 16:59:03,585 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 16:59:03,586 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 16:59:03,587 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 16:59:03,588 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 16:59:03,589 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 16:59:03,590 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 16:59:03,591 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 16:59:03,592 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 16:59:03,593 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 16:59:03,594 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 16:59:03,595 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 16:59:03,597 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 16:59:04,011 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 16:59:04,044 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 16:59:04,104 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 16:59:04,109 - CRDS - INFO - Syncing 6 files
2026-07-28 16:59:04,109 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf 125.1 K bytes (1 / 6 files) (0 / 105.9 M bytes)
2026-07-28 16:59:04,587 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits 21.2 M bytes (2 / 6 files) (125.1 K / 105.9 M bytes)
2026-07-28 16:59:05,873 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits 12.7 M bytes (3 / 6 files) (21.3 M / 105.9 M bytes)
2026-07-28 16:59:06,960 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits 33.9 M bytes (4 / 6 files) (34.0 M / 105.9 M bytes)
2026-07-28 16:59:08,422 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 105.9 M bytes)
2026-07-28 16:59:09,888 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf 40.4 K bytes (6 / 6 files) (105.9 M / 105.9 M bytes)
2026-07-28 16:59:10,164 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 16:59:10,165 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 16:59:10,166 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 16:59:10,166 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 16:59:10,167 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 16:59:10,167 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 16:59:10,167 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 16:59:10,168 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf'.
2026-07-28 16:59:10,169 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 16:59:10,169 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 16:59:10,170 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits'.
2026-07-28 16:59:10,170 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 16:59:10,171 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 16:59:10,172 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2026-07-28 16:59:10,172 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 16:59:10,173 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 16:59:10,173 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 16:59:10,174 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 16:59:10,175 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 16:59:10,175 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 16:59:10,175 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 16:59:10,176 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 16:59:10,176 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits'.
2026-07-28 16:59:10,177 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf'.
2026-07-28 16:59:10,178 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 16:59:10,178 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf'.
2026-07-28 16:59:10,178 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 16:59:10,179 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 16:59:10,180 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 16:59:10,187 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong
2026-07-28 16:59:10,187 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits ...
2026-07-28 16:59:10,395 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:10,872 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 16:59:12,069 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 16:59:12,736 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.081970046 -70.085622316 81.089744449 -70.085622316 81.089744449 -70.082973266 81.081970046 -70.082973266
2026-07-28 16:59:12,738 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 16:59:12,742 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 16:59:12,944 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits']).
2026-07-28 16:59:12,946 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:13,139 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:13,140 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:13,332 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:13,333 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:13,525 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>, []).
2026-07-28 16:59:13,526 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:13,716 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', []).
2026-07-28 16:59:13,717 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:13,906 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', []).
2026-07-28 16:59:13,907 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:14,094 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits']).
2026-07-28 16:59:14,094 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:14,283 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:14,283 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 16:59:14,284 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 16:59:14,284 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 16:59:14,287 - stpipe.step - INFO - Step srctype done
2026-07-28 16:59:14,474 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:14,475 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:14,664 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:14,669 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 16:59:14,813 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 16:59:35,980 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 16:59:56,868 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03494076803326607 DN/s
2026-07-28 16:59:56,868 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 16:59:56,872 - stpipe.step - INFO - Step straylight done
2026-07-28 16:59:57,061 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:57,121 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:59:57,128 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits
2026-07-28 16:59:57,129 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 16:59:57,129 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 16:59:57,130 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 16:59:57,198 - stpipe.step - INFO - Step flat_field done
2026-07-28 16:59:57,387 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:57,392 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2026-07-28 16:59:57,432 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:59:57,432 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:59:57,433 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:59:57,474 - stpipe.step - INFO - Step fringe done
2026-07-28 16:59:57,659 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:57,660 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:57,845 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:57,846 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:58,034 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:58,042 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits
2026-07-28 16:59:58,043 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 16:59:58,044 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 16:59:58,044 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 16:59:58,044 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 16:59:58,045 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 16:59:58,131 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 16:59:58,152 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 16:59:58,152 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 16:59:58,189 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 16:59:58,709 - stpipe.step - INFO - Step photom done
2026-07-28 16:59:58,897 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2026-07-28 16:59:58,898 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:59,702 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits>,).
2026-07-28 16:59:59,703 - stpipe.step - INFO - Step skipped.
2026-07-28 16:59:59,911 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits>,).
2026-07-28 16:59:59,912 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:00,128 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits>,).
2026-07-28 17:00:00,129 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:00,944 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits>,).
2026-07-28 17:00:00,945 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:00,949 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong
2026-07-28 17:00:00,950 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:00:00,951 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:00:01,323 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits
2026-07-28 17:00:01,324 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:00:01,325 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:00:01,707 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:00:01,716 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:00:01,724 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:00:01,733 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:00:01,741 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:00:01,750 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:00:01,758 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:00:01,781 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:00:01,782 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:00:01,784 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:00:01,785 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:00:01,786 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:00:01,787 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:00:01,787 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:00:01,788 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:00:01,793 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:00:01,794 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:00:01,795 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:00:01,796 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:00:01,797 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:00:01,798 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:00:01,799 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:00:01,800 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:00:01,801 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:00:01,802 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:00:01,803 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:00:01,804 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:00:01,805 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:00:01,806 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:00:01,807 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:00:01,808 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:00:01,809 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:00:01,810 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:00:01,811 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:00:01,812 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:00:01,812 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:00:01,814 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:00:01,815 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:00:01,817 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:00:02,152 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:00:02,185 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:00:02,244 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:00:02,248 - CRDS - INFO - Syncing 6 files
2026-07-28 17:00:02,249 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf 166.3 K bytes (1 / 6 files) (0 / 106.0 M bytes)
2026-07-28 17:00:02,675 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits 21.2 M bytes (2 / 6 files) (166.3 K / 106.0 M bytes)
2026-07-28 17:00:04,191 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits 12.7 M bytes (3 / 6 files) (21.3 M / 106.0 M bytes)
2026-07-28 17:00:05,509 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits 33.9 M bytes (4 / 6 files) (34.0 M / 106.0 M bytes)
2026-07-28 17:00:07,195 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 106.0 M bytes)
2026-07-28 17:00:08,819 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf 53.7 K bytes (6 / 6 files) (105.9 M / 106.0 M bytes)
2026-07-28 17:00:09,146 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:00:09,147 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:00:09,147 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:00:09,148 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:00:09,149 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:00:09,149 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:00:09,150 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:00:09,150 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf'.
2026-07-28 17:00:09,151 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:00:09,151 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:00:09,152 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2026-07-28 17:00:09,152 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:00:09,153 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:00:09,153 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2026-07-28 17:00:09,154 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:00:09,155 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:00:09,155 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:00:09,155 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:00:09,156 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:00:09,157 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:00:09,157 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:00:09,158 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:00:09,158 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits'.
2026-07-28 17:00:09,159 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf'.
2026-07-28 17:00:09,159 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:00:09,160 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf'.
2026-07-28 17:00:09,160 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:00:09,161 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:00:09,162 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:00:09,168 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort
2026-07-28 17:00:09,169 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits ...
2026-07-28 17:00:09,379 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:09,983 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:00:11,448 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:00:12,218 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083833334 -70.085031228 81.088275348 -70.085031228 81.088275348 -70.083425112 81.083833334 -70.083425112
2026-07-28 17:00:12,220 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:00:12,224 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:00:12,500 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits']).
2026-07-28 17:00:12,503 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:12,699 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:12,699 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:12,895 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:12,896 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:13,092 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>, []).
2026-07-28 17:00:13,093 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:13,294 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', []).
2026-07-28 17:00:13,295 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:13,488 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', []).
2026-07-28 17:00:13,489 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:13,681 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits']).
2026-07-28 17:00:13,681 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:13,878 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:13,879 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:00:13,880 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:00:13,880 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:00:13,883 - stpipe.step - INFO - Step srctype done
2026-07-28 17:00:14,076 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:14,077 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:14,274 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:14,279 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:00:14,424 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:00:36,234 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:00:57,134 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.043493556615697496 DN/s
2026-07-28 17:00:57,134 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:00:57,138 - stpipe.step - INFO - Step straylight done
2026-07-28 17:00:57,334 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:57,394 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:00:57,401 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2026-07-28 17:00:57,402 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:00:57,402 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:00:57,402 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:00:57,472 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:00:57,668 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:57,672 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2026-07-28 17:00:57,713 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:00:57,714 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:00:57,714 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:00:57,755 - stpipe.step - INFO - Step fringe done
2026-07-28 17:00:57,948 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:57,949 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:58,145 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:58,146 - stpipe.step - INFO - Step skipped.
2026-07-28 17:00:58,344 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:58,352 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits
2026-07-28 17:00:58,353 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:00:58,353 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:00:58,354 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:00:58,354 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:00:58,354 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:00:58,442 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:00:58,463 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:00:58,464 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:00:58,501 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:00:59,072 - stpipe.step - INFO - Step photom done
2026-07-28 17:00:59,270 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2026-07-28 17:00:59,271 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:00,296 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits>,).
2026-07-28 17:01:00,297 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:00,531 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits>,).
2026-07-28 17:01:00,532 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:00,764 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits>,).
2026-07-28 17:01:00,765 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:01,823 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits>,).
2026-07-28 17:01:01,824 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:01,827 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort
2026-07-28 17:01:01,829 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:01:01,829 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:01:02,282 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits
2026-07-28 17:01:02,283 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:01:02,284 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:01:02,674 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:01:02,682 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:01:02,690 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:01:02,699 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:01:02,707 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:01:02,716 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:01:02,724 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:01:02,747 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:01:02,748 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:01:02,749 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:01:02,750 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:01:02,751 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:01:02,752 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:01:02,753 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:01:02,754 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:01:02,758 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:01:02,759 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:01:02,760 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:01:02,761 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:01:02,762 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:01:02,763 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:01:02,764 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:01:02,765 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:01:02,766 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:01:02,767 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:01:02,768 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:01:02,768 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:01:02,769 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:01:02,770 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:01:02,773 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:01:02,773 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:01:02,774 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:01:02,775 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:01:02,776 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:01:02,777 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:01:02,778 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:01:02,779 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:01:02,781 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:01:02,782 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:01:03,184 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:01:03,217 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:01:03,275 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:01:03,278 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:01:03,279 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:01:03,279 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:01:03,280 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:01:03,280 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:01:03,281 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:01:03,281 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:01:03,281 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf'.
2026-07-28 17:01:03,283 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:01:03,283 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:01:03,283 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits'.
2026-07-28 17:01:03,284 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:01:03,284 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:01:03,285 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2026-07-28 17:01:03,285 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:01:03,286 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:01:03,287 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:01:03,287 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:01:03,288 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:01:03,288 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:01:03,289 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:01:03,289 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:01:03,289 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits'.
2026-07-28 17:01:03,290 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf'.
2026-07-28 17:01:03,291 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:01:03,291 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf'.
2026-07-28 17:01:03,292 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:01:03,292 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:01:03,293 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:01:03,300 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong
2026-07-28 17:01:03,300 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits ...
2026-07-28 17:01:03,511 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:03,977 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:01:05,149 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:01:05,803 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.082703676 -70.084789229 81.090477809 -70.084789229 81.090477809 -70.082140161 81.082703676 -70.082140161
2026-07-28 17:01:05,805 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:01:05,808 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:01:06,008 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits']).
2026-07-28 17:01:06,010 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:06,195 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:06,196 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:06,384 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:06,385 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:06,577 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>, []).
2026-07-28 17:01:06,578 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:06,768 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', []).
2026-07-28 17:01:06,768 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:06,958 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', []).
2026-07-28 17:01:06,958 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:07,146 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits']).
2026-07-28 17:01:07,147 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:07,335 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:07,336 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:01:07,337 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:01:07,337 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:01:07,340 - stpipe.step - INFO - Step srctype done
2026-07-28 17:01:07,529 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:07,530 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:07,720 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:07,724 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:01:07,868 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:01:29,057 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:01:49,951 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.0384264700114727 DN/s
2026-07-28 17:01:49,952 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:01:49,955 - stpipe.step - INFO - Step straylight done
2026-07-28 17:01:50,140 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:50,199 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:01:50,207 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits
2026-07-28 17:01:50,208 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:01:50,208 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:01:50,209 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:01:50,278 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:01:50,463 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:50,469 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2026-07-28 17:01:50,512 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:01:50,513 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:01:50,514 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:01:50,554 - stpipe.step - INFO - Step fringe done
2026-07-28 17:01:50,736 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:50,736 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:50,920 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:50,921 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:51,104 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:51,112 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits
2026-07-28 17:01:51,113 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:01:51,113 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:01:51,114 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:01:51,114 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:01:51,115 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:01:51,200 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:01:51,220 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:01:51,221 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:01:51,257 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:01:51,774 - stpipe.step - INFO - Step photom done
2026-07-28 17:01:51,959 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2026-07-28 17:01:51,960 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:52,764 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits>,).
2026-07-28 17:01:52,764 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:52,975 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits>,).
2026-07-28 17:01:52,976 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:53,188 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits>,).
2026-07-28 17:01:53,188 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:54,017 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits>,).
2026-07-28 17:01:54,018 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:54,021 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong
2026-07-28 17:01:54,022 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:01:54,023 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:01:54,391 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits
2026-07-28 17:01:54,392 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:01:54,393 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:01:54,770 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:01:54,778 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:01:54,786 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:01:54,794 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:01:54,803 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:01:54,811 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:01:54,819 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:01:54,842 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:01:54,844 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:01:54,845 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:01:54,846 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:01:54,847 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:01:54,848 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:01:54,849 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:01:54,850 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:01:54,855 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:01:54,856 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:01:54,857 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:01:54,858 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:01:54,859 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:01:54,859 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:01:54,860 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:01:54,862 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:01:54,863 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:01:54,864 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:01:54,864 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:01:54,865 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:01:54,866 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:01:54,868 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:01:54,869 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:01:54,870 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:01:54,870 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:01:54,872 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:01:54,872 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:01:54,873 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:01:54,874 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:01:54,876 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:01:54,877 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:01:54,879 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:01:55,183 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:01:55,215 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:01:55,272 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:01:55,276 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:01:55,276 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:01:55,277 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:01:55,277 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:01:55,278 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:01:55,278 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:01:55,279 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:01:55,279 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf'.
2026-07-28 17:01:55,280 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:01:55,280 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:01:55,281 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2026-07-28 17:01:55,281 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:01:55,282 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:01:55,282 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2026-07-28 17:01:55,283 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:01:55,283 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:01:55,284 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:01:55,284 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:01:55,285 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:01:55,285 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:01:55,286 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:01:55,286 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:01:55,287 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits'.
2026-07-28 17:01:55,287 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf'.
2026-07-28 17:01:55,288 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:01:55,288 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf'.
2026-07-28 17:01:55,289 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:01:55,289 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:01:55,290 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:01:55,297 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort
2026-07-28 17:01:55,297 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits ...
2026-07-28 17:01:55,503 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:01:56,101 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:01:57,551 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:01:58,310 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084566892 -70.084198133 81.089008762 -70.084198133 81.089008762 -70.082592008 81.084566892 -70.082592008
2026-07-28 17:01:58,312 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:01:58,316 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:01:58,567 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits']).
2026-07-28 17:01:58,570 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:58,761 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:01:58,762 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:58,955 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:01:58,956 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:59,145 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>, []).
2026-07-28 17:01:59,146 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:59,336 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', []).
2026-07-28 17:01:59,337 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:59,524 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', []).
2026-07-28 17:01:59,525 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:59,710 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits']).
2026-07-28 17:01:59,711 - stpipe.step - INFO - Step skipped.
2026-07-28 17:01:59,902 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:01:59,902 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:01:59,903 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:01:59,903 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:01:59,906 - stpipe.step - INFO - Step srctype done
2026-07-28 17:02:00,098 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:02:00,099 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:00,293 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:02:00,297 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:02:00,441 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:02:22,266 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:02:43,160 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.02330242997044443 DN/s
2026-07-28 17:02:43,161 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:02:43,164 - stpipe.step - INFO - Step straylight done
2026-07-28 17:02:43,357 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:02:43,416 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:02:43,423 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2026-07-28 17:02:43,424 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:02:43,425 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:02:43,425 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:02:43,495 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:02:43,688 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:02:43,692 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2026-07-28 17:02:43,733 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:02:43,733 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:02:43,734 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:02:43,775 - stpipe.step - INFO - Step fringe done
2026-07-28 17:02:43,970 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:02:43,971 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:44,168 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:02:44,169 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:44,364 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:02:44,373 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits
2026-07-28 17:02:44,373 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:02:44,374 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:02:44,374 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:02:44,375 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:02:44,375 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:02:44,462 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:02:44,483 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:02:44,484 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:02:44,521 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:02:45,096 - stpipe.step - INFO - Step photom done
2026-07-28 17:02:45,289 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2026-07-28 17:02:45,290 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:46,317 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits>,).
2026-07-28 17:02:46,318 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:46,546 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits>,).
2026-07-28 17:02:46,546 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:46,775 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits>,).
2026-07-28 17:02:46,776 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:47,814 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits>,).
2026-07-28 17:02:47,815 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:47,818 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort
2026-07-28 17:02:47,820 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:02:47,820 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:02:48,268 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits
2026-07-28 17:02:48,269 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:02:48,270 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:02:48,658 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:02:48,666 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:02:48,674 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:02:48,682 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:02:48,691 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:02:48,699 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:02:48,707 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:02:48,730 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:02:48,731 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:02:48,732 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:02:48,733 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:02:48,734 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:02:48,735 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:02:48,736 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:02:48,737 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:02:48,742 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:02:48,743 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:02:48,744 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:02:48,744 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:02:48,745 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:02:48,746 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:02:48,747 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:02:48,749 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:02:48,750 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:02:48,750 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:02:48,751 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:02:48,752 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:02:48,753 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:02:48,755 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:02:48,755 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:02:48,756 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:02:48,757 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:02:48,758 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:02:48,759 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:02:48,760 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:02:48,761 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:02:48,762 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:02:48,763 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:02:48,765 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:02:49,163 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:02:49,196 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:02:49,256 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:02:49,259 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:02:49,259 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:02:49,260 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:02:49,260 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:02:49,261 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:02:49,261 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:02:49,261 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:02:49,262 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf'.
2026-07-28 17:02:49,263 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:02:49,263 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:02:49,263 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits'.
2026-07-28 17:02:49,264 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:02:49,265 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:02:49,265 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2026-07-28 17:02:49,265 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:02:49,266 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:02:49,266 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:02:49,266 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:02:49,267 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:02:49,268 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:02:49,268 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:02:49,268 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:02:49,269 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits'.
2026-07-28 17:02:49,269 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf'.
2026-07-28 17:02:49,270 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:02:49,270 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf'.
2026-07-28 17:02:49,271 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:02:49,272 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:02:49,273 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:02:49,279 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong
2026-07-28 17:02:49,280 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits ...
2026-07-28 17:02:49,486 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:02:49,951 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:02:51,131 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:02:51,798 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.082048045 -70.085483519 81.089822386 -70.085483519 81.089822386 -70.082834473 81.082048045 -70.082834473
2026-07-28 17:02:51,800 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:02:51,804 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:02:52,004 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits']).
2026-07-28 17:02:52,007 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:52,196 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:02:52,197 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:52,387 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:02:52,388 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:52,575 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>, []).
2026-07-28 17:02:52,576 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:52,765 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', []).
2026-07-28 17:02:52,765 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:52,949 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', []).
2026-07-28 17:02:52,950 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:53,135 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits']).
2026-07-28 17:02:53,136 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:53,325 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:02:53,326 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:02:53,326 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:02:53,327 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:02:53,329 - stpipe.step - INFO - Step srctype done
2026-07-28 17:02:53,514 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:02:53,514 - stpipe.step - INFO - Step skipped.
2026-07-28 17:02:53,704 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:02:53,709 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:02:53,852 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:03:15,058 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:03:35,926 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.032305872067809105 DN/s
2026-07-28 17:03:35,927 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:03:35,931 - stpipe.step - INFO - Step straylight done
2026-07-28 17:03:36,116 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:03:36,175 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:03:36,182 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits
2026-07-28 17:03:36,183 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:03:36,183 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:03:36,184 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:03:36,251 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:03:36,435 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:03:36,439 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2026-07-28 17:03:36,479 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:03:36,479 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:03:36,480 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:03:36,520 - stpipe.step - INFO - Step fringe done
2026-07-28 17:03:36,703 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:03:36,703 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:36,891 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:03:36,891 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:37,079 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:03:37,088 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits
2026-07-28 17:03:37,089 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:03:37,089 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:03:37,090 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:03:37,090 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:03:37,091 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:03:37,177 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:03:37,197 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:03:37,198 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:03:37,235 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:03:37,756 - stpipe.step - INFO - Step photom done
2026-07-28 17:03:37,943 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2026-07-28 17:03:37,944 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:38,751 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits>,).
2026-07-28 17:03:38,752 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:38,962 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits>,).
2026-07-28 17:03:38,963 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:39,171 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits>,).
2026-07-28 17:03:39,172 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:39,992 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits>,).
2026-07-28 17:03:39,993 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:39,997 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong
2026-07-28 17:03:39,998 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:03:39,998 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:03:40,365 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits
2026-07-28 17:03:40,366 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:03:40,367 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:03:40,748 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:03:40,756 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:03:40,765 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:03:40,773 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:03:40,782 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:03:40,791 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:03:40,799 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:03:40,821 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:03:40,822 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:03:40,823 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:03:40,824 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:03:40,825 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:03:40,827 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:03:40,827 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:03:40,828 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:03:40,833 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:03:40,834 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:03:40,835 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:03:40,835 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:03:40,836 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:03:40,837 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:03:40,838 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:03:40,840 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:03:40,841 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:03:40,841 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:03:40,842 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:03:40,843 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:03:40,844 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:03:40,845 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:03:40,846 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:03:40,847 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:03:40,848 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:03:40,849 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:03:40,850 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:03:40,851 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:03:40,851 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:03:40,853 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:03:40,854 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:03:40,855 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:03:41,165 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:03:41,198 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:03:41,257 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:03:41,261 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:03:41,261 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:03:41,262 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:03:41,262 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:03:41,262 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:03:41,263 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:03:41,263 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:03:41,264 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf'.
2026-07-28 17:03:41,264 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:03:41,265 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:03:41,265 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2026-07-28 17:03:41,266 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:03:41,266 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:03:41,266 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2026-07-28 17:03:41,267 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:03:41,268 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:03:41,268 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:03:41,268 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:03:41,269 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:03:41,270 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:03:41,270 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:03:41,270 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:03:41,271 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits'.
2026-07-28 17:03:41,271 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf'.
2026-07-28 17:03:41,272 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:03:41,272 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf'.
2026-07-28 17:03:41,273 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:03:41,273 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:03:41,274 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:03:41,280 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort
2026-07-28 17:03:41,281 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits ...
2026-07-28 17:03:41,490 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:03:42,095 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:03:43,558 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:03:44,327 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083911317 -70.084892431 81.088353293 -70.084892431 81.088353293 -70.083286318 81.083911317 -70.083286318
2026-07-28 17:03:44,329 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:03:44,332 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:03:44,594 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits']).
2026-07-28 17:03:44,596 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:44,786 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:03:44,787 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:44,978 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:03:44,979 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:45,172 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>, []).
2026-07-28 17:03:45,173 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:45,368 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', []).
2026-07-28 17:03:45,369 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:45,559 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', []).
2026-07-28 17:03:45,560 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:45,749 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits']).
2026-07-28 17:03:45,749 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:45,943 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:03:45,943 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:03:45,944 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:03:45,944 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:03:45,947 - stpipe.step - INFO - Step srctype done
2026-07-28 17:03:46,138 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:03:46,139 - stpipe.step - INFO - Step skipped.
2026-07-28 17:03:46,331 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:03:46,336 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:03:46,479 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:04:08,261 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:04:29,143 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03315040839770971 DN/s
2026-07-28 17:04:29,144 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:04:29,148 - stpipe.step - INFO - Step straylight done
2026-07-28 17:04:29,339 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:04:29,399 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:04:29,407 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2026-07-28 17:04:29,408 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:04:29,408 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:04:29,408 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:04:29,478 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:04:29,669 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:04:29,674 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2026-07-28 17:04:29,714 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:04:29,715 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:04:29,715 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:04:29,755 - stpipe.step - INFO - Step fringe done
2026-07-28 17:04:29,946 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:04:29,947 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:30,139 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:04:30,140 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:30,332 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:04:30,340 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits
2026-07-28 17:04:30,341 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:04:30,342 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:04:30,342 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:04:30,343 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:04:30,343 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:04:30,429 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:04:30,450 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:04:30,451 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:04:30,488 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:04:31,071 - stpipe.step - INFO - Step photom done
2026-07-28 17:04:31,265 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2026-07-28 17:04:31,266 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:32,287 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits>,).
2026-07-28 17:04:32,288 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:32,517 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits>,).
2026-07-28 17:04:32,518 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:32,747 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits>,).
2026-07-28 17:04:32,747 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:33,771 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits>,).
2026-07-28 17:04:33,772 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:33,776 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort
2026-07-28 17:04:33,777 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:04:33,777 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:04:34,227 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits
2026-07-28 17:04:34,228 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:04:34,229 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:04:34,613 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:04:34,621 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:04:34,629 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:04:34,637 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:04:34,646 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:04:34,655 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:04:34,662 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:04:34,685 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:04:34,686 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:04:34,687 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:04:34,688 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:04:34,689 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:04:34,690 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:04:34,691 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:04:34,692 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:04:34,696 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:04:34,697 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:04:34,698 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:04:34,699 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:04:34,700 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:04:34,700 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:04:34,701 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:04:34,703 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:04:34,704 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:04:34,705 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:04:34,705 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:04:34,706 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:04:34,707 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:04:34,708 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:04:34,709 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:04:34,710 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:04:34,711 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:04:34,714 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:04:34,714 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:04:34,715 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:04:34,716 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:04:34,717 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:04:34,719 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:04:34,720 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:04:35,107 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:04:35,139 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:04:35,198 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:04:35,201 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:04:35,202 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:04:35,203 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:04:35,203 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:04:35,203 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:04:35,204 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:04:35,205 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:04:35,205 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf'.
2026-07-28 17:04:35,206 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:04:35,206 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:04:35,207 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits'.
2026-07-28 17:04:35,208 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:04:35,208 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:04:35,208 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2026-07-28 17:04:35,209 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:04:35,209 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:04:35,210 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:04:35,210 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:04:35,211 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:04:35,211 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:04:35,212 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:04:35,212 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:04:35,213 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits'.
2026-07-28 17:04:35,213 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf'.
2026-07-28 17:04:35,214 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:04:35,214 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf'.
2026-07-28 17:04:35,215 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:04:35,215 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:04:35,216 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:04:35,222 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong
2026-07-28 17:04:35,223 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits ...
2026-07-28 17:04:35,433 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:04:35,897 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2026-07-28 17:04:37,075 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:04:37,735 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.082783604 -70.084650973 81.090557685 -70.084650973 81.090557685 -70.082001906 81.082783604 -70.082001906
2026-07-28 17:04:37,736 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:04:37,740 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:04:37,935 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits']).
2026-07-28 17:04:37,936 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:38,121 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:04:38,122 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:38,308 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:04:38,309 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:38,496 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>, []).
2026-07-28 17:04:38,497 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:38,682 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', []).
2026-07-28 17:04:38,682 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:38,865 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', []).
2026-07-28 17:04:38,866 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:39,048 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits']).
2026-07-28 17:04:39,049 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:39,234 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:04:39,235 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:04:39,236 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:04:39,236 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:04:39,239 - stpipe.step - INFO - Step srctype done
2026-07-28 17:04:39,425 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:04:39,426 - stpipe.step - INFO - Step skipped.
2026-07-28 17:04:39,613 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:04:39,618 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:04:39,760 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:05:00,975 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:05:21,866 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03911658003926277 DN/s
2026-07-28 17:05:21,867 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:05:21,870 - stpipe.step - INFO - Step straylight done
2026-07-28 17:05:22,052 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:05:22,110 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:05:22,117 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits
2026-07-28 17:05:22,118 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:05:22,118 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:05:22,119 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:05:22,185 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:05:22,367 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:05:22,373 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2026-07-28 17:05:22,412 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:05:22,413 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:05:22,413 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:05:22,452 - stpipe.step - INFO - Step fringe done
2026-07-28 17:05:22,633 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:05:22,634 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:22,819 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:05:22,820 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:23,006 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:05:23,014 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits
2026-07-28 17:05:23,015 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:05:23,015 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:05:23,016 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:05:23,016 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:05:23,017 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:05:23,102 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:05:23,123 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:05:23,123 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:05:23,159 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:05:23,681 - stpipe.step - INFO - Step photom done
2026-07-28 17:05:23,865 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2026-07-28 17:05:23,866 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:24,673 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits>,).
2026-07-28 17:05:24,674 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:24,883 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits>,).
2026-07-28 17:05:24,884 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:25,093 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits>,).
2026-07-28 17:05:25,094 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:25,912 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits>,).
2026-07-28 17:05:25,913 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:25,917 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong
2026-07-28 17:05:25,918 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:05:25,918 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:05:26,287 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits
2026-07-28 17:05:26,288 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:05:26,289 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:05:26,670 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:05:26,678 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:05:26,687 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:05:26,695 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:05:26,704 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:05:26,713 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:05:26,721 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:05:26,743 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:05:26,745 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:05:26,746 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:05:26,747 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:05:26,748 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:05:26,749 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:05:26,750 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:05:26,751 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:05:26,756 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:05:26,756 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:05:26,758 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:05:26,758 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:05:26,759 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:05:26,760 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:05:26,761 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:05:26,762 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:05:26,763 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:05:26,764 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:05:26,765 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:05:26,765 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:05:26,766 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:05:26,768 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:05:26,769 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:05:26,770 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:05:26,771 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:05:26,772 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:05:26,773 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:05:26,774 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:05:26,775 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:05:26,776 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:05:26,777 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:05:26,779 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:05:27,112 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:05:27,144 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:05:27,203 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:05:27,206 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:05:27,207 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:05:27,207 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:05:27,208 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:05:27,209 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:05:27,209 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:05:27,210 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:05:27,210 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf'.
2026-07-28 17:05:27,211 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:05:27,211 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:05:27,212 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2026-07-28 17:05:27,212 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:05:27,213 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:05:27,213 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2026-07-28 17:05:27,214 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:05:27,214 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:05:27,215 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:05:27,215 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:05:27,216 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:05:27,217 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:05:27,217 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:05:27,217 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:05:27,218 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits'.
2026-07-28 17:05:27,218 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf'.
2026-07-28 17:05:27,219 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:05:27,220 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf'.
2026-07-28 17:05:27,220 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:05:27,221 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:05:27,221 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:05:27,228 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort
2026-07-28 17:05:27,228 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits ...
2026-07-28 17:05:27,434 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:05:28,034 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:05:29,495 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:05:30,265 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084646809 -70.084059877 81.089088648 -70.084059877 81.089088648 -70.082453752 81.084646809 -70.082453752
2026-07-28 17:05:30,266 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:05:30,270 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:05:30,524 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits']).
2026-07-28 17:05:30,526 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:30,717 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:05:30,718 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:30,908 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:05:30,909 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:31,099 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>, []).
2026-07-28 17:05:31,100 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:31,290 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', []).
2026-07-28 17:05:31,291 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:31,478 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', []).
2026-07-28 17:05:31,479 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:31,666 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits']).
2026-07-28 17:05:31,667 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:31,856 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:05:31,857 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:05:31,857 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:05:31,858 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:05:31,861 - stpipe.step - INFO - Step srctype done
2026-07-28 17:05:32,049 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:05:32,050 - stpipe.step - INFO - Step skipped.
2026-07-28 17:05:32,239 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:05:32,243 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:05:32,388 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:05:54,173 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:06:15,043 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.02808541157250882 DN/s
2026-07-28 17:06:15,044 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:06:15,047 - stpipe.step - INFO - Step straylight done
2026-07-28 17:06:15,237 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:06:15,296 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:06:15,303 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2026-07-28 17:06:15,304 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:06:15,304 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:06:15,305 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:06:15,373 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:06:15,565 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:06:15,570 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2026-07-28 17:06:15,610 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:06:15,611 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:06:15,612 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:06:15,655 - stpipe.step - INFO - Step fringe done
2026-07-28 17:06:15,842 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:06:15,843 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:16,035 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:06:16,036 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:16,229 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:06:16,237 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits
2026-07-28 17:06:16,238 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:06:16,238 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:06:16,239 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:06:16,240 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:06:16,240 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:06:16,326 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:06:16,347 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:06:16,347 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:06:16,384 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:06:16,940 - stpipe.step - INFO - Step photom done
2026-07-28 17:06:17,131 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2026-07-28 17:06:17,132 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:18,143 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits>,).
2026-07-28 17:06:18,144 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:18,370 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits>,).
2026-07-28 17:06:18,371 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:18,593 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits>,).
2026-07-28 17:06:18,594 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:19,612 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits>,).
2026-07-28 17:06:19,613 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:19,616 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort
2026-07-28 17:06:19,617 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:06:19,617 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:06:20,065 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits
2026-07-28 17:06:20,065 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:06:20,066 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:06:20,452 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:06:20,460 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:06:20,469 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:06:20,477 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:06:20,486 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:06:20,494 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:06:20,502 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:06:20,524 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:06:20,526 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:06:20,527 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:06:20,528 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:06:20,529 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:06:20,530 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:06:20,531 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:06:20,532 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:06:20,536 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:06:20,537 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:06:20,538 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:06:20,539 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:06:20,540 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:06:20,541 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:06:20,542 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:06:20,543 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:06:20,544 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:06:20,545 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:06:20,546 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:06:20,547 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:06:20,548 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:06:20,549 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:06:20,550 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:06:20,551 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:06:20,552 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:06:20,553 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:06:20,554 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:06:20,555 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:06:20,557 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:06:20,557 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:06:20,559 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:06:20,560 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:06:20,940 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:06:20,972 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:06:21,030 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:06:21,034 - CRDS - INFO - Syncing 6 files
2026-07-28 17:06:21,035 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf 125.0 K bytes (1 / 6 files) (0 / 105.9 M bytes)
2026-07-28 17:06:21,502 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits 21.2 M bytes (2 / 6 files) (125.0 K / 105.9 M bytes)
2026-07-28 17:06:22,717 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits 12.7 M bytes (3 / 6 files) (21.3 M / 105.9 M bytes)
2026-07-28 17:06:23,891 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits 33.9 M bytes (4 / 6 files) (34.0 M / 105.9 M bytes)
2026-07-28 17:06:25,598 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 105.9 M bytes)
2026-07-28 17:06:27,165 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf 40.4 K bytes (6 / 6 files) (105.9 M / 105.9 M bytes)
2026-07-28 17:06:27,419 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:06:27,419 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:06:27,420 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:06:27,421 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:06:27,421 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:06:27,422 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:06:27,422 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:06:27,423 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf'.
2026-07-28 17:06:27,424 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:06:27,424 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:06:27,425 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2026-07-28 17:06:27,426 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:06:27,426 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:06:27,426 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2026-07-28 17:06:27,427 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:06:27,427 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:06:27,428 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:06:27,428 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:06:27,429 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:06:27,430 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:06:27,430 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:06:27,430 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:06:27,431 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits'.
2026-07-28 17:06:27,431 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf'.
2026-07-28 17:06:27,432 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:06:27,433 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf'.
2026-07-28 17:06:27,433 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:06:27,434 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:06:27,435 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:06:27,441 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong
2026-07-28 17:06:27,442 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits ...
2026-07-28 17:06:27,646 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:06:28,110 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:06:29,264 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:06:29,920 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.081895218 -70.085603352 81.089830477 -70.085603352 81.089830477 -70.082960725 81.081895218 -70.082960725
2026-07-28 17:06:29,922 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:06:29,925 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:06:30,118 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits']).
2026-07-28 17:06:30,120 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:30,307 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:06:30,307 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:30,489 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:06:30,490 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:30,673 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>, []).
2026-07-28 17:06:30,674 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:30,857 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', []).
2026-07-28 17:06:30,859 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:31,037 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits', []).
2026-07-28 17:06:31,038 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:31,217 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits']).
2026-07-28 17:06:31,217 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:31,400 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:06:31,401 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:06:31,401 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:06:31,402 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:06:31,405 - stpipe.step - INFO - Step srctype done
2026-07-28 17:06:31,588 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:06:31,589 - stpipe.step - INFO - Step skipped.
2026-07-28 17:06:31,773 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:06:31,778 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:06:31,921 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:06:53,129 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:07:14,039 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03528253361582756 DN/s
2026-07-28 17:07:14,040 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:07:14,043 - stpipe.step - INFO - Step straylight done
2026-07-28 17:07:14,227 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:07:14,286 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:07:14,293 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2026-07-28 17:07:14,294 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:07:14,294 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:07:14,295 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:07:14,363 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:07:14,546 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:07:14,551 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2026-07-28 17:07:14,591 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:07:14,591 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:07:14,592 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:07:14,631 - stpipe.step - INFO - Step fringe done
2026-07-28 17:07:14,813 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:07:14,814 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:15,001 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:07:15,002 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:15,187 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:07:15,195 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits
2026-07-28 17:07:15,196 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:07:15,196 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:07:15,197 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:07:15,197 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:07:15,198 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:07:15,283 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:07:15,304 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:07:15,304 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:07:15,340 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:07:15,859 - stpipe.step - INFO - Step photom done
2026-07-28 17:07:16,043 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2026-07-28 17:07:16,044 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:16,841 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits>,).
2026-07-28 17:07:16,842 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:17,053 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits>,).
2026-07-28 17:07:17,054 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:17,265 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits>,).
2026-07-28 17:07:17,266 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:18,081 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits>,).
2026-07-28 17:07:18,082 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:18,085 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong
2026-07-28 17:07:18,086 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:07:18,087 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:07:18,458 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits
2026-07-28 17:07:18,459 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:07:18,459 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:07:18,847 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:07:18,855 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:07:18,864 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:07:18,873 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:07:18,882 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:07:18,891 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:07:18,899 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:07:18,921 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:07:18,922 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:07:18,923 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:07:18,924 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:07:18,925 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:07:18,926 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:07:18,927 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:07:18,928 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:07:18,932 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:07:18,933 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:07:18,934 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:07:18,935 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:07:18,936 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:07:18,937 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:07:18,938 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:07:18,940 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:07:18,942 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:07:18,942 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:07:18,943 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:07:18,944 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:07:18,945 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:07:18,947 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:07:18,948 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:07:18,948 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:07:18,949 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:07:18,950 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:07:18,951 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:07:18,952 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:07:18,953 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:07:18,954 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:07:18,955 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:07:18,957 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:07:19,285 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:07:19,318 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:07:19,377 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:07:19,381 - CRDS - INFO - Syncing 6 files
2026-07-28 17:07:19,382 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf 166.4 K bytes (1 / 6 files) (0 / 106.0 M bytes)
2026-07-28 17:07:19,774 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits 21.2 M bytes (2 / 6 files) (166.4 K / 106.0 M bytes)
2026-07-28 17:07:21,192 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits 12.7 M bytes (3 / 6 files) (21.3 M / 106.0 M bytes)
2026-07-28 17:07:22,333 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits 33.9 M bytes (4 / 6 files) (34.0 M / 106.0 M bytes)
2026-07-28 17:07:23,854 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 106.0 M bytes)
2026-07-28 17:07:25,537 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf 53.7 K bytes (6 / 6 files) (105.9 M / 106.0 M bytes)
2026-07-28 17:07:25,879 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:07:25,880 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:07:25,881 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:07:25,882 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:07:25,883 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:07:25,883 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:07:25,884 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:07:25,884 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf'.
2026-07-28 17:07:25,885 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:07:25,886 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:07:25,886 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2026-07-28 17:07:25,888 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:07:25,888 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:07:25,889 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2026-07-28 17:07:25,889 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:07:25,890 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:07:25,890 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:07:25,890 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:07:25,891 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:07:25,891 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:07:25,892 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:07:25,892 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:07:25,893 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits'.
2026-07-28 17:07:25,893 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf'.
2026-07-28 17:07:25,894 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:07:25,895 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf'.
2026-07-28 17:07:25,896 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:07:25,896 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:07:25,897 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:07:25,903 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort
2026-07-28 17:07:25,904 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits ...
2026-07-28 17:07:26,106 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:07:26,709 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:07:28,164 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:07:28,930 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083830182 -70.085111400 81.088370896 -70.085111400 81.088370896 -70.083515133 81.083830182 -70.083515133
2026-07-28 17:07:28,932 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:07:28,935 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:07:29,197 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits']).
2026-07-28 17:07:29,199 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:29,398 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:07:29,399 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:29,594 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:07:29,594 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:29,791 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>, []).
2026-07-28 17:07:29,792 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:29,988 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', []).
2026-07-28 17:07:29,989 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:30,181 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits', []).
2026-07-28 17:07:30,182 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:30,372 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits']).
2026-07-28 17:07:30,373 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:30,565 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:07:30,565 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:07:30,566 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:07:30,566 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:07:30,569 - stpipe.step - INFO - Step srctype done
2026-07-28 17:07:30,759 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:07:30,760 - stpipe.step - INFO - Step skipped.
2026-07-28 17:07:30,950 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:07:30,954 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:07:31,098 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:07:52,598 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:08:13,472 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.037959573376245254 DN/s
2026-07-28 17:08:13,473 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:08:13,476 - stpipe.step - INFO - Step straylight done
2026-07-28 17:08:13,669 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:08:13,727 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:08:13,735 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2026-07-28 17:08:13,735 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:08:13,736 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:08:13,737 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:08:13,806 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:08:14,000 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:08:14,005 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2026-07-28 17:08:14,045 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:08:14,046 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:08:14,047 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:08:14,088 - stpipe.step - INFO - Step fringe done
2026-07-28 17:08:14,280 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:08:14,281 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:14,475 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:08:14,476 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:14,670 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:08:14,679 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits
2026-07-28 17:08:14,679 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:08:14,680 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:08:14,681 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:08:14,681 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:08:14,682 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:08:14,767 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:08:14,787 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:08:14,788 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:08:14,824 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:08:15,395 - stpipe.step - INFO - Step photom done
2026-07-28 17:08:15,587 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2026-07-28 17:08:15,588 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:16,620 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits>,).
2026-07-28 17:08:16,621 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:16,856 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits>,).
2026-07-28 17:08:16,857 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:17,097 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits>,).
2026-07-28 17:08:17,098 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:18,138 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits>,).
2026-07-28 17:08:18,139 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:18,143 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort
2026-07-28 17:08:18,144 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:08:18,144 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:08:18,597 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits
2026-07-28 17:08:18,598 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:08:18,598 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:08:18,984 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:08:18,992 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:08:19,001 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:08:19,009 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:08:19,017 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:08:19,026 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:08:19,033 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:08:19,055 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:08:19,057 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:08:19,058 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:08:19,059 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:08:19,060 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:08:19,061 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:08:19,062 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:08:19,063 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:08:19,067 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:08:19,068 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:08:19,069 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:08:19,070 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:08:19,070 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:08:19,071 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:08:19,072 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:08:19,074 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:08:19,076 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:08:19,076 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:08:19,077 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:08:19,078 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:08:19,079 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:08:19,080 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:08:19,082 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:08:19,083 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:08:19,084 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:08:19,085 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:08:19,086 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:08:19,087 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:08:19,088 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:08:19,089 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:08:19,090 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:08:19,092 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:08:19,478 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:08:19,510 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:08:19,569 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:08:19,572 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:08:19,573 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:08:19,573 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:08:19,574 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:08:19,574 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:08:19,575 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:08:19,575 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:08:19,576 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf'.
2026-07-28 17:08:19,577 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:08:19,577 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:08:19,577 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2026-07-28 17:08:19,578 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:08:19,578 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:08:19,579 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2026-07-28 17:08:19,580 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:08:19,580 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:08:19,581 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:08:19,581 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:08:19,581 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:08:19,582 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:08:19,583 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:08:19,583 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:08:19,584 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits'.
2026-07-28 17:08:19,584 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf'.
2026-07-28 17:08:19,585 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:08:19,585 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf'.
2026-07-28 17:08:19,586 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:08:19,587 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:08:19,587 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:08:19,594 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong
2026-07-28 17:08:19,594 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits ...
2026-07-28 17:08:19,792 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:08:20,254 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2026-07-28 17:08:21,424 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:08:22,094 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.082628860 -70.084770835 81.090563839 -70.084770835 81.090563839 -70.082128193 81.082628860 -70.082128193
2026-07-28 17:08:22,095 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:08:22,099 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:08:22,297 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits']).
2026-07-28 17:08:22,300 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:22,482 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:08:22,483 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:22,669 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:08:22,670 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:22,854 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>, []).
2026-07-28 17:08:22,856 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:23,040 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', []).
2026-07-28 17:08:23,041 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:23,224 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits', []).
2026-07-28 17:08:23,225 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:23,407 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits']).
2026-07-28 17:08:23,408 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:23,591 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:08:23,592 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:08:23,592 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:08:23,593 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:08:23,595 - stpipe.step - INFO - Step srctype done
2026-07-28 17:08:23,779 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:08:23,779 - stpipe.step - INFO - Step skipped.
2026-07-28 17:08:23,965 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:08:23,970 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:08:24,115 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:08:45,303 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:09:06,199 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.005848990753293037 DN/s
2026-07-28 17:09:06,200 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:09:06,203 - stpipe.step - INFO - Step straylight done
2026-07-28 17:09:06,384 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:09:06,442 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:06,449 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2026-07-28 17:09:06,449 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:09:06,450 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:09:06,451 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:09:06,517 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:09:06,700 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:09:06,704 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2026-07-28 17:09:06,744 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:06,745 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:06,746 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:06,787 - stpipe.step - INFO - Step fringe done
2026-07-28 17:09:06,971 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:09:06,972 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:07,158 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:09:07,159 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:07,343 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:09:07,352 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits
2026-07-28 17:09:07,353 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:09:07,353 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:09:07,353 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:09:07,354 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:09:07,355 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:09:07,441 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:07,462 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:09:07,462 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:09:07,498 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:09:08,025 - stpipe.step - INFO - Step photom done
2026-07-28 17:09:08,208 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2026-07-28 17:09:08,209 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:09,012 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits>,).
2026-07-28 17:09:09,013 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:09,227 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits>,).
2026-07-28 17:09:09,227 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:09,439 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits>,).
2026-07-28 17:09:09,440 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:10,260 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits>,).
2026-07-28 17:09:10,261 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:10,264 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong
2026-07-28 17:09:10,265 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:09:10,266 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:09:10,636 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits
2026-07-28 17:09:10,637 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:09:10,637 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:09:11,022 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:09:11,030 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:09:11,039 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:09:11,048 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:09:11,056 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:09:11,065 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:09:11,073 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:09:11,096 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:09:11,098 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:09:11,099 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:09:11,100 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:09:11,101 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:09:11,103 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:09:11,104 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:09:11,105 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:09:11,109 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:09:11,110 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:09:11,111 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:09:11,112 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:09:11,113 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:09:11,113 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:09:11,115 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:09:11,116 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:09:11,117 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:09:11,118 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:09:11,119 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:09:11,120 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:09:11,120 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:09:11,122 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:09:11,123 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:09:11,124 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:09:11,124 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:09:11,125 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:09:11,126 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:09:11,127 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:09:11,128 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:09:11,129 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:09:11,131 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:09:11,132 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:09:11,461 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:09:11,495 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:09:11,554 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:09:11,557 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:09:11,558 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:09:11,558 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:09:11,559 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:09:11,560 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:09:11,560 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:09:11,561 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:09:11,561 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf'.
2026-07-28 17:09:11,562 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:09:11,562 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:09:11,562 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2026-07-28 17:09:11,564 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:09:11,564 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:09:11,564 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2026-07-28 17:09:11,565 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:09:11,565 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:09:11,566 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:09:11,566 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:09:11,567 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:09:11,567 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:09:11,568 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:09:11,568 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:09:11,568 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits'.
2026-07-28 17:09:11,569 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf'.
2026-07-28 17:09:11,570 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:09:11,570 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf'.
2026-07-28 17:09:11,571 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:09:11,571 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:09:11,572 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:09:11,578 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort
2026-07-28 17:09:11,579 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits ...
2026-07-28 17:09:11,781 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:12,384 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2026-07-28 17:09:13,852 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:09:14,633 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084563754 -70.084278877 81.089104314 -70.084278877 81.089104314 -70.082682602 81.084563754 -70.082682602
2026-07-28 17:09:14,635 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:09:14,639 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:09:14,907 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits']).
2026-07-28 17:09:14,909 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:15,102 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:15,103 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:15,294 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:15,294 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:15,486 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>, []).
2026-07-28 17:09:15,487 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:15,680 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', []).
2026-07-28 17:09:15,681 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:15,876 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits', []).
2026-07-28 17:09:15,877 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:16,070 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits']).
2026-07-28 17:09:16,071 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:16,264 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:16,265 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:09:16,265 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:09:16,266 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:09:16,269 - stpipe.step - INFO - Step srctype done
2026-07-28 17:09:16,460 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:16,460 - stpipe.step - INFO - Step skipped.
2026-07-28 17:09:16,655 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:16,660 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:09:16,805 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:09:38,310 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:09:59,186 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.023702734653519165 DN/s
2026-07-28 17:09:59,187 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:09:59,191 - stpipe.step - INFO - Step straylight done
2026-07-28 17:09:59,379 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:59,437 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:59,445 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2026-07-28 17:09:59,445 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:09:59,446 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:09:59,446 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:09:59,514 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:09:59,704 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:59,709 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2026-07-28 17:09:59,748 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:59,749 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:59,750 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:09:59,789 - stpipe.step - INFO - Step fringe done
2026-07-28 17:09:59,979 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:09:59,980 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:00,173 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:10:00,174 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:00,366 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:10:00,375 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits
2026-07-28 17:10:00,375 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:10:00,376 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:10:00,376 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:10:00,377 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:10:00,377 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:10:00,464 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:10:00,484 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:10:00,484 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:10:00,520 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:10:01,085 - stpipe.step - INFO - Step photom done
2026-07-28 17:10:01,284 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2026-07-28 17:10:01,285 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:02,309 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits>,).
2026-07-28 17:10:02,310 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:02,544 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits>,).
2026-07-28 17:10:02,545 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:02,777 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits>,).
2026-07-28 17:10:02,777 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:03,816 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits>,).
2026-07-28 17:10:03,817 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:03,820 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort
2026-07-28 17:10:03,821 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:10:03,821 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:10:04,275 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits
2026-07-28 17:10:04,275 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:10:04,276 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:10:04,663 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:10:04,671 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:10:04,680 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:10:04,688 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:10:04,696 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:10:04,705 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:10:04,713 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:10:04,735 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:10:04,737 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:10:04,738 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:10:04,739 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:10:04,740 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:10:04,741 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:10:04,742 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:10:04,743 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:10:04,748 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:10:04,748 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:10:04,749 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:10:04,750 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:10:04,751 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:10:04,753 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:10:04,754 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:10:04,755 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:10:04,756 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:10:04,758 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:10:04,758 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:10:04,759 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:10:04,760 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:10:04,762 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:10:04,763 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:10:04,764 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:10:04,764 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:10:04,766 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:10:04,767 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:10:04,767 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:10:04,768 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:10:04,769 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:10:04,771 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:10:04,773 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:10:05,144 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:10:05,181 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:10:05,239 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:10:05,243 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:10:05,243 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:10:05,244 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:10:05,244 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:10:05,245 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:10:05,245 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:10:05,246 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:10:05,246 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf'.
2026-07-28 17:10:05,247 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:10:05,248 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:10:05,248 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2026-07-28 17:10:05,249 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:10:05,249 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:10:05,250 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2026-07-28 17:10:05,250 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:10:05,251 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:10:05,251 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:10:05,252 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:10:05,253 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:10:05,253 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:10:05,254 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:10:05,254 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:10:05,254 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits'.
2026-07-28 17:10:05,255 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf'.
2026-07-28 17:10:05,256 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:10:05,256 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf'.
2026-07-28 17:10:05,257 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:10:05,257 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:10:05,258 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:10:05,264 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong
2026-07-28 17:10:05,265 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits ...
2026-07-28 17:10:05,463 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:05,925 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2026-07-28 17:10:07,097 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:10:07,757 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.081973335 -70.085465028 81.089908525 -70.085465028 81.089908525 -70.082822408 81.081973335 -70.082822408
2026-07-28 17:10:07,759 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:10:07,763 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:10:07,960 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits']).
2026-07-28 17:10:07,963 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:08,147 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:08,148 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:08,332 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:08,333 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:08,517 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>, []).
2026-07-28 17:10:08,517 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:08,702 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', []).
2026-07-28 17:10:08,704 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:08,887 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits', []).
2026-07-28 17:10:08,888 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:09,073 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits']).
2026-07-28 17:10:09,074 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:09,260 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:09,261 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:10:09,262 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:10:09,263 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:10:09,265 - stpipe.step - INFO - Step srctype done
2026-07-28 17:10:09,450 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:09,451 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:09,637 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:09,642 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:10:09,785 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:10:30,956 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:10:51,829 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.009363008663058281 DN/s
2026-07-28 17:10:51,830 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:10:51,833 - stpipe.step - INFO - Step straylight done
2026-07-28 17:10:52,018 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:52,075 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:10:52,082 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2026-07-28 17:10:52,083 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:10:52,083 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:10:52,084 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:10:52,151 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:10:52,336 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:52,341 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2026-07-28 17:10:52,381 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:10:52,382 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:10:52,382 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:10:52,422 - stpipe.step - INFO - Step fringe done
2026-07-28 17:10:52,607 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:52,608 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:52,793 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:52,794 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:52,981 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:52,989 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits
2026-07-28 17:10:52,990 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:10:52,990 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:10:52,991 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:10:52,991 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:10:52,992 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:10:53,079 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:10:53,100 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:10:53,100 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:10:53,137 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:10:53,649 - stpipe.step - INFO - Step photom done
2026-07-28 17:10:53,837 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2026-07-28 17:10:53,838 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:54,644 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits>,).
2026-07-28 17:10:54,645 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:54,858 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits>,).
2026-07-28 17:10:54,859 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:55,072 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits>,).
2026-07-28 17:10:55,073 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:55,884 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits>,).
2026-07-28 17:10:55,885 - stpipe.step - INFO - Step skipped.
2026-07-28 17:10:55,889 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong
2026-07-28 17:10:55,890 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:10:55,890 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:10:56,259 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits
2026-07-28 17:10:56,260 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:10:56,260 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:10:56,643 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:10:56,651 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:10:56,660 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:10:56,668 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:10:56,677 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:10:56,686 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:10:56,694 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:10:56,717 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:10:56,718 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:10:56,720 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:10:56,721 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:10:56,722 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:10:56,723 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:10:56,724 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:10:56,725 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:10:56,729 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:10:56,730 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:10:56,732 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:10:56,733 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:10:56,734 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:10:56,735 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:10:56,736 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:10:56,737 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:10:56,738 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:10:56,739 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:10:56,740 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:10:56,741 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:10:56,741 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:10:56,743 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:10:56,745 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:10:56,745 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:10:56,746 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:10:56,748 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:10:56,749 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:10:56,750 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:10:56,751 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:10:56,752 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:10:56,753 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:10:56,755 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:10:57,080 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:10:57,112 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:10:57,170 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:10:57,174 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:10:57,174 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:10:57,175 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:10:57,175 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:10:57,175 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:10:57,176 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:10:57,176 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:10:57,177 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf'.
2026-07-28 17:10:57,178 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:10:57,178 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:10:57,179 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2026-07-28 17:10:57,179 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:10:57,180 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:10:57,180 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2026-07-28 17:10:57,181 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:10:57,182 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:10:57,182 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:10:57,182 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:10:57,183 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:10:57,183 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:10:57,184 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:10:57,184 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:10:57,185 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits'.
2026-07-28 17:10:57,185 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf'.
2026-07-28 17:10:57,186 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:10:57,187 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf'.
2026-07-28 17:10:57,188 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:10:57,188 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:10:57,188 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:10:57,195 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort
2026-07-28 17:10:57,196 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits ...
2026-07-28 17:10:57,398 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:10:58,000 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:10:59,467 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:11:00,244 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083908282 -70.084973079 81.088448955 -70.084973079 81.088448955 -70.083376815 81.083908282 -70.083376815
2026-07-28 17:11:00,245 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:11:00,249 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:11:00,507 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits']).
2026-07-28 17:11:00,510 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:00,706 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:00,707 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:00,900 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:00,901 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:01,096 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>, []).
2026-07-28 17:11:01,096 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:01,295 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', []).
2026-07-28 17:11:01,296 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:01,492 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits', []).
2026-07-28 17:11:01,492 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:01,687 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits']).
2026-07-28 17:11:01,688 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:01,884 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:01,885 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:11:01,885 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:11:01,886 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:11:01,888 - stpipe.step - INFO - Step srctype done
2026-07-28 17:11:02,082 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:02,083 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:02,279 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:02,283 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:11:02,429 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:11:23,918 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:11:44,789 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03591747025164387 DN/s
2026-07-28 17:11:44,789 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:11:44,793 - stpipe.step - INFO - Step straylight done
2026-07-28 17:11:44,986 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:45,045 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:11:45,053 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2026-07-28 17:11:45,054 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:11:45,054 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:11:45,055 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:11:45,125 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:11:45,319 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:45,324 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2026-07-28 17:11:45,364 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:11:45,364 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:11:45,365 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:11:45,406 - stpipe.step - INFO - Step fringe done
2026-07-28 17:11:45,597 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:45,598 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:45,793 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:45,794 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:45,990 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:45,999 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits
2026-07-28 17:11:45,999 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:11:46,000 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:11:46,001 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:11:46,001 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:11:46,002 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:11:46,092 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:11:46,112 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:11:46,113 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:11:46,152 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:11:46,740 - stpipe.step - INFO - Step photom done
2026-07-28 17:11:46,937 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2026-07-28 17:11:46,937 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:47,954 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits>,).
2026-07-28 17:11:47,955 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:48,183 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits>,).
2026-07-28 17:11:48,184 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:48,412 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits>,).
2026-07-28 17:11:48,413 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:49,447 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits>,).
2026-07-28 17:11:49,448 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:49,452 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort
2026-07-28 17:11:49,454 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:11:49,454 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:11:49,904 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits
2026-07-28 17:11:49,905 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:11:49,905 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:11:50,294 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:11:50,302 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:11:50,310 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:11:50,319 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:11:50,327 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:11:50,336 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:11:50,344 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:11:50,366 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:11:50,367 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:11:50,368 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:11:50,369 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:11:50,371 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:11:50,372 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:11:50,373 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:11:50,374 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:11:50,379 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:11:50,380 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:11:50,381 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:11:50,382 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:11:50,383 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:11:50,384 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:11:50,385 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:11:50,387 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:11:50,388 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:11:50,389 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:11:50,389 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:11:50,390 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:11:50,391 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:11:50,393 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:11:50,394 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:11:50,395 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:11:50,396 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:11:50,397 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:11:50,398 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:11:50,399 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:11:50,400 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:11:50,401 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:11:50,402 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:11:50,404 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:11:50,804 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:11:50,837 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:11:50,896 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:11:50,899 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:11:50,899 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:11:50,900 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:11:50,900 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:11:50,901 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:11:50,901 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:11:50,902 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:11:50,902 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf'.
2026-07-28 17:11:50,903 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:11:50,904 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:11:50,904 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2026-07-28 17:11:50,905 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:11:50,905 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:11:50,906 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2026-07-28 17:11:50,906 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:11:50,907 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:11:50,907 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:11:50,908 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:11:50,908 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:11:50,909 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:11:50,909 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:11:50,910 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:11:50,910 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits'.
2026-07-28 17:11:50,911 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf'.
2026-07-28 17:11:50,911 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:11:50,912 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf'.
2026-07-28 17:11:50,913 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:11:50,913 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:11:50,914 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:11:50,920 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong
2026-07-28 17:11:50,921 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits ...
2026-07-28 17:11:51,125 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:11:51,599 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2026-07-28 17:11:52,767 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:11:53,433 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.082708732 -70.084632184 81.090643663 -70.084632184 81.090643663 -70.081989541 81.082708732 -70.081989541
2026-07-28 17:11:53,435 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:11:53,439 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:11:53,635 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits']).
2026-07-28 17:11:53,637 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:53,824 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:11:53,825 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:54,010 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:11:54,011 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:54,199 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>, []).
2026-07-28 17:11:54,200 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:54,387 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', []).
2026-07-28 17:11:54,388 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:54,572 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits', []).
2026-07-28 17:11:54,573 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:54,755 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits']).
2026-07-28 17:11:54,755 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:54,945 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:11:54,945 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:11:54,946 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:11:54,946 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:11:54,949 - stpipe.step - INFO - Step srctype done
2026-07-28 17:11:55,133 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:11:55,135 - stpipe.step - INFO - Step skipped.
2026-07-28 17:11:55,321 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:11:55,325 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:11:55,470 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:12:16,642 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:12:37,519 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.026375921443104744 DN/s
2026-07-28 17:12:37,520 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:12:37,524 - stpipe.step - INFO - Step straylight done
2026-07-28 17:12:37,707 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:12:37,765 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:12:37,772 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2026-07-28 17:12:37,773 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:12:37,773 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:12:37,774 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:12:37,840 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:12:38,019 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:12:38,024 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2026-07-28 17:12:38,063 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:12:38,063 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:12:38,064 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:12:38,103 - stpipe.step - INFO - Step fringe done
2026-07-28 17:12:38,282 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:12:38,283 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:38,467 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:12:38,468 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:38,651 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:12:38,659 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits
2026-07-28 17:12:38,660 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:12:38,660 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:12:38,661 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:12:38,661 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:12:38,661 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:12:38,750 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:12:38,770 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:12:38,770 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:12:38,806 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:12:39,317 - stpipe.step - INFO - Step photom done
2026-07-28 17:12:39,498 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2026-07-28 17:12:39,498 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:40,290 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits>,).
2026-07-28 17:12:40,291 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:40,496 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits>,).
2026-07-28 17:12:40,497 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:40,704 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits>,).
2026-07-28 17:12:40,705 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:41,536 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits>,).
2026-07-28 17:12:41,537 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:41,540 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong
2026-07-28 17:12:41,541 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:12:41,542 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:12:41,913 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits
2026-07-28 17:12:41,914 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:12:41,914 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:12:42,296 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:12:42,304 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:12:42,313 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:12:42,322 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:12:42,331 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:12:42,341 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:12:42,349 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:12:42,375 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:12:42,377 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:12:42,378 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:12:42,379 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:12:42,380 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:12:42,381 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:12:42,382 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:12:42,383 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:12:42,390 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:12:42,391 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:12:42,392 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:12:42,393 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:12:42,394 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:12:42,396 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:12:42,397 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:12:42,399 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:12:42,400 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:12:42,401 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:12:42,402 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:12:42,403 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:12:42,404 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:12:42,405 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:12:42,406 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:12:42,407 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:12:42,408 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:12:42,409 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:12:42,410 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:12:42,411 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:12:42,412 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:12:42,413 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:12:42,414 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:12:42,416 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:12:42,706 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2026-07-28 17:12:42,739 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:12:42,797 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:12:42,801 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:12:42,801 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:12:42,802 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:12:42,802 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:12:42,803 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:12:42,803 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:12:42,804 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:12:42,804 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf'.
2026-07-28 17:12:42,805 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:12:42,806 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:12:42,806 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2026-07-28 17:12:42,807 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:12:42,807 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:12:42,808 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2026-07-28 17:12:42,808 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:12:42,809 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:12:42,809 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:12:42,809 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:12:42,811 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:12:42,811 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:12:42,811 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:12:42,812 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:12:42,812 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits'.
2026-07-28 17:12:42,813 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf'.
2026-07-28 17:12:42,813 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:12:42,814 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf'.
2026-07-28 17:12:42,815 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:12:42,815 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:12:42,816 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:12:42,822 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort
2026-07-28 17:12:42,823 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits ...
2026-07-28 17:12:43,028 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:12:43,634 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2026-07-28 17:12:45,098 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:12:45,855 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084643613 -70.084140230 81.089184145 -70.084140230 81.089184145 -70.082543955 81.084643613 -70.082543955
2026-07-28 17:12:45,856 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:12:45,860 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:12:46,127 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits']).
2026-07-28 17:12:46,129 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:46,322 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:12:46,323 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:46,515 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:12:46,516 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:46,708 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>, []).
2026-07-28 17:12:46,709 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:46,904 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', []).
2026-07-28 17:12:46,905 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:47,096 - stpipe.step - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits', []).
2026-07-28 17:12:47,097 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:47,296 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits']).
2026-07-28 17:12:47,296 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:47,494 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:12:47,495 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:12:47,495 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:12:47,496 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:12:47,499 - stpipe.step - INFO - Step srctype done
2026-07-28 17:12:47,691 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:12:47,691 - stpipe.step - INFO - Step skipped.
2026-07-28 17:12:47,884 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:12:47,889 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:12:48,032 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:13:09,602 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:13:30,526 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.02836487739802967 DN/s
2026-07-28 17:13:30,526 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:13:30,530 - stpipe.step - INFO - Step straylight done
2026-07-28 17:13:30,728 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:13:30,788 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:13:30,795 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2026-07-28 17:13:30,796 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:13:30,796 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:13:30,797 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:13:30,867 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:13:31,065 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:13:31,070 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2026-07-28 17:13:31,111 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:13:31,111 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:13:31,112 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:13:31,157 - stpipe.step - INFO - Step fringe done
2026-07-28 17:13:31,351 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:13:31,352 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:31,551 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:13:31,552 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:31,749 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:13:31,757 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits
2026-07-28 17:13:31,758 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:13:31,758 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:13:31,759 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:13:31,759 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:13:31,760 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:13:31,847 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:13:31,868 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:13:31,869 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:13:31,906 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:13:32,481 - stpipe.step - INFO - Step photom done
2026-07-28 17:13:32,678 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2026-07-28 17:13:32,679 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:33,713 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits>,).
2026-07-28 17:13:33,714 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:33,950 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits>,).
2026-07-28 17:13:33,951 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:34,186 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits>,).
2026-07-28 17:13:34,187 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:35,235 - stpipe.step - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits>,).
2026-07-28 17:13:35,235 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:35,239 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort
2026-07-28 17:13:35,240 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:13:35,240 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:13:35,690 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits
2026-07-28 17:13:35,691 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:13:35,692 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
Reduce the backgrounds individually. This will be needed for the Master Background step in calwebb_spec3, but is unnecessary if doing calwebb_spec2 pixel based background instead.
if dospec2bg:
for file in bgfiles:
asnfile = os.path.join(bg_dir, 'l2asn.json')
writel2asn(file, '', selfcalfiles, asnfile, 'Level2')
Spec2Pipeline.call(asnfile, steps=spec2dict, save_results=True, output_dir=spec2_bgdir)
else:
print('Skipping Spec2 processing for BG data')
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:13:36,004 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:13:36,012 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:13:36,021 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:13:36,030 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:13:36,038 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:13:36,047 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:13:36,055 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:13:36,078 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:13:36,079 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:13:36,080 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:13:36,081 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:13:36,082 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:13:36,083 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:13:36,084 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:13:36,085 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:13:36,090 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:13:36,090 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:13:36,091 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:13:36,092 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:13:36,094 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:13:36,094 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:13:36,095 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:13:36,097 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:13:36,098 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:13:36,098 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:13:36,099 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:13:36,100 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:13:36,101 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:13:36,102 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:13:36,103 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:13:36,104 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:13:36,105 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:13:36,106 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:13:36,107 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:13:36,108 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:13:36,109 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:13:36,110 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:13:36,111 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:13:36,113 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:13:36,521 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:13:36,553 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:13:36,612 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:13:36,616 - CRDS - INFO - Syncing 3 files
2026-07-28 17:13:36,616 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf 810.3 K bytes (1 / 3 files) (0 / 1.6 M bytes)
2026-07-28 17:13:37,293 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits 555.8 K bytes (2 / 3 files) (810.3 K / 1.6 M bytes)
2026-07-28 17:13:37,930 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf 250.9 K bytes (3 / 3 files) (1.4 M / 1.6 M bytes)
2026-07-28 17:13:38,415 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:13:38,416 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:13:38,416 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:13:38,417 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:13:38,418 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:13:38,418 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:13:38,419 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:13:38,420 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:13:38,420 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:13:38,421 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf'.
2026-07-28 17:13:38,421 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:13:38,422 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:13:38,423 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:13:38,423 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2026-07-28 17:13:38,424 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:13:38,424 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:13:38,425 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2026-07-28 17:13:38,426 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:13:38,426 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:13:38,427 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:13:38,427 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:13:38,428 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:13:38,428 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:13:38,429 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:13:38,429 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:13:38,430 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:13:38,430 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits'.
2026-07-28 17:13:38,431 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:13:38,431 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf'.
2026-07-28 17:13:38,432 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:13:38,432 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:13:38,433 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:13:38,433 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf'.
2026-07-28 17:13:38,435 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:13:38,435 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:13:38,436 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:13:38,443 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong
2026-07-28 17:13:38,443 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits ...
2026-07-28 17:13:38,659 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:13:39,124 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757701947
2026-07-28 17:13:40,290 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:13:40,964 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.026388733 -70.078928397 81.034183346 -70.078928397 81.034183346 -70.076269606 81.026388733 -70.076269606
2026-07-28 17:13:40,965 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:13:40,969 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:13:41,170 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], []).
2026-07-28 17:13:41,172 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:41,359 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:13:41,360 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:41,551 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:13:41,552 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:41,738 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>, []).
2026-07-28 17:13:41,739 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:41,928 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>, []).
2026-07-28 17:13:41,929 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:42,119 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:13:42,119 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:13:42,120 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:13:42,121 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:13:42,124 - stpipe.step - INFO - Step srctype done
2026-07-28 17:13:42,308 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:13:42,309 - stpipe.step - INFO - Step skipped.
2026-07-28 17:13:42,495 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:13:42,500 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:13:42,643 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:14:03,832 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:14:24,718 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.036642756313085556 DN/s
2026-07-28 17:14:24,718 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:14:24,722 - stpipe.step - INFO - Step straylight done
2026-07-28 17:14:24,908 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:14:24,967 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:14:24,974 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2026-07-28 17:14:24,975 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:14:24,975 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:14:24,976 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:14:25,044 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:14:25,227 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:14:25,232 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2026-07-28 17:14:25,273 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:14:25,274 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:14:25,275 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:14:25,315 - stpipe.step - INFO - Step fringe done
2026-07-28 17:14:25,498 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:14:25,499 - stpipe.step - INFO - Step skipped.
2026-07-28 17:14:25,684 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:14:25,685 - stpipe.step - INFO - Step skipped.
2026-07-28 17:14:25,871 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:14:25,879 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits
2026-07-28 17:14:25,880 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:14:25,880 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:14:25,881 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:14:25,881 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:14:25,882 - jwst.photom.photom - INFO - band: LONG
2026-07-28 17:14:25,967 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:14:25,988 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:14:25,989 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:14:26,024 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:14:26,555 - stpipe.step - INFO - Step photom done
2026-07-28 17:14:26,741 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2026-07-28 17:14:26,742 - stpipe.step - INFO - Step skipped.
2026-07-28 17:14:27,540 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_cal.fits>,).
2026-07-28 17:14:27,541 - stpipe.step - INFO - Step skipped.
2026-07-28 17:14:27,753 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_cal.fits>,).
2026-07-28 17:14:27,753 - stpipe.step - INFO - Step skipped.
2026-07-28 17:14:27,966 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_cal.fits>,).
2026-07-28 17:14:27,967 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:14:27,967 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:14:27,968 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:14:27,968 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:14:27,985 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2026-07-28 17:14:27,986 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['long', 'long']
2026-07-28 17:14:27,986 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:14:28,277 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:14:28,278 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:14:28,280 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:14:28,282 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:14:28,283 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:14:28,283 - jwst.cube_build.ifu_cube - INFO - Axis 1 51 26.00 81.03028604 0.20000000 -5.10000008 5.10000008
2026-07-28 17:14:28,284 - jwst.cube_build.ifu_cube - INFO - Axis 2 51 26.00 -70.07759900 0.20000000 -5.10000008 5.10000008
2026-07-28 17:14:28,284 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:14:28,285 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:14:28,285 - jwst.cube_build.ifu_cube - INFO - Axis 3 2486 1.00 15.40774059 15.40774059 28.69605064
2026-07-28 17:14:28,286 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, long
2026-07-28 17:14:28,286 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, long
2026-07-28 17:14:28,286 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['long']
2026-07-28 17:14:29,281 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 638 with wavelength below 15.404848098754883
2026-07-28 17:14:38,934 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:14:38,934 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:14:38,947 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 2
2026-07-28 17:14:39,252 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.026209757 -70.078987844 81.026209757 -70.076210066 81.034362322 -70.076210066 81.034362322 -70.078987844
2026-07-28 17:14:39,257 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:14:39,399 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_s3d.fits
2026-07-28 17:14:39,649 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81ae09bd0>,).
2026-07-28 17:14:39,665 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:14:39,670 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:14:39,674 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:14:39,675 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:14:40,105 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:14:40,120 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:14:40,339 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/daofinder.py:343: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:14:40,340 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:14:40,341 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:14:40,344 - jwst.extract_1d.ifu - INFO - Using x_center = 19, y_center = 29, based on TARG_RA and TARG_DEC
2026-07-28 17:14:51,981 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:14:53,432 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:14:55,056 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_x1d.fits
2026-07-28 17:14:55,057 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:14:55,058 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong
2026-07-28 17:14:55,063 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:14:55,064 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:14:55,442 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_cal.fits
2026-07-28 17:14:55,443 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:14:55,443 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:14:55,762 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:14:55,770 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:14:55,778 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:14:55,786 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:14:55,794 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:14:55,803 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:14:55,811 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:14:55,833 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:14:55,834 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:14:55,835 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:14:55,836 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:14:55,837 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:14:55,838 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:14:55,839 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:14:55,840 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:14:55,844 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:14:55,845 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:14:55,846 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:14:55,847 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:14:55,848 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:14:55,849 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:14:55,850 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:14:55,852 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:14:55,852 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:14:55,853 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:14:55,854 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:14:55,855 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:14:55,856 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:14:55,857 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:14:55,858 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:14:55,859 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:14:55,860 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:14:55,861 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:14:55,862 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:14:55,863 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:14:55,864 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:14:55,865 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:14:55,866 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:14:55,867 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:14:56,073 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:14:56,106 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:14:56,163 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:14:56,167 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:14:56,168 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:14:56,168 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:14:56,169 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:14:56,169 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:14:56,169 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:14:56,170 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:14:56,170 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:14:56,171 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:14:56,171 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf'.
2026-07-28 17:14:56,171 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:14:56,173 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:14:56,173 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:14:56,173 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2026-07-28 17:14:56,174 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:14:56,174 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:14:56,175 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2026-07-28 17:14:56,175 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:14:56,176 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:14:56,176 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:14:56,177 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:14:56,177 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:14:56,178 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:14:56,178 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:14:56,178 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:14:56,179 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:14:56,179 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits'.
2026-07-28 17:14:56,180 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:14:56,181 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf'.
2026-07-28 17:14:56,182 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:14:56,182 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:14:56,182 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:14:56,183 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf'.
2026-07-28 17:14:56,184 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:14:56,184 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:14:56,184 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:14:56,191 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort
2026-07-28 17:14:56,191 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits ...
2026-07-28 17:14:56,401 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:14:57,002 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757701947
2026-07-28 17:14:58,458 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:14:59,224 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.028254684 -70.078388227 81.032754141 -70.078388227 81.032754141 -70.076785915 81.028254684 -70.076785915
2026-07-28 17:14:59,225 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:14:59,229 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:14:59,490 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], []).
2026-07-28 17:14:59,491 - stpipe.step - INFO - Step skipped.
2026-07-28 17:14:59,685 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:14:59,686 - stpipe.step - INFO - Step skipped.
2026-07-28 17:14:59,881 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:14:59,881 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:00,079 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>, []).
2026-07-28 17:15:00,080 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:00,286 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>, []).
2026-07-28 17:15:00,287 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:00,489 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:00,490 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:15:00,490 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:15:00,491 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:15:00,493 - stpipe.step - INFO - Step srctype done
2026-07-28 17:15:00,685 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:00,686 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:00,883 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:00,888 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:15:01,033 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:15:22,950 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:15:43,854 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.04428004712530226 DN/s
2026-07-28 17:15:43,855 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:15:43,859 - stpipe.step - INFO - Step straylight done
2026-07-28 17:15:44,054 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:44,114 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:15:44,121 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2026-07-28 17:15:44,122 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:15:44,122 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:15:44,123 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:15:44,191 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:15:44,387 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:44,391 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2026-07-28 17:15:44,431 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:15:44,432 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:15:44,432 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:15:44,472 - stpipe.step - INFO - Step fringe done
2026-07-28 17:15:44,666 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:44,666 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:44,862 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:44,862 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:45,058 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:45,066 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits
2026-07-28 17:15:45,066 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:15:45,067 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:15:45,068 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:15:45,068 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:15:45,069 - jwst.photom.photom - INFO - band: LONG
2026-07-28 17:15:45,156 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:15:45,177 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:15:45,178 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:15:45,215 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:15:45,781 - stpipe.step - INFO - Step photom done
2026-07-28 17:15:45,977 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2026-07-28 17:15:45,977 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:46,994 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_cal.fits>,).
2026-07-28 17:15:46,995 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:47,227 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_cal.fits>,).
2026-07-28 17:15:47,228 - stpipe.step - INFO - Step skipped.
2026-07-28 17:15:47,459 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_cal.fits>,).
2026-07-28 17:15:47,460 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:15:47,461 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:15:47,461 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:15:47,462 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:15:47,476 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2026-07-28 17:15:47,477 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['long', 'long']
2026-07-28 17:15:47,478 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:15:47,766 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:15:47,767 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:15:47,770 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:15:47,773 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:15:47,773 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:15:47,774 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.03050441 0.13000000 -3.05499989 3.05499989
2026-07-28 17:15:47,774 - jwst.cube_build.ifu_cube - INFO - Axis 2 49 25.00 -70.07758707 0.13000000 -3.18499988 3.18499988
2026-07-28 17:15:47,775 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:15:47,776 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:15:47,776 - jwst.cube_build.ifu_cube - INFO - Axis 3 4068 1.00 6.52953386 6.52953386 11.70048332
2026-07-28 17:15:47,777 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, long
2026-07-28 17:15:47,777 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, long
2026-07-28 17:15:47,778 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['long']
2026-07-28 17:15:48,862 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3145 with wavelength below 6.5286736488342285
2026-07-28 17:15:54,945 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2150 with wavelength above 11.702359199523926
2026-07-28 17:16:01,065 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:16:01,065 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:16:01,084 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 1
2026-07-28 17:16:01,463 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.028066858 -70.078453721 81.028066858 -70.076720388 81.032941967 -70.076720388 81.032941967 -70.078453721
2026-07-28 17:16:01,468 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:16:01,638 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_s3d.fits
2026-07-28 17:16:01,930 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81aeb4770>,).
2026-07-28 17:16:01,936 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:16:01,940 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:16:01,944 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:16:01,944 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:16:02,362 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:16:02,386 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:16:02,783 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/daofinder.py:343: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:16:02,784 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:16:02,785 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:16:02,787 - jwst.extract_1d.ifu - INFO - Using x_center = 15, y_center = 29, based on TARG_RA and TARG_DEC
2026-07-28 17:16:22,330 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:16:23,724 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:16:26,162 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_x1d.fits
2026-07-28 17:16:26,163 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:16:26,164 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort
2026-07-28 17:16:26,169 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:16:26,170 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:16:26,625 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_cal.fits
2026-07-28 17:16:26,626 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:16:26,626 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:16:26,951 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:16:26,959 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:16:26,967 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:16:26,975 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:16:26,984 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:16:26,993 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:16:27,001 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:16:27,022 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:16:27,024 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:16:27,025 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:16:27,026 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:16:27,027 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:16:27,028 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:16:27,029 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:16:27,030 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:16:27,034 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:16:27,036 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:16:27,037 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:16:27,038 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:16:27,039 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:16:27,040 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:16:27,041 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:16:27,043 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:16:27,044 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:16:27,045 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:16:27,046 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:16:27,047 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:16:27,050 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:16:27,051 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:16:27,052 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:16:27,053 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:16:27,054 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:16:27,055 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:16:27,056 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:16:27,058 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:16:27,059 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:16:27,060 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:16:27,061 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:16:27,063 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:16:27,281 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:16:27,313 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:16:27,373 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:16:27,377 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:16:27,377 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:16:27,378 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:16:27,378 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:16:27,379 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:16:27,379 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:16:27,380 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:16:27,380 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:16:27,381 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:16:27,381 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf'.
2026-07-28 17:16:27,382 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:16:27,383 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:16:27,383 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:16:27,384 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2026-07-28 17:16:27,384 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:16:27,385 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:16:27,385 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2026-07-28 17:16:27,386 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:16:27,386 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:16:27,386 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:16:27,387 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:16:27,388 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:16:27,388 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:16:27,389 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:16:27,389 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:16:27,390 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:16:27,390 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits'.
2026-07-28 17:16:27,390 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:16:27,391 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf'.
2026-07-28 17:16:27,392 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:16:27,392 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:16:27,393 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:16:27,393 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf'.
2026-07-28 17:16:27,394 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:16:27,394 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:16:27,395 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:16:27,402 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong
2026-07-28 17:16:27,402 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits ...
2026-07-28 17:16:27,607 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:16:28,074 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757068164
2026-07-28 17:16:29,255 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0145.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0144.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0143.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:16:29,944 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.027562329 -70.078457705 81.035356794 -70.078457705 81.035356794 -70.075798903 81.027562329 -70.075798903
2026-07-28 17:16:29,945 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:16:29,949 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:16:30,149 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], []).
2026-07-28 17:16:30,151 - stpipe.step - INFO - Step skipped.
2026-07-28 17:16:30,338 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:16:30,339 - stpipe.step - INFO - Step skipped.
2026-07-28 17:16:30,527 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:16:30,527 - stpipe.step - INFO - Step skipped.
2026-07-28 17:16:30,717 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>, []).
2026-07-28 17:16:30,717 - stpipe.step - INFO - Step skipped.
2026-07-28 17:16:30,910 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>, []).
2026-07-28 17:16:30,910 - stpipe.step - INFO - Step skipped.
2026-07-28 17:16:31,103 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:16:31,104 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:16:31,105 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:16:31,105 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:16:31,108 - stpipe.step - INFO - Step srctype done
2026-07-28 17:16:31,295 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:16:31,295 - stpipe.step - INFO - Step skipped.
2026-07-28 17:16:31,484 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:16:31,489 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:16:31,632 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:16:52,827 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:17:13,723 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.032489631325006485 DN/s
2026-07-28 17:17:13,724 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:17:13,728 - stpipe.step - INFO - Step straylight done
2026-07-28 17:17:13,914 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:17:13,974 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:17:13,981 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2026-07-28 17:17:13,982 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:17:13,983 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:17:13,983 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:17:14,051 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:17:14,241 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:17:14,246 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2026-07-28 17:17:14,286 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:17:14,287 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:17:14,288 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:17:14,329 - stpipe.step - INFO - Step fringe done
2026-07-28 17:17:14,513 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:17:14,514 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:14,700 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:17:14,701 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:14,889 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:17:14,897 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits
2026-07-28 17:17:14,898 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:17:14,898 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:17:14,899 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:17:14,899 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:17:14,900 - jwst.photom.photom - INFO - band: LONG
2026-07-28 17:17:14,986 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:17:15,007 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:17:15,008 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:17:15,044 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:17:15,574 - stpipe.step - INFO - Step photom done
2026-07-28 17:17:15,758 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2026-07-28 17:17:15,759 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:16,563 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_cal.fits>,).
2026-07-28 17:17:16,564 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:16,778 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_cal.fits>,).
2026-07-28 17:17:16,779 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:16,994 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_cal.fits>,).
2026-07-28 17:17:16,994 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:17:16,995 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:17:16,995 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:17:16,996 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:17:17,009 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2026-07-28 17:17:17,010 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['long', 'long']
2026-07-28 17:17:17,011 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:17:17,294 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:17:17,294 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:17:17,297 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:17:17,299 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:17:17,300 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:17:17,300 - jwst.cube_build.ifu_cube - INFO - Axis 1 51 26.00 81.03145956 0.20000000 -5.10000008 5.10000008
2026-07-28 17:17:17,301 - jwst.cube_build.ifu_cube - INFO - Axis 2 51 26.00 -70.07712830 0.20000000 -5.10000008 5.10000008
2026-07-28 17:17:17,301 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:17:17,302 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:17:17,302 - jwst.cube_build.ifu_cube - INFO - Axis 3 2486 1.00 15.40774059 15.40774059 28.69605064
2026-07-28 17:17:17,303 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, long
2026-07-28 17:17:17,304 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, long
2026-07-28 17:17:17,304 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['long']
2026-07-28 17:17:18,313 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 638 with wavelength below 15.404848098754883
2026-07-28 17:17:28,042 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:17:28,043 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:17:28,056 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 2
2026-07-28 17:17:28,347 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.027383371 -70.078517146 81.027383371 -70.075739369 81.035535752 -70.075739369 81.035535752 -70.078517146
2026-07-28 17:17:28,352 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:17:28,494 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_s3d.fits
2026-07-28 17:17:28,747 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa818295480>,).
2026-07-28 17:17:28,753 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:17:28,757 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:17:28,761 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:17:28,762 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:17:29,177 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:17:29,191 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:17:29,409 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/daofinder.py:343: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:17:29,410 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:17:29,410 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:17:29,413 - jwst.extract_1d.ifu - INFO - Using x_center = 26, y_center = 20, based on TARG_RA and TARG_DEC
2026-07-28 17:17:41,118 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:17:42,504 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:17:44,143 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_x1d.fits
2026-07-28 17:17:44,144 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:17:44,145 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong
2026-07-28 17:17:44,151 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:17:44,151 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:17:44,524 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_cal.fits
2026-07-28 17:17:44,525 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:17:44,526 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:17:44,847 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:17:44,855 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:17:44,864 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:17:44,872 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:17:44,880 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:17:44,889 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:17:44,897 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:17:44,919 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:17:44,920 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:17:44,921 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:17:44,922 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:17:44,924 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:17:44,925 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:17:44,926 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:17:44,927 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:17:44,931 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:17:44,932 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:17:44,933 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:17:44,934 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:17:44,935 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:17:44,936 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:17:44,937 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:17:44,938 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:17:44,939 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:17:44,940 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:17:44,941 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:17:44,942 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:17:44,943 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:17:44,945 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:17:44,946 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:17:44,947 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:17:44,948 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:17:44,949 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:17:44,949 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:17:44,950 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:17:44,951 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:17:44,952 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:17:44,953 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:17:44,955 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:17:45,165 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:17:45,198 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:17:45,257 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:17:45,261 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:17:45,261 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:17:45,262 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:17:45,262 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:17:45,263 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:17:45,263 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:17:45,264 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:17:45,265 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:17:45,265 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:17:45,265 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf'.
2026-07-28 17:17:45,266 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:17:45,267 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:17:45,267 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:17:45,268 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2026-07-28 17:17:45,268 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:17:45,269 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:17:45,269 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2026-07-28 17:17:45,270 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:17:45,270 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:17:45,270 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:17:45,271 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:17:45,271 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:17:45,272 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:17:45,272 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:17:45,272 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:17:45,273 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:17:45,273 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits'.
2026-07-28 17:17:45,274 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:17:45,274 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf'.
2026-07-28 17:17:45,275 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:17:45,276 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:17:45,276 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:17:45,276 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf'.
2026-07-28 17:17:45,277 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:17:45,277 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:17:45,278 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:17:45,284 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort
2026-07-28 17:17:45,285 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits ...
2026-07-28 17:17:45,488 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:17:46,092 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757701947
2026-07-28 17:17:47,553 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0146.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0143.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0146.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:17:48,329 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.029428240 -70.077917531 81.033927617 -70.077917531 81.033927617 -70.076315214 81.029428240 -70.076315214
2026-07-28 17:17:48,331 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:17:48,335 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:17:48,608 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], []).
2026-07-28 17:17:48,611 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:48,807 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:17:48,808 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:49,002 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:17:49,003 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:49,198 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>, []).
2026-07-28 17:17:49,199 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:49,397 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>, []).
2026-07-28 17:17:49,398 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:49,593 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:17:49,594 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:17:49,594 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:17:49,595 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:17:49,598 - stpipe.step - INFO - Step srctype done
2026-07-28 17:17:49,793 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:17:49,794 - stpipe.step - INFO - Step skipped.
2026-07-28 17:17:49,987 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:17:49,992 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:17:50,133 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:18:12,034 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:18:32,913 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.025583457754886917 DN/s
2026-07-28 17:18:32,913 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:18:32,917 - stpipe.step - INFO - Step straylight done
2026-07-28 17:18:33,113 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:18:33,173 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:18:33,180 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2026-07-28 17:18:33,181 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:18:33,181 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:18:33,182 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:18:33,249 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:18:33,444 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:18:33,449 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2026-07-28 17:18:33,489 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:18:33,490 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:18:33,490 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:18:33,531 - stpipe.step - INFO - Step fringe done
2026-07-28 17:18:33,725 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:18:33,726 - stpipe.step - INFO - Step skipped.
2026-07-28 17:18:33,922 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:18:33,923 - stpipe.step - INFO - Step skipped.
2026-07-28 17:18:34,118 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:18:34,126 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0222.fits
2026-07-28 17:18:34,127 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:18:34,128 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:18:34,128 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:18:34,129 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:18:34,129 - jwst.photom.photom - INFO - band: LONG
2026-07-28 17:18:34,215 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:18:34,236 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:18:34,237 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:18:34,274 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:18:34,825 - stpipe.step - INFO - Step photom done
2026-07-28 17:18:35,019 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2026-07-28 17:18:35,020 - stpipe.step - INFO - Step skipped.
2026-07-28 17:18:36,040 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_cal.fits>,).
2026-07-28 17:18:36,041 - stpipe.step - INFO - Step skipped.
2026-07-28 17:18:36,266 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_cal.fits>,).
2026-07-28 17:18:36,267 - stpipe.step - INFO - Step skipped.
2026-07-28 17:18:36,494 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_cal.fits>,).
2026-07-28 17:18:36,495 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:18:36,496 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:18:36,496 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:18:36,497 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:18:36,511 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2026-07-28 17:18:36,511 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['long', 'long']
2026-07-28 17:18:36,512 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:18:36,795 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:18:36,796 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:18:36,799 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:18:36,802 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:18:36,802 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:18:36,803 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.03167793 0.13000000 -3.05499989 3.05499989
2026-07-28 17:18:36,803 - jwst.cube_build.ifu_cube - INFO - Axis 2 49 25.00 -70.07711637 0.13000000 -3.18499988 3.18499988
2026-07-28 17:18:36,804 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:18:36,804 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:18:36,805 - jwst.cube_build.ifu_cube - INFO - Axis 3 4068 1.00 6.52953386 6.52953386 11.70048332
2026-07-28 17:18:36,805 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, long
2026-07-28 17:18:36,807 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, long
2026-07-28 17:18:36,807 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['long']
2026-07-28 17:18:37,869 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3145 with wavelength below 6.5286736488342285
2026-07-28 17:18:43,943 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2150 with wavelength above 11.702359199523926
2026-07-28 17:18:50,051 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:18:50,052 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:18:50,071 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 1
2026-07-28 17:18:50,457 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.029240429 -70.077983023 81.029240429 -70.076249689 81.034115428 -70.076249689 81.034115428 -70.077983023
2026-07-28 17:18:50,461 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:18:50,635 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_s3d.fits
2026-07-28 17:18:50,934 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81b2ba3f0>,).
2026-07-28 17:18:50,940 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:18:50,944 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:18:50,948 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:18:50,949 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:18:51,369 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:18:51,394 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:18:51,794 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/daofinder.py:343: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:18:51,795 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:18:51,795 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:18:51,798 - jwst.extract_1d.ifu - INFO - Using x_center = 26, y_center = 16, based on TARG_RA and TARG_DEC
2026-07-28 17:19:11,074 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:19:12,482 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:19:14,936 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_x1d.fits
2026-07-28 17:19:14,937 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:19:14,938 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort
2026-07-28 17:19:14,940 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:19:14,941 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:19:15,392 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_cal.fits
2026-07-28 17:19:15,393 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:19:15,393 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:19:15,717 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:19:15,725 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:19:15,734 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:19:15,742 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:19:15,751 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:19:15,759 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:19:15,767 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:19:15,789 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:19:15,791 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:19:15,792 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:19:15,792 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:19:15,794 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:19:15,795 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:19:15,796 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:19:15,797 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:19:15,801 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:19:15,802 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:19:15,803 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:19:15,804 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:19:15,805 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:19:15,806 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:19:15,807 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:19:15,809 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:19:15,810 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:19:15,811 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:19:15,813 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:19:15,814 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:19:15,814 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:19:15,816 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:19:15,817 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:19:15,817 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:19:15,818 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:19:15,819 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:19:15,820 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:19:15,821 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:19:15,822 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:19:15,823 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:19:15,825 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:19:15,826 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:19:16,043 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:19:16,076 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:19:16,136 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:19:16,140 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:19:16,140 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:19:16,141 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:19:16,141 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:19:16,141 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:19:16,142 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:19:16,142 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:19:16,143 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:19:16,144 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:19:16,144 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf'.
2026-07-28 17:19:16,145 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:19:16,145 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:19:16,145 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:19:16,146 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits'.
2026-07-28 17:19:16,146 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:19:16,147 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:19:16,147 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2026-07-28 17:19:16,148 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:19:16,148 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:19:16,148 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:19:16,149 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:19:16,150 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:19:16,150 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:19:16,150 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:19:16,151 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:19:16,151 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:19:16,152 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits'.
2026-07-28 17:19:16,152 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:19:16,153 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf'.
2026-07-28 17:19:16,153 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:19:16,154 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:19:16,154 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:19:16,154 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf'.
2026-07-28 17:19:16,156 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:19:16,156 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:19:16,157 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:19:16,163 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong
2026-07-28 17:19:16,164 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits ...
2026-07-28 17:19:16,368 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:19:16,834 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757701947
2026-07-28 17:19:18,013 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:19:18,711 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.026536733 -70.078933291 81.034302997 -70.078933291 81.034302997 -70.076286558 81.026536733 -70.076286558
2026-07-28 17:19:18,712 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:19:18,717 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:19:18,916 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], []).
2026-07-28 17:19:18,918 - stpipe.step - INFO - Step skipped.
2026-07-28 17:19:19,104 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:19:19,105 - stpipe.step - INFO - Step skipped.
2026-07-28 17:19:19,290 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:19:19,291 - stpipe.step - INFO - Step skipped.
2026-07-28 17:19:19,477 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>, []).
2026-07-28 17:19:19,477 - stpipe.step - INFO - Step skipped.
2026-07-28 17:19:19,666 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>, []).
2026-07-28 17:19:19,667 - stpipe.step - INFO - Step skipped.
2026-07-28 17:19:19,855 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:19:19,856 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:19:19,856 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:19:19,857 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:19:19,860 - stpipe.step - INFO - Step srctype done
2026-07-28 17:19:20,045 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:19:20,046 - stpipe.step - INFO - Step skipped.
2026-07-28 17:19:20,237 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:19:20,242 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:19:20,385 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:19:41,600 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:20:02,504 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.026767294853925705 DN/s
2026-07-28 17:20:02,505 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:20:02,508 - stpipe.step - INFO - Step straylight done
2026-07-28 17:20:02,697 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:20:02,755 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:20:02,762 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits
2026-07-28 17:20:02,763 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:20:02,764 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:20:02,764 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:20:02,833 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:20:03,023 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:20:03,027 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2026-07-28 17:20:03,067 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:20:03,068 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:20:03,068 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:20:03,108 - stpipe.step - INFO - Step fringe done
2026-07-28 17:20:03,294 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:20:03,295 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:03,484 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:20:03,485 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:03,671 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:20:03,679 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits
2026-07-28 17:20:03,680 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:20:03,680 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:20:03,681 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:20:03,681 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:20:03,681 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:20:03,768 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:20:03,789 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:20:03,790 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:20:03,826 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:20:04,356 - stpipe.step - INFO - Step photom done
2026-07-28 17:20:04,541 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2026-07-28 17:20:04,542 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:05,351 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_cal.fits>,).
2026-07-28 17:20:05,352 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:05,562 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_cal.fits>,).
2026-07-28 17:20:05,563 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:05,773 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_cal.fits>,).
2026-07-28 17:20:05,773 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:20:05,774 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:20:05,774 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:20:05,775 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:20:05,788 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2026-07-28 17:20:05,788 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['medium', 'medium']
2026-07-28 17:20:05,789 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:20:06,069 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:20:06,070 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:20:06,072 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:20:06,075 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:20:06,075 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:20:06,076 - jwst.cube_build.ifu_cube - INFO - Axis 1 51 26.00 81.03041986 0.20000000 -5.10000008 5.10000008
2026-07-28 17:20:06,076 - jwst.cube_build.ifu_cube - INFO - Axis 2 51 26.00 -70.07760992 0.20000000 -5.10000008 5.10000008
2026-07-28 17:20:06,077 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:20:06,078 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:20:06,078 - jwst.cube_build.ifu_cube - INFO - Axis 3 2830 1.00 13.33861923 13.33861923 24.48033714
2026-07-28 17:20:06,079 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, medium
2026-07-28 17:20:06,079 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, medium
2026-07-28 17:20:06,080 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['medium']
2026-07-28 17:20:07,084 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 967 with wavelength below 13.33633041381836
2026-07-28 17:20:17,832 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:20:17,833 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:20:17,847 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:20:18,169 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.026343580 -70.078998767 81.026343580 -70.076220989 81.034496150 -70.076220989 81.034496150 -70.078998767
2026-07-28 17:20:18,174 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:20:18,323 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_s3d.fits
2026-07-28 17:20:18,572 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa818549e10>,).
2026-07-28 17:20:18,577 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:20:18,581 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:20:18,586 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:20:18,586 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:20:19,003 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:20:19,018 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:20:19,315 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/daofinder.py:343: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:20:19,316 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:20:19,317 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:20:19,320 - jwst.extract_1d.ifu - INFO - Using x_center = 19, y_center = 29, based on TARG_RA and TARG_DEC
2026-07-28 17:20:32,678 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:20:34,061 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:20:35,881 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_x1d.fits
2026-07-28 17:20:35,881 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:20:35,882 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong
2026-07-28 17:20:35,888 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:20:35,889 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:20:36,266 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_cal.fits
2026-07-28 17:20:36,267 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:20:36,267 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:20:36,587 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:20:36,595 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:20:36,604 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:20:36,612 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:20:36,621 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:20:36,630 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:20:36,638 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:20:36,660 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:20:36,661 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:20:36,662 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:20:36,663 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:20:36,664 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:20:36,665 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:20:36,666 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:20:36,667 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:20:36,672 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:20:36,673 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:20:36,674 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:20:36,674 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:20:36,675 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:20:36,676 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:20:36,677 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:20:36,679 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:20:36,680 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:20:36,680 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:20:36,681 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:20:36,682 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:20:36,683 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:20:36,684 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:20:36,685 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:20:36,686 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:20:36,687 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:20:36,688 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:20:36,689 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:20:36,690 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:20:36,691 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:20:36,692 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:20:36,693 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:20:36,694 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:20:36,899 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:20:36,932 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:20:36,990 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:20:36,994 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:20:36,995 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:20:36,995 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:20:36,995 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:20:36,996 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:20:36,996 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:20:36,997 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:20:36,998 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:20:36,998 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:20:36,998 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf'.
2026-07-28 17:20:36,999 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:20:37,000 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:20:37,000 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:20:37,000 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2026-07-28 17:20:37,001 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:20:37,001 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:20:37,002 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2026-07-28 17:20:37,002 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:20:37,003 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:20:37,003 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:20:37,004 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:20:37,004 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:20:37,005 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:20:37,005 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:20:37,006 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:20:37,006 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:20:37,007 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits'.
2026-07-28 17:20:37,007 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:20:37,008 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf'.
2026-07-28 17:20:37,008 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:20:37,009 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:20:37,009 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:20:37,009 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf'.
2026-07-28 17:20:37,010 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:20:37,011 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:20:37,012 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:20:37,018 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort
2026-07-28 17:20:37,018 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits ...
2026-07-28 17:20:37,222 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:20:37,825 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757068164
2026-07-28 17:20:39,281 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:20:40,044 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.028398651 -70.078343125 81.032834725 -70.078343125 81.032834725 -70.076738250 81.028398651 -70.076738250
2026-07-28 17:20:40,045 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:20:40,049 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:20:40,305 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], []).
2026-07-28 17:20:40,307 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:40,500 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:20:40,501 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:40,694 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:20:40,695 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:40,887 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>, []).
2026-07-28 17:20:40,888 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:41,080 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>, []).
2026-07-28 17:20:41,081 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:41,276 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:20:41,278 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:20:41,279 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:20:41,280 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:20:41,284 - stpipe.step - INFO - Step srctype done
2026-07-28 17:20:41,479 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:20:41,480 - stpipe.step - INFO - Step skipped.
2026-07-28 17:20:41,673 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:20:41,678 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:20:41,823 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:21:03,570 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:21:24,451 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.04248149069825808 DN/s
2026-07-28 17:21:24,452 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:21:24,455 - stpipe.step - INFO - Step straylight done
2026-07-28 17:21:24,648 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:21:24,707 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:21:24,715 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2026-07-28 17:21:24,715 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:21:24,716 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:21:24,716 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:21:24,787 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:21:24,981 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:21:24,985 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2026-07-28 17:21:25,025 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:21:25,026 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:21:25,026 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:21:25,067 - stpipe.step - INFO - Step fringe done
2026-07-28 17:21:25,260 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:21:25,261 - stpipe.step - INFO - Step skipped.
2026-07-28 17:21:25,457 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:21:25,457 - stpipe.step - INFO - Step skipped.
2026-07-28 17:21:25,651 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:21:25,660 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits
2026-07-28 17:21:25,660 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:21:25,661 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:21:25,661 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:21:25,662 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:21:25,662 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:21:25,747 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:21:25,766 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:21:25,767 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:21:25,803 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:21:26,371 - stpipe.step - INFO - Step photom done
2026-07-28 17:21:26,567 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2026-07-28 17:21:26,567 - stpipe.step - INFO - Step skipped.
2026-07-28 17:21:27,589 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_cal.fits>,).
2026-07-28 17:21:27,590 - stpipe.step - INFO - Step skipped.
2026-07-28 17:21:27,826 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_cal.fits>,).
2026-07-28 17:21:27,827 - stpipe.step - INFO - Step skipped.
2026-07-28 17:21:28,057 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_cal.fits>,).
2026-07-28 17:21:28,058 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:21:28,059 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:21:28,059 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:21:28,060 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:21:28,077 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2026-07-28 17:21:28,077 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['medium', 'medium']
2026-07-28 17:21:28,078 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:21:28,369 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:21:28,370 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:21:28,373 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:21:28,376 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:21:28,376 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:21:28,377 - jwst.cube_build.ifu_cube - INFO - Axis 1 45 23.00 81.03061669 0.13000000 -2.92499989 2.92499989
2026-07-28 17:21:28,377 - jwst.cube_build.ifu_cube - INFO - Axis 2 49 25.00 -70.07754069 0.13000000 -3.18499988 3.18499988
2026-07-28 17:21:28,378 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:21:28,378 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:21:28,379 - jwst.cube_build.ifu_cube - INFO - Axis 3 4243 1.00 5.65960693 5.65960693 10.13073730
2026-07-28 17:21:28,379 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, medium
2026-07-28 17:21:28,382 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, medium
2026-07-28 17:21:28,382 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['medium']
2026-07-28 17:21:29,467 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3801 with wavelength below 5.658884048461914
2026-07-28 17:21:35,694 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2469 with wavelength above 10.13226318359375
2026-07-28 17:21:42,030 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:21:42,031 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:21:42,050 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 1
2026-07-28 17:21:42,437 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.028285119 -70.078407339 81.028285119 -70.076674006 81.032948257 -70.076674006 81.032948257 -70.078407339
2026-07-28 17:21:42,441 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:21:42,618 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_s3d.fits
2026-07-28 17:21:42,916 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa818765490>,).
2026-07-28 17:21:42,921 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:21:42,926 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:21:42,930 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:21:42,930 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:21:43,348 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:21:43,373 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:21:43,789 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/core.py:656: NoDetectionsWarning: Sources were found, but none pass the filtering criteria
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:21:43,790 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:21:43,790 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:21:43,793 - jwst.extract_1d.ifu - INFO - Using x_center = 15, y_center = 28, based on TARG_RA and TARG_DEC
2026-07-28 17:22:03,907 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:22:05,311 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:22:07,843 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_x1d.fits
2026-07-28 17:22:07,844 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:22:07,846 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort
2026-07-28 17:22:07,847 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:22:07,848 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:22:08,299 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_cal.fits
2026-07-28 17:22:08,299 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:22:08,300 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:22:08,628 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:22:08,637 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:22:08,645 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:22:08,654 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:22:08,662 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:22:08,671 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:22:08,679 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:22:08,702 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:22:08,703 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:22:08,704 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:22:08,705 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:22:08,706 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:22:08,708 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:22:08,709 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:22:08,710 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:22:08,715 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:22:08,716 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:22:08,717 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:22:08,718 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:22:08,719 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:22:08,720 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:22:08,721 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:22:08,723 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:22:08,724 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:22:08,724 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:22:08,725 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:22:08,726 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:22:08,727 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:22:08,728 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:22:08,729 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:22:08,730 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:22:08,731 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:22:08,732 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:22:08,733 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:22:08,734 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:22:08,735 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:22:08,736 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:22:08,738 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:22:08,739 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:22:08,961 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:22:08,993 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:22:09,052 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:22:09,056 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:22:09,057 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:22:09,058 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:22:09,058 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:22:09,059 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:22:09,060 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:22:09,060 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:22:09,061 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:22:09,062 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:22:09,062 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf'.
2026-07-28 17:22:09,063 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:22:09,064 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:22:09,064 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:22:09,065 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits'.
2026-07-28 17:22:09,065 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:22:09,065 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:22:09,066 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2026-07-28 17:22:09,067 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:22:09,067 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:22:09,067 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:22:09,068 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:22:09,068 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:22:09,069 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:22:09,069 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:22:09,070 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:22:09,070 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:22:09,071 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits'.
2026-07-28 17:22:09,072 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:22:09,072 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf'.
2026-07-28 17:22:09,073 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:22:09,073 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:22:09,073 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:22:09,074 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf'.
2026-07-28 17:22:09,075 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:22:09,075 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:22:09,076 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:22:09,082 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong
2026-07-28 17:22:09,083 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits ...
2026-07-28 17:22:09,289 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:09,756 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757068164
2026-07-28 17:22:10,939 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0143.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0142.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0144.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:22:11,601 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.027709521 -70.078460935 81.035475657 -70.078460935 81.035475657 -70.075814183 81.027709521 -70.075814183
2026-07-28 17:22:11,603 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:22:11,607 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:22:11,805 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], []).
2026-07-28 17:22:11,807 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:11,996 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:11,997 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:12,187 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:12,187 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:12,376 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>, []).
2026-07-28 17:22:12,376 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:12,561 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>, []).
2026-07-28 17:22:12,562 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:12,746 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:12,747 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:22:12,747 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:22:12,748 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:22:12,750 - stpipe.step - INFO - Step srctype done
2026-07-28 17:22:12,935 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:12,936 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:13,124 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:13,129 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:22:13,271 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:22:34,485 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:22:55,394 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.015758185647428036 DN/s
2026-07-28 17:22:55,395 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:22:55,398 - stpipe.step - INFO - Step straylight done
2026-07-28 17:22:55,581 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:55,638 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:22:55,645 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0840.fits
2026-07-28 17:22:55,646 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:22:55,646 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:22:55,647 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:22:55,713 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:22:55,893 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:55,898 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2026-07-28 17:22:55,936 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:22:55,937 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:22:55,938 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:22:55,976 - stpipe.step - INFO - Step fringe done
2026-07-28 17:22:56,163 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:56,164 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:56,352 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:56,352 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:56,543 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:56,551 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0221.fits
2026-07-28 17:22:56,552 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:22:56,552 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:22:56,553 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:22:56,553 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:22:56,554 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:22:56,638 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:22:56,658 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:22:56,659 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:22:56,694 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:22:57,203 - stpipe.step - INFO - Step photom done
2026-07-28 17:22:57,389 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2026-07-28 17:22:57,390 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:58,201 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_cal.fits>,).
2026-07-28 17:22:58,202 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:58,416 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_cal.fits>,).
2026-07-28 17:22:58,417 - stpipe.step - INFO - Step skipped.
2026-07-28 17:22:58,629 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_cal.fits>,).
2026-07-28 17:22:58,630 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:22:58,630 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:22:58,631 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:22:58,631 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:22:58,644 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2026-07-28 17:22:58,645 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['medium', 'medium']
2026-07-28 17:22:58,645 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:22:58,934 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:22:58,934 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:22:58,937 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:22:58,939 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:22:58,940 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:22:58,941 - jwst.cube_build.ifu_cube - INFO - Axis 1 51 26.00 81.03159259 0.20000000 -5.10000008 5.10000008
2026-07-28 17:22:58,941 - jwst.cube_build.ifu_cube - INFO - Axis 2 51 26.00 -70.07713756 0.20000000 -5.10000008 5.10000008
2026-07-28 17:22:58,941 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:22:58,942 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:22:58,942 - jwst.cube_build.ifu_cube - INFO - Axis 3 2830 1.00 13.33861923 13.33861923 24.48033714
2026-07-28 17:22:58,943 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, medium
2026-07-28 17:22:58,944 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, medium
2026-07-28 17:22:58,944 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['medium']
2026-07-28 17:22:59,958 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 967 with wavelength below 13.33633041381836
2026-07-28 17:23:10,698 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:23:10,698 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:23:10,713 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:23:11,032 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.027516397 -70.078526401 81.027516397 -70.075748624 81.035668781 -70.075748624 81.035668781 -70.078526401
2026-07-28 17:23:11,037 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:23:11,185 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_s3d.fits
2026-07-28 17:23:11,436 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa8180a5ef0>,).
2026-07-28 17:23:11,441 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:23:11,446 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:23:11,451 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:23:11,451 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:23:11,866 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:23:11,886 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:23:12,189 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/daofinder.py:343: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:23:12,189 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:23:12,190 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:23:12,193 - jwst.extract_1d.ifu - INFO - Using x_center = 27, y_center = 20, based on TARG_RA and TARG_DEC
2026-07-28 17:23:25,429 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:23:26,808 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:23:28,621 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_x1d.fits
2026-07-28 17:23:28,621 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:23:28,622 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong
2026-07-28 17:23:28,628 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:23:28,629 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:23:29,002 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_cal.fits
2026-07-28 17:23:29,003 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:23:29,004 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:23:29,328 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:23:29,336 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:23:29,345 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:23:29,353 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:23:29,362 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:23:29,371 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:23:29,378 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:23:29,400 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:23:29,401 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:23:29,403 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:23:29,404 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:23:29,405 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:23:29,406 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:23:29,407 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:23:29,408 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:23:29,412 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:23:29,414 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:23:29,414 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:23:29,415 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:23:29,416 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:23:29,417 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:23:29,418 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:23:29,420 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:23:29,421 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:23:29,422 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:23:29,422 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:23:29,423 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:23:29,424 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:23:29,425 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:23:29,426 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:23:29,427 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:23:29,429 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:23:29,430 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:23:29,431 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:23:29,432 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:23:29,433 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:23:29,434 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:23:29,435 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:23:29,437 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:23:29,638 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:23:29,669 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:23:29,728 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:23:29,732 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:23:29,732 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:23:29,733 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:23:29,733 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:23:29,734 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:23:29,734 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:23:29,734 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:23:29,735 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:23:29,735 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:23:29,736 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf'.
2026-07-28 17:23:29,736 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:23:29,737 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:23:29,737 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:23:29,738 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2026-07-28 17:23:29,738 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:23:29,739 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:23:29,739 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2026-07-28 17:23:29,740 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:23:29,740 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:23:29,741 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:23:29,741 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:23:29,741 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:23:29,742 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:23:29,742 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:23:29,743 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:23:29,743 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:23:29,744 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits'.
2026-07-28 17:23:29,745 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:23:29,745 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf'.
2026-07-28 17:23:29,746 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:23:29,746 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:23:29,746 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:23:29,747 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf'.
2026-07-28 17:23:29,748 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:23:29,748 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:23:29,749 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:23:29,755 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort
2026-07-28 17:23:29,755 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits ...
2026-07-28 17:23:29,951 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:23:30,552 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757068164
2026-07-28 17:23:31,997 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0144.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0141.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0141.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:23:32,739 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.029571400 -70.077870762 81.034007412 -70.077870762 81.034007412 -70.076265876 81.029571400 -70.076265876
2026-07-28 17:23:32,740 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:23:32,744 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:23:32,997 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], []).
2026-07-28 17:23:33,000 - stpipe.step - INFO - Step skipped.
2026-07-28 17:23:33,193 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:23:33,194 - stpipe.step - INFO - Step skipped.
2026-07-28 17:23:33,386 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:23:33,387 - stpipe.step - INFO - Step skipped.
2026-07-28 17:23:33,578 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>, []).
2026-07-28 17:23:33,578 - stpipe.step - INFO - Step skipped.
2026-07-28 17:23:33,770 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>, []).
2026-07-28 17:23:33,771 - stpipe.step - INFO - Step skipped.
2026-07-28 17:23:33,975 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:23:33,976 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:23:33,977 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:23:33,977 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:23:33,980 - stpipe.step - INFO - Step srctype done
2026-07-28 17:23:34,173 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:23:34,174 - stpipe.step - INFO - Step skipped.
2026-07-28 17:23:34,371 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:23:34,375 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:23:34,516 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:23:56,287 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:24:17,194 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03500558336587109 DN/s
2026-07-28 17:24:17,195 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:24:17,198 - stpipe.step - INFO - Step straylight done
2026-07-28 17:24:17,389 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:24:17,447 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:24:17,455 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2026-07-28 17:24:17,455 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:24:17,456 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:24:17,456 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:24:17,524 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:24:17,718 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:24:17,723 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2026-07-28 17:24:17,763 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:24:17,764 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:24:17,764 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:24:17,805 - stpipe.step - INFO - Step fringe done
2026-07-28 17:24:17,998 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:24:17,999 - stpipe.step - INFO - Step skipped.
2026-07-28 17:24:18,195 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:24:18,195 - stpipe.step - INFO - Step skipped.
2026-07-28 17:24:18,393 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:24:18,402 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0226.fits
2026-07-28 17:24:18,402 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:24:18,403 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:24:18,403 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:24:18,403 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:24:18,404 - jwst.photom.photom - INFO - band: MEDIUM
2026-07-28 17:24:18,490 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:24:18,511 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:24:18,512 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:24:18,550 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:24:19,096 - stpipe.step - INFO - Step photom done
2026-07-28 17:24:19,290 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2026-07-28 17:24:19,291 - stpipe.step - INFO - Step skipped.
2026-07-28 17:24:20,323 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_cal.fits>,).
2026-07-28 17:24:20,324 - stpipe.step - INFO - Step skipped.
2026-07-28 17:24:20,554 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_cal.fits>,).
2026-07-28 17:24:20,555 - stpipe.step - INFO - Step skipped.
2026-07-28 17:24:20,786 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_cal.fits>,).
2026-07-28 17:24:20,787 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:24:20,787 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:24:20,788 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:24:20,788 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:24:20,802 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2026-07-28 17:24:20,803 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['medium', 'medium']
2026-07-28 17:24:20,803 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:24:21,088 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:24:21,089 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:24:21,093 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:24:21,095 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:24:21,096 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:24:21,096 - jwst.cube_build.ifu_cube - INFO - Axis 1 45 23.00 81.03178941 0.13000000 -2.92499989 2.92499989
2026-07-28 17:24:21,097 - jwst.cube_build.ifu_cube - INFO - Axis 2 49 25.00 -70.07706832 0.13000000 -3.18499988 3.18499988
2026-07-28 17:24:21,097 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:24:21,098 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:24:21,098 - jwst.cube_build.ifu_cube - INFO - Axis 3 4243 1.00 5.65960693 5.65960693 10.13073730
2026-07-28 17:24:21,099 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, medium
2026-07-28 17:24:21,099 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, medium
2026-07-28 17:24:21,100 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['medium']
2026-07-28 17:24:22,185 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3801 with wavelength below 5.658884048461914
2026-07-28 17:24:28,389 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2469 with wavelength above 10.13226318359375
2026-07-28 17:24:34,707 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:24:34,708 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:24:34,727 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 1
2026-07-28 17:24:35,113 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.029457890 -70.077934970 81.029457890 -70.076201637 81.034120922 -70.076201637 81.034120922 -70.077934970
2026-07-28 17:24:35,118 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:24:35,294 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_s3d.fits
2026-07-28 17:24:35,598 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81a0cb650>,).
2026-07-28 17:24:35,603 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:24:35,608 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:24:35,612 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:24:35,612 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:24:36,030 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:24:36,056 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:24:36,474 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/core.py:656: NoDetectionsWarning: Sources were found, but none pass the filtering criteria
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:24:36,475 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:24:36,476 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:24:36,478 - jwst.extract_1d.ifu - INFO - Using x_center = 26, y_center = 15, based on TARG_RA and TARG_DEC
2026-07-28 17:24:56,578 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:24:57,970 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:25:00,516 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_x1d.fits
2026-07-28 17:25:00,517 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:25:00,518 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort
2026-07-28 17:25:00,520 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:25:00,520 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:25:00,974 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_cal.fits
2026-07-28 17:25:00,975 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:25:00,976 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:25:01,296 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:25:01,304 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:25:01,312 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:25:01,320 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:25:01,329 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:25:01,337 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:25:01,345 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:25:01,367 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:25:01,368 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:25:01,369 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:25:01,370 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:25:01,371 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:25:01,372 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:25:01,373 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:25:01,374 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:25:01,378 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:25:01,379 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:25:01,380 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:25:01,381 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:25:01,381 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:25:01,382 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:25:01,383 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:25:01,385 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:25:01,386 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:25:01,386 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:25:01,387 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:25:01,388 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:25:01,389 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:25:01,390 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:25:01,391 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:25:01,392 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:25:01,393 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:25:01,394 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:25:01,395 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:25:01,395 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:25:01,396 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:25:01,397 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:25:01,399 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:25:01,400 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:25:01,622 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:25:01,656 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:25:01,715 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:25:01,719 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:25:01,719 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:25:01,720 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:25:01,720 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:25:01,721 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:25:01,721 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:25:01,722 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:25:01,722 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:25:01,723 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:25:01,723 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf'.
2026-07-28 17:25:01,724 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:25:01,725 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:25:01,725 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:25:01,725 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2026-07-28 17:25:01,726 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:25:01,726 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:25:01,727 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2026-07-28 17:25:01,728 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:25:01,728 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:25:01,729 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:25:01,729 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:25:01,730 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:25:01,730 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:25:01,731 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:25:01,731 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:25:01,732 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:25:01,732 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits'.
2026-07-28 17:25:01,733 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:25:01,733 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf'.
2026-07-28 17:25:01,734 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:25:01,734 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:25:01,735 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:25:01,735 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf'.
2026-07-28 17:25:01,736 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:25:01,736 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:25:01,737 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:25:01,743 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong
2026-07-28 17:25:01,744 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits ...
2026-07-28 17:25:01,947 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:02,413 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757068164
2026-07-28 17:25:03,588 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:25:04,256 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.026462176 -70.078914856 81.034388803 -70.078914856 81.034388803 -70.076274551 81.026462176 -70.076274551
2026-07-28 17:25:04,258 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:25:04,261 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:25:04,464 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], []).
2026-07-28 17:25:04,466 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:04,655 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:04,655 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:04,844 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:04,845 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:05,033 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>, []).
2026-07-28 17:25:05,034 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:05,226 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>, []).
2026-07-28 17:25:05,227 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:05,418 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:05,419 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:25:05,419 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:25:05,420 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:25:05,423 - stpipe.step - INFO - Step srctype done
2026-07-28 17:25:05,609 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:05,609 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:05,799 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:05,803 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:25:05,948 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:25:27,125 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:25:47,984 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.008650952950119972 DN/s
2026-07-28 17:25:47,985 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:25:47,988 - stpipe.step - INFO - Step straylight done
2026-07-28 17:25:48,170 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:48,228 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:25:48,235 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2026-07-28 17:25:48,236 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:25:48,236 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:25:48,237 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:25:48,314 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:25:48,497 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:48,502 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2026-07-28 17:25:48,540 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:25:48,541 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:25:48,541 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:25:48,579 - stpipe.step - INFO - Step fringe done
2026-07-28 17:25:48,764 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:48,765 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:48,954 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:48,954 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:49,141 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:49,148 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits
2026-07-28 17:25:49,149 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:25:49,150 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:25:49,150 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:25:49,150 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:25:49,151 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:25:49,235 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:25:49,255 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:25:49,256 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:25:49,292 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:25:49,797 - stpipe.step - INFO - Step photom done
2026-07-28 17:25:49,980 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2026-07-28 17:25:49,981 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:50,784 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_cal.fits>,).
2026-07-28 17:25:50,785 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:50,994 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_cal.fits>,).
2026-07-28 17:25:50,995 - stpipe.step - INFO - Step skipped.
2026-07-28 17:25:51,203 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_cal.fits>,).
2026-07-28 17:25:51,204 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:25:51,205 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:25:51,205 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:25:51,206 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:25:51,219 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2026-07-28 17:25:51,219 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'short']
2026-07-28 17:25:51,220 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:25:51,504 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:25:51,505 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:25:51,508 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:25:51,510 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:25:51,511 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:25:51,512 - jwst.cube_build.ifu_cube - INFO - Axis 1 53 27.00 81.03042549 0.20000000 -5.30000008 5.30000008
2026-07-28 17:25:51,512 - jwst.cube_build.ifu_cube - INFO - Axis 2 51 26.00 -70.07759470 0.20000000 -5.10000008 5.10000008
2026-07-28 17:25:51,513 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:25:51,513 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:25:51,514 - jwst.cube_build.ifu_cube - INFO - Axis 3 3128 1.00 11.54997730 11.54997730 20.95471191
2026-07-28 17:25:51,514 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, short
2026-07-28 17:25:51,514 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, short
2026-07-28 17:25:51,515 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['short']
2026-07-28 17:25:52,502 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2079 with wavelength below 11.548135757446289
2026-07-28 17:26:03,986 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:26:03,987 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:26:04,004 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:26:04,358 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.026186156 -70.078983542 81.026186156 -70.076205764 81.034664823 -70.076205764 81.034664823 -70.078983542
2026-07-28 17:26:04,362 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:26:04,528 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_s3d.fits
2026-07-28 17:26:04,798 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa8185a6650>,).
2026-07-28 17:26:04,804 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:26:04,808 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:26:04,812 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:26:04,813 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:26:05,230 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:26:05,251 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:26:05,602 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/daofinder.py:343: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:26:05,603 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:26:05,603 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:26:05,606 - jwst.extract_1d.ifu - INFO - Using x_center = 20, y_center = 29, based on TARG_RA and TARG_DEC
2026-07-28 17:26:20,239 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:26:21,622 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:26:23,584 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_x1d.fits
2026-07-28 17:26:23,585 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:26:23,586 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong
2026-07-28 17:26:23,588 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:26:23,588 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:26:23,956 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_cal.fits
2026-07-28 17:26:23,956 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:26:23,957 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:26:24,275 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:26:24,283 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:26:24,292 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:26:24,300 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:26:24,308 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:26:24,317 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:26:24,325 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:26:24,347 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:26:24,349 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:26:24,350 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:26:24,351 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:26:24,352 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:26:24,353 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:26:24,354 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:26:24,355 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:26:24,360 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:26:24,361 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:26:24,362 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:26:24,363 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:26:24,363 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:26:24,364 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:26:24,365 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:26:24,367 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:26:24,367 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:26:24,368 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:26:24,370 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:26:24,371 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:26:24,372 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:26:24,373 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:26:24,374 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:26:24,375 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:26:24,376 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:26:24,378 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:26:24,378 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:26:24,379 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:26:24,380 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:26:24,382 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:26:24,383 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:26:24,385 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:26:24,591 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:26:24,623 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:26:24,681 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:26:24,685 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:26:24,686 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:26:24,686 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:26:24,686 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:26:24,687 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:26:24,687 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:26:24,688 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:26:24,688 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:26:24,689 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:26:24,689 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf'.
2026-07-28 17:26:24,690 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:26:24,691 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:26:24,691 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:26:24,692 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2026-07-28 17:26:24,692 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:26:24,693 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:26:24,693 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2026-07-28 17:26:24,694 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:26:24,694 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:26:24,695 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:26:24,695 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:26:24,696 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:26:24,696 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:26:24,697 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:26:24,697 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:26:24,697 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:26:24,698 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits'.
2026-07-28 17:26:24,699 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:26:24,699 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf'.
2026-07-28 17:26:24,700 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:26:24,700 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:26:24,701 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:26:24,701 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf'.
2026-07-28 17:26:24,701 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:26:24,702 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:26:24,703 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:26:24,709 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort
2026-07-28 17:26:24,710 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits ...
2026-07-28 17:26:24,913 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:26:25,515 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757068164
2026-07-28 17:26:26,973 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:26:27,731 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.028395073 -70.078423896 81.032929915 -70.078423896 81.032929915 -70.076828813 81.028395073 -70.076828813
2026-07-28 17:26:27,733 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:26:27,737 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:26:27,992 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], []).
2026-07-28 17:26:27,995 - stpipe.step - INFO - Step skipped.
2026-07-28 17:26:28,189 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:26:28,190 - stpipe.step - INFO - Step skipped.
2026-07-28 17:26:28,387 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:26:28,388 - stpipe.step - INFO - Step skipped.
2026-07-28 17:26:28,583 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>, []).
2026-07-28 17:26:28,584 - stpipe.step - INFO - Step skipped.
2026-07-28 17:26:28,779 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>, []).
2026-07-28 17:26:28,780 - stpipe.step - INFO - Step skipped.
2026-07-28 17:26:28,975 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:26:28,975 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:26:28,976 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:26:28,976 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:26:28,979 - stpipe.step - INFO - Step srctype done
2026-07-28 17:26:29,172 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:26:29,173 - stpipe.step - INFO - Step skipped.
2026-07-28 17:26:29,368 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:26:29,372 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:26:29,514 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:26:51,026 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:27:11,900 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.04151553678869984 DN/s
2026-07-28 17:27:11,900 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:27:11,904 - stpipe.step - INFO - Step straylight done
2026-07-28 17:27:12,097 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:27:12,156 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:27:12,163 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2026-07-28 17:27:12,163 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:27:12,164 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:27:12,164 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:27:12,233 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:27:12,428 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:27:12,432 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2026-07-28 17:27:12,475 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:27:12,476 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:27:12,476 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:27:12,522 - stpipe.step - INFO - Step fringe done
2026-07-28 17:27:12,720 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:27:12,721 - stpipe.step - INFO - Step skipped.
2026-07-28 17:27:12,913 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:27:12,914 - stpipe.step - INFO - Step skipped.
2026-07-28 17:27:13,108 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:27:13,116 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits
2026-07-28 17:27:13,116 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:27:13,117 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:27:13,117 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:27:13,118 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:27:13,118 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:27:13,204 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:27:13,224 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:27:13,225 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:27:13,262 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:27:13,832 - stpipe.step - INFO - Step photom done
2026-07-28 17:27:14,027 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2026-07-28 17:27:14,028 - stpipe.step - INFO - Step skipped.
2026-07-28 17:27:15,059 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_cal.fits>,).
2026-07-28 17:27:15,059 - stpipe.step - INFO - Step skipped.
2026-07-28 17:27:15,287 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_cal.fits>,).
2026-07-28 17:27:15,288 - stpipe.step - INFO - Step skipped.
2026-07-28 17:27:15,514 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_cal.fits>,).
2026-07-28 17:27:15,515 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:27:15,515 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:27:15,516 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:27:15,516 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:27:15,531 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2026-07-28 17:27:15,531 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'short']
2026-07-28 17:27:15,532 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:27:15,821 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:27:15,822 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:27:15,825 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:27:15,828 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:27:15,828 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:27:15,829 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.03066249 0.13000000 -3.05499989 3.05499989
2026-07-28 17:27:15,829 - jwst.cube_build.ifu_cube - INFO - Axis 2 49 25.00 -70.07762635 0.13000000 -3.18499988 3.18499988
2026-07-28 17:27:15,830 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:27:15,830 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:27:15,831 - jwst.cube_build.ifu_cube - INFO - Axis 3 4404 1.00 4.90000010 4.90000010 8.77080059
2026-07-28 17:27:15,831 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, short
2026-07-28 17:27:15,831 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, short
2026-07-28 17:27:15,832 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['short']
2026-07-28 17:27:16,930 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3697 with wavelength below 4.899390697479248
2026-07-28 17:27:23,260 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2597 with wavelength above 8.772054672241211
2026-07-28 17:27:29,800 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:27:29,801 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:27:29,821 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 1
2026-07-28 17:27:30,250 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.028224935 -70.078493005 81.028224935 -70.076759671 81.033100053 -70.076759671 81.033100053 -70.078493005
2026-07-28 17:27:30,255 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:27:30,441 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_s3d.fits
2026-07-28 17:27:30,737 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa8181df550>,).
2026-07-28 17:27:30,742 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:27:30,747 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:27:30,751 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:27:30,752 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:27:31,168 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:27:31,195 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:27:31,641 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/core.py:603: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:27:31,641 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:27:31,643 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:27:31,646 - jwst.extract_1d.ifu - INFO - Using x_center = 17, y_center = 31, based on TARG_RA and TARG_DEC
2026-07-28 17:27:52,400 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:27:53,796 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:27:56,443 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_x1d.fits
2026-07-28 17:27:56,444 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:27:56,446 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort
2026-07-28 17:27:56,448 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:27:56,449 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:27:56,901 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_cal.fits
2026-07-28 17:27:56,902 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:27:56,902 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:27:57,224 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:27:57,232 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:27:57,241 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:27:57,249 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:27:57,257 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:27:57,266 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:27:57,273 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:27:57,295 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:27:57,296 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:27:57,297 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:27:57,298 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:27:57,300 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:27:57,301 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:27:57,302 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:27:57,303 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:27:57,308 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:27:57,309 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:27:57,310 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:27:57,311 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:27:57,312 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:27:57,313 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:27:57,314 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:27:57,315 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:27:57,317 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:27:57,317 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:27:57,318 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:27:57,319 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:27:57,320 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:27:57,321 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:27:57,322 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:27:57,323 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:27:57,324 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:27:57,325 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:27:57,326 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:27:57,327 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:27:57,327 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:27:57,328 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:27:57,330 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:27:57,331 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:27:57,551 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:27:57,584 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:27:57,643 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:27:57,646 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:27:57,647 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:27:57,647 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:27:57,648 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:27:57,648 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:27:57,649 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:27:57,649 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:27:57,650 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:27:57,651 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:27:57,651 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf'.
2026-07-28 17:27:57,651 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:27:57,652 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:27:57,652 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:27:57,653 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2026-07-28 17:27:57,653 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:27:57,654 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:27:57,654 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2026-07-28 17:27:57,655 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:27:57,655 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:27:57,656 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:27:57,656 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:27:57,657 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:27:57,658 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:27:57,658 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:27:57,659 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:27:57,659 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:27:57,659 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits'.
2026-07-28 17:27:57,660 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:27:57,660 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf'.
2026-07-28 17:27:57,661 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:27:57,662 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:27:57,662 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:27:57,662 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf'.
2026-07-28 17:27:57,663 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:27:57,663 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:27:57,664 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:27:57,671 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong
2026-07-28 17:27:57,676 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits ...
2026-07-28 17:27:57,877 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:27:58,341 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.0000087564343811
2026-07-28 17:27:59,504 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0141.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0140.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0145.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:28:00,162 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.027635116 -70.078442156 81.035561620 -70.078442156 81.035561620 -70.075801829 81.027635116 -70.075801829
2026-07-28 17:28:00,163 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:28:00,167 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:28:00,365 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits'], []).
2026-07-28 17:28:00,367 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:00,556 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:00,560 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:00,747 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:00,747 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:00,935 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>, []).
2026-07-28 17:28:00,936 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:01,124 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>, []).
2026-07-28 17:28:01,125 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:01,313 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:01,314 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:28:01,314 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:28:01,314 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:28:01,317 - stpipe.step - INFO - Step srctype done
2026-07-28 17:28:01,502 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:01,502 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:01,694 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:01,699 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:28:01,848 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:28:23,036 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:28:43,967 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.03229295834898949 DN/s
2026-07-28 17:28:43,968 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:28:43,972 - stpipe.step - INFO - Step straylight done
2026-07-28 17:28:44,159 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:44,218 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:28:44,226 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2026-07-28 17:28:44,226 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:28:44,227 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:28:44,227 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:28:44,306 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:28:44,492 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:44,497 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2026-07-28 17:28:44,537 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:28:44,538 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:28:44,539 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:28:44,578 - stpipe.step - INFO - Step fringe done
2026-07-28 17:28:44,764 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:44,765 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:44,952 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:44,953 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:45,139 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:45,147 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0220.fits
2026-07-28 17:28:45,148 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:28:45,148 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:28:45,149 - jwst.photom.photom - INFO - detector: MIRIFULONG
2026-07-28 17:28:45,149 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:28:45,150 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:28:45,236 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:28:45,256 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:28:45,257 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:28:45,293 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:28:45,793 - stpipe.step - INFO - Step photom done
2026-07-28 17:28:45,977 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2026-07-28 17:28:45,978 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:46,780 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_cal.fits>,).
2026-07-28 17:28:46,781 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:46,991 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_cal.fits>,).
2026-07-28 17:28:46,992 - stpipe.step - INFO - Step skipped.
2026-07-28 17:28:47,203 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_cal.fits>,).
2026-07-28 17:28:47,204 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:28:47,204 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:28:47,205 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:28:47,205 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:28:47,219 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2026-07-28 17:28:47,219 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'short']
2026-07-28 17:28:47,220 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:28:47,505 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:28:47,505 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:28:47,508 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:28:47,510 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:28:47,511 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:28:47,511 - jwst.cube_build.ifu_cube - INFO - Axis 1 53 27.00 81.03159837 0.20000000 -5.30000008 5.30000008
2026-07-28 17:28:47,512 - jwst.cube_build.ifu_cube - INFO - Axis 2 51 26.00 -70.07712199 0.20000000 -5.10000008 5.10000008
2026-07-28 17:28:47,513 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:28:47,513 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:28:47,513 - jwst.cube_build.ifu_cube - INFO - Axis 3 3128 1.00 11.54997730 11.54997730 20.95471191
2026-07-28 17:28:47,514 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, short
2026-07-28 17:28:47,514 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, short
2026-07-28 17:28:47,515 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['short']
2026-07-28 17:28:48,510 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2079 with wavelength below 11.548135757446289
2026-07-28 17:28:59,950 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:28:59,951 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:28:59,966 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:29:00,324 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.027359131 -70.078510831 81.027359131 -70.075733053 81.035837605 -70.075733053 81.035837605 -70.078510831
2026-07-28 17:29:00,328 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:29:00,494 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_s3d.fits
2026-07-28 17:29:00,768 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81919d3d0>,).
2026-07-28 17:29:00,773 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:29:00,778 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:29:00,782 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:29:00,783 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:29:01,196 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:29:01,219 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:29:01,568 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/daofinder.py:343: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:29:01,569 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:29:01,569 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:29:01,572 - jwst.extract_1d.ifu - INFO - Using x_center = 28, y_center = 20, based on TARG_RA and TARG_DEC
2026-07-28 17:29:16,157 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:29:17,562 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:29:19,516 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_x1d.fits
2026-07-28 17:29:19,517 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:29:19,518 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong
2026-07-28 17:29:19,520 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:29:19,520 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:29:19,886 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_cal.fits
2026-07-28 17:29:19,886 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:29:19,887 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
2026-07-28 17:29:20,206 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:29:20,214 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:29:20,222 - CRDS - ERROR - Error determining best reference for 'pars-targcentroidstep' = Unknown reference type 'pars-targcentroidstep'
2026-07-28 17:29:20,230 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:29:20,239 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:29:20,247 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:29:20,255 - stpipe.pipeline - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0010.asdf
2026-07-28 17:29:20,277 - stpipe.step - INFO - Spec2Pipeline instance created.
2026-07-28 17:29:20,279 - stpipe.step - INFO - AssignWcsStep instance created.
2026-07-28 17:29:20,280 - stpipe.step - INFO - BadpixSelfcalStep instance created.
2026-07-28 17:29:20,282 - stpipe.step - INFO - MSAFlagOpenStep instance created.
2026-07-28 17:29:20,283 - stpipe.step - INFO - CleanFlickerNoiseStep instance created.
2026-07-28 17:29:20,285 - stpipe.step - INFO - BackgroundStep instance created.
2026-07-28 17:29:20,287 - stpipe.step - INFO - ImprintStep instance created.
2026-07-28 17:29:20,288 - stpipe.step - INFO - Extract2dStep instance created.
2026-07-28 17:29:20,292 - stpipe.step - INFO - MasterBackgroundMosStep instance created.
2026-07-28 17:29:20,293 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:29:20,294 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:29:20,295 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:29:20,296 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:29:20,297 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:29:20,299 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:29:20,300 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:29:20,301 - stpipe.step - INFO - TargCentroidStep instance created.
2026-07-28 17:29:20,302 - stpipe.step - INFO - WavecorrStep instance created.
2026-07-28 17:29:20,303 - stpipe.step - INFO - FlatFieldStep instance created.
2026-07-28 17:29:20,304 - stpipe.step - INFO - SourceTypeStep instance created.
2026-07-28 17:29:20,305 - stpipe.step - INFO - StraylightStep instance created.
2026-07-28 17:29:20,306 - stpipe.step - INFO - FringeStep instance created.
2026-07-28 17:29:20,307 - stpipe.step - INFO - ResidualFringeStep instance created.
2026-07-28 17:29:20,308 - stpipe.step - INFO - PathLossStep instance created.
2026-07-28 17:29:20,310 - stpipe.step - INFO - BarShadowStep instance created.
2026-07-28 17:29:20,311 - stpipe.step - INFO - WfssContamStep instance created.
2026-07-28 17:29:20,311 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:29:20,312 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:29:20,313 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:29:20,314 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:29:20,315 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:29:20,317 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:29:20,520 - stpipe.step - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2026-07-28 17:29:20,552 - stpipe.step - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs004/stage2
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
nrs_ifu_slice_wcs: False
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
autoparam: False
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_list: None
save_combined_background: False
sigma: 3.0
maxiters: None
soss_source_percentile: 35.0
soss_bkg_percentile: None
wfss_mmag_extract: None
wfss_mask: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names: None
source_ids: None
source_ra: None
source_dec: None
source_max_sep: 2.0
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
targ_centroid:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
ta_file: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
save_shower_model: False
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: '1'
orders: None
magnitude_limit: None
wl_oversample: 2
max_pixels_per_chunk: 5000
polyfit_degree: None
n_iterations: 1
l2_alpha: 0.1
rejection_threshold: 0.1
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: multi
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
2026-07-28 17:29:20,610 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l2asn.json' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'chromcorr', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange']
2026-07-28 17:29:20,614 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:29:20,615 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:29:20,615 - stpipe.pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2026-07-28 17:29:20,616 - stpipe.pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2026-07-28 17:29:20,616 - stpipe.pipeline - INFO - Prefetch for CHROMCORR reference file is 'N/A'.
2026-07-28 17:29:20,617 - stpipe.pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2026-07-28 17:29:20,617 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:29:20,618 - stpipe.pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2026-07-28 17:29:20,618 - stpipe.pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2026-07-28 17:29:20,619 - stpipe.pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf'.
2026-07-28 17:29:20,619 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:29:20,620 - stpipe.pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2026-07-28 17:29:20,621 - stpipe.pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2026-07-28 17:29:20,621 - stpipe.pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2026-07-28 17:29:20,622 - stpipe.pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2026-07-28 17:29:20,622 - stpipe.pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2026-07-28 17:29:20,623 - stpipe.pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2026-07-28 17:29:20,623 - stpipe.pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2026-07-28 17:29:20,624 - stpipe.pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2026-07-28 17:29:20,624 - stpipe.pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2026-07-28 17:29:20,624 - stpipe.pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2026-07-28 17:29:20,625 - stpipe.pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2026-07-28 17:29:20,626 - stpipe.pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2026-07-28 17:29:20,626 - stpipe.pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2026-07-28 17:29:20,627 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:29:20,627 - stpipe.pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2026-07-28 17:29:20,628 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits'.
2026-07-28 17:29:20,628 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:29:20,629 - stpipe.pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf'.
2026-07-28 17:29:20,630 - stpipe.pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2026-07-28 17:29:20,630 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:29:20,630 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:29:20,631 - stpipe.pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf'.
2026-07-28 17:29:20,632 - stpipe.pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2026-07-28 17:29:20,632 - stpipe.pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf'.
2026-07-28 17:29:20,633 - jwst.pipeline.calwebb_spec2 - INFO - Starting calwebb_spec2 ...
2026-07-28 17:29:20,639 - jwst.pipeline.calwebb_spec2 - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort
2026-07-28 17:29:20,640 - jwst.pipeline.calwebb_spec2 - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits ...
2026-07-28 17:29:20,838 - stpipe.step - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:29:21,439 - jwst.assign_wcs.miri - INFO - Applied Barycentric velocity correction : 1.000008757068164
2026-07-28 17:29:22,879 - jwst.assign_wcs.miri - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0140.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0139.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0142.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0011.asdf', 'camera': None, 'chromcorr': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2026-07-28 17:29:23,626 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.029567981 -70.077951186 81.034102761 -70.077951186 81.034102761 -70.076356092 81.029567981 -70.076356092
2026-07-28 17:29:23,628 - jwst.assign_wcs.assign_wcs - INFO - COMPLETED assign_wcs
2026-07-28 17:29:23,632 - stpipe.step - INFO - Step assign_wcs done
2026-07-28 17:29:23,882 - stpipe.step - INFO - Step badpix_selfcal running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits'], []).
2026-07-28 17:29:23,884 - stpipe.step - INFO - Step skipped.
2026-07-28 17:29:24,075 - stpipe.step - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:29:24,076 - stpipe.step - INFO - Step skipped.
2026-07-28 17:29:24,268 - stpipe.step - INFO - Step clean_flicker_noise running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:29:24,269 - stpipe.step - INFO - Step skipped.
2026-07-28 17:29:24,460 - stpipe.step - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>, []).
2026-07-28 17:29:24,461 - stpipe.step - INFO - Step skipped.
2026-07-28 17:29:24,652 - stpipe.step - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>, []).
2026-07-28 17:29:24,653 - stpipe.step - INFO - Step skipped.
2026-07-28 17:29:24,842 - stpipe.step - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:29:24,843 - jwst.srctype.srctype - INFO - Input EXP_TYPE is MIR_MRS
2026-07-28 17:29:24,844 - jwst.srctype.srctype - INFO - Input SRCTYAPT = UNKNOWN
2026-07-28 17:29:24,844 - jwst.srctype.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2026-07-28 17:29:24,847 - stpipe.step - INFO - Step srctype done
2026-07-28 17:29:25,035 - stpipe.step - INFO - Step targ_centroid running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:29:25,036 - stpipe.step - INFO - Step skipped.
2026-07-28 17:29:25,225 - stpipe.step - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:29:25,229 - jwst.straylight.straylight_step - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2026-07-28 17:29:25,369 - jwst.straylight.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2026-07-28 17:29:46,884 - jwst.straylight.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2026-07-28 17:30:07,811 - jwst.straylight.straylight - INFO - Derived pedestal correction 0.02333652326093085 DN/s
2026-07-28 17:30:07,812 - jwst.straylight.straylight - INFO - Cross-artifact model complete.
2026-07-28 17:30:07,815 - stpipe.step - INFO - Step straylight done
2026-07-28 17:30:08,006 - stpipe.step - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:30:08,065 - stdatamodels.dynamicdq - WARNING - Keyword UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:30:08,072 - jwst.flatfield.flat_field_step - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2026-07-28 17:30:08,073 - jwst.flatfield.flat_field_step - INFO - No reference found for type FFLAT
2026-07-28 17:30:08,073 - jwst.flatfield.flat_field_step - INFO - No reference found for type SFLAT
2026-07-28 17:30:08,074 - jwst.flatfield.flat_field_step - INFO - No reference found for type DFLAT
2026-07-28 17:30:08,141 - stpipe.step - INFO - Step flat_field done
2026-07-28 17:30:08,331 - stpipe.step - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:30:08,336 - jwst.fringe.fringe_step - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2026-07-28 17:30:08,376 - stdatamodels.dynamicdq - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:30:08,377 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:30:08,378 - stdatamodels.dynamicdq - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:30:08,418 - stpipe.step - INFO - Step fringe done
2026-07-28 17:30:08,611 - stpipe.step - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:30:08,611 - stpipe.step - INFO - Step skipped.
2026-07-28 17:30:08,805 - stpipe.step - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:30:08,806 - stpipe.step - INFO - Step skipped.
2026-07-28 17:30:09,002 - stpipe.step - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:30:09,010 - jwst.photom.photom_step - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0224.fits
2026-07-28 17:30:09,011 - jwst.photom.photom_step - INFO - Using area reference file: N/A
2026-07-28 17:30:09,012 - jwst.photom.photom - INFO - Using instrument: MIRI
2026-07-28 17:30:09,012 - jwst.photom.photom - INFO - detector: MIRIFUSHORT
2026-07-28 17:30:09,012 - jwst.photom.photom - INFO - exp_type: MIR_MRS
2026-07-28 17:30:09,013 - jwst.photom.photom - INFO - band: SHORT
2026-07-28 17:30:09,099 - stdatamodels.dynamicdq - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2026-07-28 17:30:09,119 - jwst.photom.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2026-07-28 17:30:09,120 - jwst.photom.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2026-07-28 17:30:09,158 - jwst.photom.photom - INFO - Applying MRS IFU time dependent correction.
2026-07-28 17:30:09,733 - stpipe.step - INFO - Step photom done
2026-07-28 17:30:09,931 - stpipe.step - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2026-07-28 17:30:09,932 - stpipe.step - INFO - Step skipped.
2026-07-28 17:30:10,957 - stpipe.step - INFO - Step adaptive_trace_model running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_cal.fits>,).
2026-07-28 17:30:10,958 - stpipe.step - INFO - Step skipped.
2026-07-28 17:30:11,191 - stpipe.step - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_cal.fits>,).
2026-07-28 17:30:11,191 - stpipe.step - INFO - Step skipped.
2026-07-28 17:30:11,424 - stpipe.step - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_cal.fits>,).
2026-07-28 17:30:11,425 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:30:11,426 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:30:11,426 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:30:11,427 - jwst.cube_build.cube_build_step - INFO - Setting output type to: multi
2026-07-28 17:30:11,441 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2026-07-28 17:30:11,441 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'short']
2026-07-28 17:30:11,442 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:30:11,733 - jwst.cube_build.cube_build - INFO - Output IFUcube are constructed from all the data
2026-07-28 17:30:11,733 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 1
2026-07-28 17:30:11,737 - jwst.cube_build.ifu_cube - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2026-07-28 17:30:11,739 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:30:11,740 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:30:11,740 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.03183537 0.13000000 -3.05499989 3.05499989
2026-07-28 17:30:11,741 - jwst.cube_build.ifu_cube - INFO - Axis 2 49 25.00 -70.07715364 0.13000000 -3.18499988 3.18499988
2026-07-28 17:30:11,741 - jwst.cube_build.ifu_cube - INFO - Non-linear wavelength dimension; CDELT3 variable
2026-07-28 17:30:11,741 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2026-07-28 17:30:11,742 - jwst.cube_build.ifu_cube - INFO - Axis 3 4404 1.00 4.90000010 4.90000010 8.77080059
2026-07-28 17:30:11,742 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, short
2026-07-28 17:30:11,743 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, short
2026-07-28 17:30:11,743 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['short']
2026-07-28 17:30:12,851 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3697 with wavelength below 4.899390697479248
2026-07-28 17:30:19,227 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2597 with wavelength above 8.772054672241211
2026-07-28 17:30:25,763 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:30:25,764 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:30:25,784 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 1
2026-07-28 17:30:26,208 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.029397867 -70.078020289 81.029397867 -70.076286956 81.034272875 -70.076286956 81.034272875 -70.078020289
2026-07-28 17:30:26,212 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:30:26,394 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_s3d.fits
2026-07-28 17:30:26,701 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa8197687d0>,).
2026-07-28 17:30:26,706 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:30:26,711 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2026-07-28 17:30:26,715 - jwst.extract_1d.extract_1d_step - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2026-07-28 17:30:26,716 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:30:27,133 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:30:27,159 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:30:27,606 - py.warnings - WARNING - /home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/photutils/detection/core.py:603: NoDetectionsWarning: No sources were found.
warnings.warn(msg, NoDetectionsWarning)
2026-07-28 17:30:27,607 - jwst.extract_1d.ifu - WARNING - Auto source detection failed.
2026-07-28 17:30:27,607 - jwst.extract_1d.ifu - INFO - Using target coordinates.
2026-07-28 17:30:27,610 - jwst.extract_1d.ifu - INFO - Using x_center = 28, y_center = 17, based on TARG_RA and TARG_DEC
2026-07-28 17:30:48,235 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:30:49,635 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:30:52,262 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_x1d.fits
2026-07-28 17:30:52,263 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:30:52,265 - jwst.pipeline.calwebb_spec2 - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort
2026-07-28 17:30:52,267 - jwst.pipeline.calwebb_spec2 - INFO - Ending calwebb_spec2
2026-07-28 17:30:52,267 - jwst.stpipe.core - INFO - Results used CRDS context: jwst_1584.pmap
2026-07-28 17:30:52,718 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_cal.fits
2026-07-28 17:30:52,719 - stpipe.step - INFO - Step Spec2Pipeline done
2026-07-28 17:30:52,719 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime so far: {time1 - time0:0.4f} seconds")
print(f"Runtime for Spec2: {time1 - time_spec2} seconds")
Runtime so far: 3401.0180 seconds
Runtime for Spec2: 2349.4126106530002 seconds
7.-Spec3 Pipeline#
In this section we’ll run the Spec3 (calwebb_spec3) pipeline to produce a
composite data cube and extracted spectrumfrom all dithered exposures.
We will need to create an association file from all science (*cal.fits)
and background (*x1d.fits) data in order for the pipeline to use them
appropriately.
Note that the data cubes created by the JWST pipeline are in SURFACE
BRIGHTNESS units (MJy/steradian), not flux units. What that means is
that if you intend to sum spectra within an aperture you need to be sure
to multiply by the pixel area in steradians first in order to get a
spectrum in flux units. This correction is already build into the pipeline
Extract1D algorithm.
The nominal pixel area in steradians is provided in the
PIXAR_SR keyword and can be found in the SCI
extension header.
Spectral extraction for point sources uses a conical aperture extraction whose radius increases with wavelength, with annular background subtraction and aperture correction. Spectral extraction for extended sources sums the entire image at each wavelength plane (note this is different for each channel).
See https://jwst-docs.stsci.edu/jwst-science-calibration-pipeline/stages-of-jwst-data-processing/calwebb_spec3
If master background subtraction was selected above this will be applied
during this stage.
To override certain steps and reference files use the examples below.
To override certain steps and reference files use the examples below.
time_spec3 = time.perf_counter()
# Set up a dictionary to define how the Spec3 pipeline should be configured
# Boilerplate dictionary setup
spec3dict = defaultdict(dict)
# Overrides for whether or not certain steps should be skipped (example)
#spec3dict['outlier_detection']['skip'] = True
# Master background usage was set up above, propagate that here
if (master_bg is True):
spec3dict['master_background']['skip'] = False
else:
spec3dict['master_background']['skip'] = True
# Overrides for various reference files
# Files should be in the base local directory or provide full path
#spec3dict['cube_build']['override_cubepar'] = 'myfile.fits' # Cube-building parameters
#spec3dict['extract_1d']['override_extract1d'] = 'myfile.asdf' # Spectral extraction parameters (ASDF file)
#spec3dict['extract_1d']['override_apcorr'] = 'myfile.asdf' # Aperture correction parameters (ASDF file)
Set certain parameters here to:
adjusting performance for the outlier detection step
adjust the cube building step
adjust the 1d spectral extraction
# Options for adjusting performance for the outlier detection step
#spec3dict['outlier_detection']['kernel_size'] = '11 1' # Dial this to adjust the detector kernel size
#spec3dict['outlier_detection']['threshold_percent'] = 99.5 # Dial this to be more/less aggressive in outlier flagging (values closer to 100% are less aggressive)
# Run adaptive trace model code if desired to mitigate resampling noise
#spec3dict['adaptive_trace_model']['skip'] = False
# Run pixel replacement code to extrapolate values for otherwise bad pixels
# This can help mitigate 5-10% negative dips in spectra of bright sources
# Use the 'mingrad' algorithm
spec3dict['pixel_replace']['skip'] = False
spec3dict['pixel_replace']['algorithm'] = 'mingrad'
#spec3dict['pixel_replace']['save_results'] = True # Enable if desired to write out these files for spot checking
# Options for adjusting the cube building step
#spec3dict['cube_build']['output_file'] = 'mycube' # Custom output name
spec3dict['cube_build']['output_type'] = 'band' # 'band', 'channel' (default), or 'multi' type cube output. 'band' is best for 1d residual fringe correction.
#spec3dict['cube_build']['channel'] = '1' # Build everything from just channel 1 into a single cube (we could also choose '2','3','4', or 'ALL')
#spec3dict['cube_build']['weighting'] = 'drizzle' # Algorithm used: 'emsm' or 'drizzle' (default)
#spec3dict['cube_build']['coord_system'] = 'ifualign' # Cube rotation: 'ifualign', 'skyalign' (default), or 'internal_cal'
#spec3dict['cube_build']['scalexy'] = 0.5 # Output cube spaxel scale (arcsec) if setting it by hand
#spec3dict['cube_build']['scalew'] = 0.002 # Output cube voxel depth in wavelength (micron) if setting it by hand
#spec3dict['cube_build']['ra_center'] = 65.0 # Force cube to be centered at this R.A.
#spec3dict['cube_build']['dec_center'] = -35.0 # Force cube to be centered at this Decl.
#spec3dict['cube_build']['cube_pa'] = 45.0 # Force cube to have this position angle
#spec3dict['cube_build']['nspax_x'] = 61 # Force cube to have this number of spaxels in cube X direction
#spec3dict['cube_build']['nspax_y'] = 61 # Force cube to have this number of spaxels in cube Y direction
#spec3dict['cube_build']['wavemin'] = 4.8 # Custom minimum wavelength for the cube
#spec3dict['cube_build']['wavemax'] = 6.3 # Custom maximum wavelength for the cube
# Options for adjusting the 1d spectral extraction
#spec3dict['extract_1d']['ifu_set_srctype'] = 'POINT' # Force a certain type of spectral extraction ('POINT' or 'EXTENDED')
#spec3dict['extract_1d']['ifu_rscale'] = 2 # Number of FWHM to use for point-source conical aperture extraction radius (default is 2)
spec3dict['extract_1d']['ifu_autocen'] = True # Enable auto-centering of the extraction aperture (default is True)
#spec3dict['extract_1d']['center_xy'] = (20,20) # Override aperture location if desired
Define a function to create association files for Stage 3.
def writel3asn(scifiles, bgfiles, asnfile, prodname):
# Define the basic association of science files
asn = afl.asn_from_list(scifiles, rule=DMS_Level3_Base, product_name=prodname)
# Add background files to the association
for file in bgfiles:
asn['products'][0]['members'].append({'expname': file, 'exptype': 'background'})
# Write the association to a json file
_, serialized = asn.dump()
with open(asnfile, 'w') as outfile:
outfile.write(serialized)
Find and sort all of the input files, ensuring use of absolute paths
# Science Files need the cal.fits files
sstring = os.path.join(spec2_dir, 'jw*mirifu*_cal.fits')
calfiles = sorted(glob.glob(sstring))
for ii in range(0, len(calfiles)):
calfiles[ii] = os.path.abspath(calfiles[ii])
calfiles = np.array(calfiles)
# Check that these are the band/channel to use
calfiles = select_ch_band_files(calfiles, use_ch, use_band)
# Background Files need the x1d.fits files for Master Background subtraction
sstring = os.path.join(spec2_bgdir, 'jw*mirifu*x1d.fits')
bgfiles = sorted(glob.glob(sstring))
for ii in range(0, len(bgfiles)):
bgfiles[ii] = os.path.abspath(bgfiles[ii])
bgfiles = np.array(bgfiles)
# Check that these are the band/channel to use
bgfiles = select_ch_band_files(bgfiles, use_ch, use_band)
print('Found ' + str(len(calfiles)) + ' science files to process')
print('Found ' + str(len(bgfiles)) + ' background files to process')
Found 24 science files to process
Found 12 background files to process
Make an association file that includes all of the different exposures. If using Master Background subtraction include the background data.
Note that science data must be of type cal.fits and background exposures must be of type x1d.fits
asnfile = os.path.join(sci_dir, 'l3asn.json')
if dospec3:
writel3asn(calfiles, bgfiles, asnfile, 'Level3')
/home/runner/micromamba/envs/ci-env/lib/python3.13/site-packages/jwst/associations/association.py:232: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning, stacklevel=1)
Run calwebb_spec3 using the call method.
if dospec3:
Spec3Pipeline.call(asnfile, steps=spec3dict, save_results=True, output_dir=spec3_dir)
else:
print('Skipping Spec3 processing')
2026-07-28 17:30:52,929 - CRDS - INFO - Syncing 1 files
2026-07-28 17:30:52,930 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-outlierdetectionstep_0052.asdf 1.2 K bytes (1 / 1 files) (0 / 1.2 K bytes)
2026-07-28 17:30:53,184 - stpipe.step - INFO - PARS-OUTLIERDETECTIONSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-outlierdetectionstep_0052.asdf
2026-07-28 17:30:53,195 - stpipe.step - INFO - PARS-ADAPTIVETRACEMODELSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-adaptivetracemodelstep_0001.asdf
2026-07-28 17:30:53,204 - stpipe.step - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2026-07-28 17:30:53,213 - stpipe.step - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2026-07-28 17:30:53,224 - CRDS - INFO - Syncing 1 files
2026-07-28 17:30:53,225 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec3pipeline_0009.asdf 2.7 K bytes (1 / 1 files) (0 / 2.7 K bytes)
2026-07-28 17:30:53,448 - stpipe.pipeline - INFO - PARS-SPEC3PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec3pipeline_0009.asdf
2026-07-28 17:30:53,465 - stpipe.step - INFO - Spec3Pipeline instance created.
2026-07-28 17:30:53,466 - stpipe.step - INFO - AssignMTWcsStep instance created.
2026-07-28 17:30:53,467 - stpipe.step - INFO - MasterBackgroundStep instance created.
2026-07-28 17:30:53,468 - stpipe.step - INFO - OutlierDetectionStep instance created.
2026-07-28 17:30:53,469 - stpipe.step - INFO - AdaptiveTraceModelStep instance created.
2026-07-28 17:30:53,470 - stpipe.step - INFO - PixelReplaceStep instance created.
2026-07-28 17:30:53,472 - stpipe.step - INFO - ResampleSpecStep instance created.
2026-07-28 17:30:53,473 - stpipe.step - INFO - CubeBuildStep instance created.
2026-07-28 17:30:53,475 - stpipe.step - INFO - Extract1dStep instance created.
2026-07-28 17:30:53,476 - stpipe.step - INFO - PhotomStep instance created.
2026-07-28 17:30:53,477 - stpipe.step - INFO - Combine1dStep instance created.
2026-07-28 17:30:53,478 - stpipe.step - INFO - SpectralLeakStep instance created.
2026-07-28 17:30:53,698 - stpipe.step - INFO - Step Spec3Pipeline running with args ('./mrs_demo_data/Obs003/l3asn.json',).
2026-07-28 17:30:53,712 - stpipe.step - INFO - Step Spec3Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mrs_demo_data/Obs003/stage3
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
steps:
assign_mtwcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: assign_mtwcs
search_output_file: True
input_dir: ''
master_background:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
median_kernel: 1
user_background: None
save_background: False
force_subtract: False
outlier_detection:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: False
input_dir: ''
weight_type: ivm
pixfrac: 1.0
kernel: square
fillval: NAN
maskpt: 0.7
snr: 5.0 4.0
scale: 1.2 0.7
backg: 0.0
kernel_size: 11 1
threshold_percent: 99.5
rolling_window_width: 25
ifu_second_check: False
save_intermediate_results: False
resample_data: True
good_bits: ~DO_NOT_USE
in_memory: True
pixmap_stepsize: 1.0
pixmap_order: 1
adaptive_trace_model:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_threshold: 10.0
oversample: 3
slope_limit: 0.1
psf_optimal: False
save_intermediate_results: False
maximum_cores: none
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: mingrad
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NAN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
propagate_dq: False
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: True
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: band
linear_wave: True
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: True
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.8
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
soss_order_3: True
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
apply_time_correction: True
combine_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
exptime_key: exposure_time
sigma_clip: None
spectral_leak:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2026-07-28 17:30:53,868 - stpipe.pipeline - INFO - Prefetching reference files for dataset: 'l3asn.json' reftypes = ['apcorr', 'area', 'cubepar', 'extract1d', 'mrsptcorr', 'pastasoss', 'photom', 'psf', 'speckernel', 'specprofile']
2026-07-28 17:30:53,871 - CRDS - INFO - Syncing 1 files
2026-07-28 17:30:53,872 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_mrsptcorr_0002.fits 49.0 K bytes (1 / 1 files) (0 / 49.0 K bytes)
2026-07-28 17:30:54,226 - stpipe.pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2026-07-28 17:30:54,227 - stpipe.pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2026-07-28 17:30:54,228 - stpipe.pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2026-07-28 17:30:54,228 - stpipe.pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2026-07-28 17:30:54,229 - stpipe.pipeline - INFO - Prefetch for MRSPTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsptcorr_0002.fits'.
2026-07-28 17:30:54,230 - stpipe.pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2026-07-28 17:30:54,230 - stpipe.pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0225.fits'.
2026-07-28 17:30:54,231 - stpipe.pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2026-07-28 17:30:54,231 - stpipe.pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2026-07-28 17:30:54,231 - stpipe.pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2026-07-28 17:30:54,232 - jwst.pipeline.calwebb_spec3 - INFO - Starting calwebb_spec3 ...
2026-07-28 17:31:17,482 - stpipe.step - INFO - Step master_background running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa817526fd0>,).
2026-07-28 17:31:17,487 - jwst.combine_1d.combine1d - INFO - Using exposure time as the weight.
2026-07-28 17:31:18,017 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 1, slit MIR_MRS
2026-07-28 17:31:18,023 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 2, slit MIR_MRS
2026-07-28 17:31:18,031 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 3, slit MIR_MRS
2026-07-28 17:31:18,037 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 4, slit MIR_MRS
2026-07-28 17:31:18,045 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 5, slit MIR_MRS
2026-07-28 17:31:18,051 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 6, slit MIR_MRS
2026-07-28 17:31:18,060 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 7, slit MIR_MRS
2026-07-28 17:31:18,067 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 8, slit MIR_MRS
2026-07-28 17:31:18,076 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 9, slit MIR_MRS
2026-07-28 17:31:18,083 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 10, slit MIR_MRS
2026-07-28 17:31:18,092 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 11, slit MIR_MRS
2026-07-28 17:31:18,099 - jwst.combine_1d.combine1d - INFO - Accumulating data from input spectrum 12, slit MIR_MRS
2026-07-28 17:31:18,111 - jwst.combine_1d.combine1d - WARNING - 6 elements of output had no corresponding input data;
2026-07-28 17:31:18,111 - jwst.combine_1d.combine1d - WARNING - these elements will be omitted.
2026-07-28 17:31:47,183 - stpipe.step - INFO - Step master_background done
2026-07-28 17:31:48,793 - stpipe.step - INFO - Step outlier_detection running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81918fd50>,).
2026-07-28 17:31:48,794 - jwst.outlier_detection.outlier_detection_step - INFO - Outlier Detection mode: ifu
2026-07-28 17:31:48,795 - jwst.outlier_detection.outlier_detection_step - INFO - Outlier Detection asn_id: a3001
2026-07-28 17:31:48,795 - jwst.outlier_detection.ifu - INFO - Performing IFU outlier_detection for exptype MIR_MRS
2026-07-28 17:31:49,786 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,803 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,820 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,837 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,854 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,870 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,887 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,904 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,921 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,938 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,955 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:49,971 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 3691 (0.35%)
2026-07-28 17:31:50,864 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:50,882 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:50,899 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:50,917 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:50,934 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:50,952 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:50,969 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:50,986 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:51,004 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:51,022 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:51,040 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:51,058 - jwst.outlier_detection.ifu - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2026-07-28 17:31:51,586 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00001_mirifulong_a3001_crf.fits
2026-07-28 17:31:52,036 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00001_mirifushort_a3001_crf.fits
2026-07-28 17:31:52,404 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00002_mirifulong_a3001_crf.fits
2026-07-28 17:31:52,859 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00002_mirifushort_a3001_crf.fits
2026-07-28 17:31:53,232 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00003_mirifulong_a3001_crf.fits
2026-07-28 17:31:53,682 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00003_mirifushort_a3001_crf.fits
2026-07-28 17:31:54,051 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00004_mirifulong_a3001_crf.fits
2026-07-28 17:31:54,499 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00004_mirifushort_a3001_crf.fits
2026-07-28 17:31:54,867 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00001_mirifulong_a3001_crf.fits
2026-07-28 17:31:55,315 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00001_mirifushort_a3001_crf.fits
2026-07-28 17:31:55,681 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00002_mirifulong_a3001_crf.fits
2026-07-28 17:31:56,133 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00002_mirifushort_a3001_crf.fits
2026-07-28 17:31:56,505 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00003_mirifulong_a3001_crf.fits
2026-07-28 17:31:56,957 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00003_mirifushort_a3001_crf.fits
2026-07-28 17:31:57,328 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00004_mirifulong_a3001_crf.fits
2026-07-28 17:31:57,783 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00004_mirifushort_a3001_crf.fits
2026-07-28 17:31:58,163 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00001_mirifulong_a3001_crf.fits
2026-07-28 17:31:59,416 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00001_mirifushort_a3001_crf.fits
2026-07-28 17:31:59,791 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00002_mirifulong_a3001_crf.fits
2026-07-28 17:32:00,251 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00002_mirifushort_a3001_crf.fits
2026-07-28 17:32:00,625 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00003_mirifulong_a3001_crf.fits
2026-07-28 17:32:01,084 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00003_mirifushort_a3001_crf.fits
2026-07-28 17:32:01,469 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00004_mirifulong_a3001_crf.fits
2026-07-28 17:32:01,922 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00004_mirifushort_a3001_crf.fits
2026-07-28 17:32:01,923 - stpipe.step - INFO - Step outlier_detection done
2026-07-28 17:32:02,708 - stpipe.step - INFO - Step adaptive_trace_model running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81918fd50>,).
2026-07-28 17:32:02,709 - stpipe.step - INFO - Step skipped.
2026-07-28 17:32:03,651 - stpipe.step - INFO - Step pixel_replace running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81918fd50>,).
2026-07-28 17:32:03,657 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:03,788 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 3971 total pixels replaced.
2026-07-28 17:32:03,793 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:03,918 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4552 total pixels replaced.
2026-07-28 17:32:03,923 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:04,049 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 3971 total pixels replaced.
2026-07-28 17:32:04,054 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:04,179 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4552 total pixels replaced.
2026-07-28 17:32:04,185 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:04,313 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 3971 total pixels replaced.
2026-07-28 17:32:04,319 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:04,442 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4552 total pixels replaced.
2026-07-28 17:32:04,447 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:04,576 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 3971 total pixels replaced.
2026-07-28 17:32:04,582 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:04,706 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4552 total pixels replaced.
2026-07-28 17:32:04,712 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:04,837 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4093 total pixels replaced.
2026-07-28 17:32:04,842 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:04,968 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4557 total pixels replaced.
2026-07-28 17:32:04,974 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:05,101 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4093 total pixels replaced.
2026-07-28 17:32:05,107 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:05,232 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4556 total pixels replaced.
2026-07-28 17:32:05,238 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:05,367 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4093 total pixels replaced.
2026-07-28 17:32:05,372 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:05,497 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4556 total pixels replaced.
2026-07-28 17:32:05,503 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:05,629 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4095 total pixels replaced.
2026-07-28 17:32:05,635 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:05,758 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4556 total pixels replaced.
2026-07-28 17:32:05,763 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:05,887 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4117 total pixels replaced.
2026-07-28 17:32:05,892 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:06,014 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4642 total pixels replaced.
2026-07-28 17:32:06,020 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:06,143 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4116 total pixels replaced.
2026-07-28 17:32:06,149 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:06,271 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4643 total pixels replaced.
2026-07-28 17:32:06,276 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:06,402 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4116 total pixels replaced.
2026-07-28 17:32:06,407 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:06,527 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4642 total pixels replaced.
2026-07-28 17:32:06,532 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:06,653 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4116 total pixels replaced.
2026-07-28 17:32:06,659 - jwst.pixel_replace.pixel_replace - INFO - Using minimum gradient method.
2026-07-28 17:32:06,782 - jwst.pixel_replace.pixel_replace - INFO - Input IFU frame had 4642 total pixels replaced.
2026-07-28 17:32:06,949 - stpipe.step - INFO - Step pixel_replace done
2026-07-28 17:32:07,761 - stpipe.step - INFO - Step cube_build running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa81918fd50>,).
2026-07-28 17:32:07,761 - jwst.cube_build.cube_build_step - INFO - Starting IFU Cube Building Step
2026-07-28 17:32:07,762 - jwst.cube_build.cube_build_step - INFO - Input interpolation: drizzle
2026-07-28 17:32:07,762 - jwst.cube_build.cube_build_step - INFO - Coordinate system to use: skyalign
2026-07-28 17:32:07,763 - jwst.cube_build.cube_build_step - INFO - Setting output type to: band
2026-07-28 17:32:08,033 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '1', '1', '2', '2', '2', '3', '3', '3', '4', '4', '4']
2026-07-28 17:32:08,034 - jwst.cube_build.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'medium', 'long', 'short', 'medium', 'long', 'short', 'medium', 'long', 'short', 'medium', 'long']
2026-07-28 17:32:08,035 - jwst.cube_build.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2026-07-28 17:32:08,366 - jwst.cube_build.cube_build - INFO - Output Cubes are single channel, single sub-channel IFU Cubes
2026-07-28 17:32:08,366 - jwst.cube_build.cube_build_step - INFO - Number of IFU cubes produced by this run = 12
2026-07-28 17:32:08,367 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:08,585 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:08,816 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:09,050 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:09,286 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:32:09,287 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:32:09,287 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.08656489 0.13000000 -3.05499989 3.05499989
2026-07-28 17:32:09,288 - jwst.cube_build.ifu_cube - INFO - Axis 2 67 34.00 -70.08390300 0.13000000 -4.35499984 4.35499984
2026-07-28 17:32:09,289 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:32:09,289 - jwst.cube_build.ifu_cube - INFO - Axis 3 1050 1.00 4.90040010 0.00080000 4.90000010 5.74000007
2026-07-28 17:32:09,290 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, short
2026-07-28 17:32:09,290 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['short']
2026-07-28 17:32:10,369 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3379 with wavelength below 4.898601539532876
2026-07-28 17:32:10,370 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3474 with wavelength above 5.741398629981802
2026-07-28 17:32:15,532 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3379 with wavelength below 4.89860153953351
2026-07-28 17:32:15,535 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3474 with wavelength above 5.741398629981169
2026-07-28 17:32:20,601 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3379 with wavelength below 4.898601539532876
2026-07-28 17:32:20,603 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3474 with wavelength above 5.741398629981802
2026-07-28 17:32:25,627 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3379 with wavelength below 4.89860153953351
2026-07-28 17:32:25,628 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3474 with wavelength above 5.741398629981169
2026-07-28 17:32:29,679 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:32:29,680 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:32:29,687 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:32:30,027 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:30,247 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:30,478 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:30,707 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:30,941 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:32:30,942 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:32:30,942 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.08648228 0.13000000 -3.05499989 3.05499989
2026-07-28 17:32:30,943 - jwst.cube_build.ifu_cube - INFO - Axis 2 67 34.00 -70.08388400 0.13000000 -4.35499984 4.35499984
2026-07-28 17:32:30,943 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:32:30,944 - jwst.cube_build.ifu_cube - INFO - Axis 3 1213 1.00 5.66039985 0.00080000 5.65999985 6.63039982
2026-07-28 17:32:30,944 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, medium
2026-07-28 17:32:30,945 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['medium']
2026-07-28 17:32:32,010 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3662 with wavelength below 5.658443765540777
2026-07-28 17:32:32,011 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3170 with wavelength above 6.631955904769076
2026-07-28 17:32:37,382 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3662 with wavelength below 5.658443765540777
2026-07-28 17:32:37,383 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3170 with wavelength above 6.631955904769076
2026-07-28 17:32:42,784 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3662 with wavelength below 5.658443765540777
2026-07-28 17:32:42,785 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3170 with wavelength above 6.631955904769076
2026-07-28 17:32:48,164 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3662 with wavelength below 5.658443765540777
2026-07-28 17:32:48,165 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3170 with wavelength above 6.631955904769076
2026-07-28 17:32:52,604 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:32:52,604 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:32:52,613 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:32:52,955 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:53,170 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:53,404 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:53,637 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:32:53,868 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:32:53,871 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:32:53,872 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.08657274 0.13000000 -3.05499989 3.05499989
2026-07-28 17:32:53,873 - jwst.cube_build.ifu_cube - INFO - Axis 2 67 34.00 -70.08395599 0.13000000 -4.35499984 4.35499984
2026-07-28 17:32:53,874 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:32:53,875 - jwst.cube_build.ifu_cube - INFO - Axis 3 1400 1.00 6.53040021 0.00080000 6.53000021 7.65000018
2026-07-28 17:32:53,876 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 1, long
2026-07-28 17:32:53,878 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['long']
2026-07-28 17:32:54,931 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3033 with wavelength below 6.528268498504163
2026-07-28 17:32:54,932 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 4193 with wavelength above 7.651731892818956
2026-07-28 17:33:00,708 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3033 with wavelength below 6.528268498504163
2026-07-28 17:33:00,709 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 4193 with wavelength above 7.651731892818956
2026-07-28 17:33:06,509 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3033 with wavelength below 6.528268498504163
2026-07-28 17:33:06,510 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 4193 with wavelength above 7.651731892818956
2026-07-28 17:33:12,304 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 3033 with wavelength below 6.528268498505007
2026-07-28 17:33:12,306 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 4193 with wavelength above 7.651731892818113
2026-07-28 17:33:17,186 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:33:17,186 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:33:17,196 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:33:17,556 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:33:17,556 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:33:17,557 - jwst.cube_build.ifu_cube - INFO - Axis 1 43 22.00 81.08650716 0.17000000 -3.65500004 3.65500004
2026-07-28 17:33:17,557 - jwst.cube_build.ifu_cube - INFO - Axis 2 59 30.00 -70.08382768 0.17000000 -5.01500005 5.01500005
2026-07-28 17:33:17,558 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:33:17,558 - jwst.cube_build.ifu_cube - INFO - Axis 3 970 1.00 7.51065023 0.00130000 7.51000023 8.77100023
2026-07-28 17:33:17,559 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, short
2026-07-28 17:33:17,559 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['short']
2026-07-28 17:33:18,531 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2433 with wavelength below 7.507832450399061
2026-07-28 17:33:18,532 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2271 with wavelength above 8.773168010797466
2026-07-28 17:33:23,133 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2433 with wavelength below 7.507832450400023
2026-07-28 17:33:23,135 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2271 with wavelength above 8.773168010796503
2026-07-28 17:33:27,802 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2433 with wavelength below 7.507832450399061
2026-07-28 17:33:27,804 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2271 with wavelength above 8.773168010797466
2026-07-28 17:33:32,388 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2433 with wavelength below 7.507832450400023
2026-07-28 17:33:32,388 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2271 with wavelength above 8.773168010796503
2026-07-28 17:33:36,060 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:33:36,061 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:33:36,068 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:33:36,380 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:33:36,380 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:33:36,381 - jwst.cube_build.ifu_cube - INFO - Axis 1 41 21.00 81.08646099 0.17000000 -3.48500004 3.48500004
2026-07-28 17:33:36,381 - jwst.cube_build.ifu_cube - INFO - Axis 2 59 30.00 -70.08374249 0.17000000 -5.01500005 5.01500005
2026-07-28 17:33:36,382 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:33:36,382 - jwst.cube_build.ifu_cube - INFO - Axis 3 1124 1.00 8.67065008 0.00130000 8.67000008 10.13120008
2026-07-28 17:33:36,382 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, medium
2026-07-28 17:33:36,383 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['medium']
2026-07-28 17:33:37,370 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 1537 with wavelength below 8.667601400109556
2026-07-28 17:33:37,372 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2126 with wavelength above 10.1335987564562
2026-07-28 17:33:42,405 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 1537 with wavelength below 8.667601400109556
2026-07-28 17:33:42,406 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2126 with wavelength above 10.1335987564562
2026-07-28 17:33:47,358 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 1537 with wavelength below 8.667601400109556
2026-07-28 17:33:47,359 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2126 with wavelength above 10.1335987564562
2026-07-28 17:33:52,304 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 1537 with wavelength below 8.667601400109556
2026-07-28 17:33:52,305 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2126 with wavelength above 10.1335987564562
2026-07-28 17:33:56,338 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:33:56,339 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:33:56,345 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:33:56,660 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:33:56,661 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:33:56,661 - jwst.cube_build.ifu_cube - INFO - Axis 1 43 22.00 81.08634942 0.17000000 -3.65500004 3.65500004
2026-07-28 17:33:56,662 - jwst.cube_build.ifu_cube - INFO - Axis 2 59 30.00 -70.08379061 0.17000000 -5.01500005 5.01500005
2026-07-28 17:33:56,662 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:33:56,663 - jwst.cube_build.ifu_cube - INFO - Axis 3 1300 1.00 10.01065023 0.00130000 10.01000023 11.70000023
2026-07-28 17:33:56,663 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 2, long
2026-07-28 17:33:56,664 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['long']
2026-07-28 17:33:57,634 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 984 with wavelength below 10.007327663197035
2026-07-28 17:33:57,635 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2080 with wavelength above 11.70267279916737
2026-07-28 17:34:02,949 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 984 with wavelength below 10.007327663197035
2026-07-28 17:34:02,950 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2080 with wavelength above 11.70267279916737
2026-07-28 17:34:08,225 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 984 with wavelength below 10.007327663197035
2026-07-28 17:34:08,227 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2080 with wavelength above 11.70267279916737
2026-07-28 17:34:13,502 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 984 with wavelength below 10.007327663198316
2026-07-28 17:34:13,502 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 2080 with wavelength above 11.70267279916609
2026-07-28 17:34:17,853 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:34:17,854 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:34:17,862 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:34:18,190 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:18,391 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:18,608 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:18,823 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:19,045 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:34:19,046 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:34:19,047 - jwst.cube_build.ifu_cube - INFO - Axis 1 49 25.00 81.08704168 0.20000000 -4.90000007 4.90000007
2026-07-28 17:34:19,047 - jwst.cube_build.ifu_cube - INFO - Axis 2 59 30.00 -70.08381667 0.20000000 -5.90000009 5.90000009
2026-07-28 17:34:19,048 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:34:19,049 - jwst.cube_build.ifu_cube - INFO - Axis 3 769 1.00 11.55125019 0.00250000 11.55000019 13.47250015
2026-07-28 17:34:19,049 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, short
2026-07-28 17:34:19,050 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['short']
2026-07-28 17:34:20,030 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 1806 with wavelength below 11.546439300025126
2026-07-28 17:34:20,031 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 157 with wavelength above 13.476061038473377
2026-07-28 17:34:24,786 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 1806 with wavelength below 11.54643930002659
2026-07-28 17:34:24,788 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 157 with wavelength above 13.476061038471913
2026-07-28 17:34:29,512 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 1806 with wavelength below 11.54643930002659
2026-07-28 17:34:29,513 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 157 with wavelength above 13.476061038471913
2026-07-28 17:34:34,264 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 1806 with wavelength below 11.546439300025126
2026-07-28 17:34:34,265 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 157 with wavelength above 13.476061038473377
2026-07-28 17:34:38,109 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:34:38,110 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:34:38,115 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:34:38,420 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:38,619 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:38,837 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:39,057 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:39,282 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:34:39,283 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:34:39,283 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.08699522 0.20000000 -4.70000007 4.70000007
2026-07-28 17:34:39,284 - jwst.cube_build.ifu_cube - INFO - Axis 2 59 30.00 -70.08375904 0.20000000 -5.90000009 5.90000009
2026-07-28 17:34:39,285 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:34:39,285 - jwst.cube_build.ifu_cube - INFO - Axis 3 892 1.00 13.34125015 0.00250000 13.34000015 15.57000010
2026-07-28 17:34:39,286 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, medium
2026-07-28 17:34:39,287 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['medium']
2026-07-28 17:34:40,250 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 936 with wavelength below 13.336085437749636
2026-07-28 17:34:40,251 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 456 with wavelength above 15.57391481758176
2026-07-28 17:34:45,276 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 936 with wavelength below 13.336085437749636
2026-07-28 17:34:45,278 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 456 with wavelength above 15.57391481758176
2026-07-28 17:34:50,304 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 936 with wavelength below 13.336085437749636
2026-07-28 17:34:50,305 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 456 with wavelength above 15.57391481758176
2026-07-28 17:34:55,308 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 936 with wavelength below 13.336085437751324
2026-07-28 17:34:55,309 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 456 with wavelength above 15.573914817580073
2026-07-28 17:34:59,417 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:34:59,418 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:34:59,425 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:34:59,734 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:34:59,936 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:35:00,153 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:35:00,370 - jwst.cube_build.ifu_cube - INFO - Mapping all pixels to output to determine IFU foot print
2026-07-28 17:35:00,588 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:35:00,590 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:35:00,591 - jwst.cube_build.ifu_cube - INFO - Axis 1 47 24.00 81.08691251 0.20000000 -4.70000007 4.70000007
2026-07-28 17:35:00,592 - jwst.cube_build.ifu_cube - INFO - Axis 2 59 30.00 -70.08378264 0.20000000 -5.90000009 5.90000009
2026-07-28 17:35:00,593 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:35:00,596 - jwst.cube_build.ifu_cube - INFO - Axis 3 1028 1.00 15.41124985 0.00250000 15.40999985 17.97999979
2026-07-28 17:35:00,596 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 3, long
2026-07-28 17:35:00,597 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['long']
2026-07-28 17:35:01,592 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 754 with wavelength below 15.405681102293547
2026-07-28 17:35:01,593 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 968 with wavelength above 17.984318535086693
2026-07-28 17:35:06,885 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 754 with wavelength below 15.405681102295494
2026-07-28 17:35:06,887 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 968 with wavelength above 17.984318535084746
2026-07-28 17:35:12,248 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 754 with wavelength below 15.405681102293547
2026-07-28 17:35:12,252 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 968 with wavelength above 17.984318535086693
2026-07-28 17:35:17,590 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 754 with wavelength below 15.405681102295494
2026-07-28 17:35:17,591 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 968 with wavelength above 17.984318535084746
2026-07-28 17:35:22,025 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:35:22,026 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:35:22,033 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:35:22,371 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:35:22,371 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:35:22,372 - jwst.cube_build.ifu_cube - INFO - Axis 1 35 18.00 81.08626944 0.34999999 -6.12499990 6.12499990
2026-07-28 17:35:22,373 - jwst.cube_build.ifu_cube - INFO - Axis 2 41 21.00 -70.08379645 0.34999999 -7.17499988 7.17499988
2026-07-28 17:35:22,373 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:35:22,374 - jwst.cube_build.ifu_cube - INFO - Axis 3 542 1.00 17.70300076 0.00600000 17.70000076 20.95200079
2026-07-28 17:35:22,374 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, short
2026-07-28 17:35:22,375 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['short']
2026-07-28 17:35:34,823 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:35:34,824 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:35:34,827 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:35:35,106 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:35:35,106 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:35:35,107 - jwst.cube_build.ifu_cube - INFO - Axis 1 35 18.00 81.08626387 0.34999999 -6.12499990 6.12499990
2026-07-28 17:35:35,107 - jwst.cube_build.ifu_cube - INFO - Axis 2 41 21.00 -70.08381211 0.34999999 -7.17499988 7.17499988
2026-07-28 17:35:35,108 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:35:35,108 - jwst.cube_build.ifu_cube - INFO - Axis 3 632 1.00 20.69300053 0.00600000 20.69000053 24.48200057
2026-07-28 17:35:35,109 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, medium
2026-07-28 17:35:35,110 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['medium']
2026-07-28 17:35:35,965 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 249 with wavelength below 20.682598635781634
2026-07-28 17:35:39,177 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 249 with wavelength below 20.682598635781634
2026-07-28 17:35:42,369 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 249 with wavelength below 20.682598635781634
2026-07-28 17:35:45,572 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 249 with wavelength below 20.682598635784423
2026-07-28 17:35:47,934 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:35:47,935 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:35:47,938 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:35:48,217 - jwst.cube_build.ifu_cube - INFO - Cube Geometry:
2026-07-28 17:35:48,218 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2026-07-28 17:35:48,218 - jwst.cube_build.ifu_cube - INFO - Axis 1 35 18.00 81.08613067 0.34999999 -6.12499990 6.12499990
2026-07-28 17:35:48,219 - jwst.cube_build.ifu_cube - INFO - Axis 2 41 21.00 -70.08380297 0.34999999 -7.17499988 7.17499988
2026-07-28 17:35:48,220 - jwst.cube_build.ifu_cube - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2026-07-28 17:35:48,220 - jwst.cube_build.ifu_cube - INFO - Axis 3 717 1.00 24.40299962 0.00600000 24.39999962 28.70199966
2026-07-28 17:35:48,221 - jwst.cube_build.ifu_cube - INFO - Cube covers channel, subchannel: 4, long
2026-07-28 17:35:48,221 - jwst.cube_build.ifu_cube - INFO - Subchannel listing: ['long']
2026-07-28 17:35:49,065 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 13075 with wavelength below 24.391886480783615
2026-07-28 17:35:52,312 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 13075 with wavelength below 24.391886480786855
2026-07-28 17:35:55,644 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 13075 with wavelength below 24.391886480783615
2026-07-28 17:35:58,913 - jwst.cube_build.ifu_cube - INFO - # of detector pixels not mapped to output plane: 13075 with wavelength below 24.391886480786855
2026-07-28 17:36:01,356 - jwst.cube_build.ifu_cube - INFO - Average # of holes/wavelength plane is < 1
2026-07-28 17:36:01,357 - jwst.cube_build.ifu_cube - INFO - Total # of holes for IFU cube is : 0
2026-07-28 17:36:01,360 - jwst.cube_build.ifu_cube - INFO - Number of spectral tear planes adjusted: 0
2026-07-28 17:36:01,654 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084126557 -70.085094649 81.084126557 -70.082711316 81.089003226 -70.082711316 81.089003226 -70.085094649
2026-07-28 17:36:01,656 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084043948 -70.085075654 81.084043948 -70.082692321 81.088920612 -70.082692321 81.088920612 -70.085075654
2026-07-28 17:36:01,658 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.084134400 -70.085147637 81.084134400 -70.082764303 81.089011081 -70.082764303 81.089011081 -70.085147637
2026-07-28 17:36:01,660 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083595827 -70.085197098 81.083595827 -70.082458209 81.089418500 -70.082458209 81.089418500 -70.085197098
2026-07-28 17:36:01,661 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083688301 -70.085111913 81.083688301 -70.082373024 81.089233681 -70.082373024 81.089233681 -70.085111913
2026-07-28 17:36:01,663 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083438092 -70.085160032 81.083438092 -70.082421143 81.089260754 -70.082421143 81.089260754 -70.085160032
2026-07-28 17:36:01,664 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083127237 -70.085427735 81.083127237 -70.082205512 81.090956129 -70.082205512 81.090956129 -70.085427735
2026-07-28 17:36:01,666 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083243890 -70.085370110 81.083243890 -70.082147888 81.090746557 -70.082147888 81.090746557 -70.085370110
2026-07-28 17:36:01,668 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.083161176 -70.085393717 81.083161176 -70.082171494 81.090663851 -70.082171494 81.090663851 -70.085393717
2026-07-28 17:36:01,669 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.081417086 -70.085740825 81.081417086 -70.081851936 81.091121795 -70.081851936 81.091121795 -70.085740825
2026-07-28 17:36:01,671 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.081411507 -70.085756490 81.081411507 -70.081867601 81.091116224 -70.081867601 81.091116224 -70.085756490
2026-07-28 17:36:01,672 - stcal.alignment.util - INFO - Update S_REGION to POLYGON ICRS 81.081278318 -70.085747347 81.081278318 -70.081858458 81.090983030 -70.081858458 81.090983030 -70.085747347
2026-07-28 17:36:02,012 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-short_s3d.fits
2026-07-28 17:36:02,270 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-medium_s3d.fits
2026-07-28 17:36:02,531 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-long_s3d.fits
2026-07-28 17:36:02,773 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-short_s3d.fits
2026-07-28 17:36:03,020 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-medium_s3d.fits
2026-07-28 17:36:03,274 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-long_s3d.fits
2026-07-28 17:36:03,516 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-short_s3d.fits
2026-07-28 17:36:03,760 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-medium_s3d.fits
2026-07-28 17:36:04,024 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-long_s3d.fits
2026-07-28 17:36:04,252 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-short_s3d.fits
2026-07-28 17:36:04,480 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-medium_s3d.fits
2026-07-28 17:36:04,733 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-long_s3d.fits
2026-07-28 17:36:04,734 - stpipe.step - INFO - Step cube_build done
2026-07-28 17:36:05,559 - stpipe.step - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa7d50847d0>,).
2026-07-28 17:36:05,670 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:36:05,677 - CRDS - INFO - Syncing 1 files
2026-07-28 17:36:05,678 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0007.asdf 810.3 K bytes (1 / 1 files) (0 / 810.3 K bytes)
2026-07-28 17:36:06,427 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0007.asdf
2026-07-28 17:36:06,435 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:36:06,864 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:36:06,870 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:36:07,019 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:36:07,019 - jwst.extract_1d.ifu - INFO - Using x_center = 24.0244, y_center = 36.4082
2026-07-28 17:36:12,492 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:36:13,264 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:36:14,452 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:36:15,270 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:36:15,277 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0007.asdf
2026-07-28 17:36:15,284 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:36:15,719 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:36:15,726 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:36:15,904 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:36:15,904 - jwst.extract_1d.ifu - INFO - Using x_center = 23.1468, y_center = 35.929
2026-07-28 17:36:22,285 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:36:23,517 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:36:24,708 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:36:25,610 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:36:25,617 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0007.asdf
2026-07-28 17:36:25,623 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:36:26,058 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:36:26,065 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:36:26,271 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:36:26,272 - jwst.extract_1d.ifu - INFO - Using x_center = 24.3219, y_center = 37.7782
2026-07-28 17:36:33,609 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:36:35,398 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:36:36,593 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:36:37,595 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:36:37,602 - CRDS - INFO - Syncing 1 files
2026-07-28 17:36:37,602 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0005.asdf 810.3 K bytes (1 / 1 files) (0 / 810.3 K bytes)
2026-07-28 17:36:38,315 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0005.asdf
2026-07-28 17:36:38,322 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:36:38,747 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:36:38,751 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:36:38,863 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:36:38,863 - jwst.extract_1d.ifu - INFO - Using x_center = 21.543, y_center = 29.8383
2026-07-28 17:36:43,803 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:36:45,833 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:36:47,846 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:36:48,616 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:36:48,622 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0005.asdf
2026-07-28 17:36:48,629 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:36:49,057 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:36:49,062 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:36:49,188 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:36:49,188 - jwst.extract_1d.ifu - INFO - Using x_center = 20.479, y_center = 27.9365
2026-07-28 17:36:54,967 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:36:59,381 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:37:00,571 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:37:01,425 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:37:01,431 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0005.asdf
2026-07-28 17:37:01,438 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:37:01,867 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:37:01,873 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:37:02,020 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:37:02,021 - jwst.extract_1d.ifu - INFO - Using x_center = 20.2756, y_center = 29.1419
2026-07-28 17:37:08,726 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:37:10,506 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:37:11,691 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:37:12,630 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:37:12,637 - CRDS - INFO - Syncing 1 files
2026-07-28 17:37:12,638 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0006.asdf 810.3 K bytes (1 / 1 files) (0 / 810.3 K bytes)
2026-07-28 17:37:13,314 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0006.asdf
2026-07-28 17:37:13,321 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:37:13,746 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:37:13,751 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:37:13,853 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:37:13,854 - jwst.extract_1d.ifu - INFO - Using x_center = 27.7428, y_center = 29.5821
2026-07-28 17:37:17,812 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:37:19,280 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:37:20,463 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:37:21,130 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:37:21,137 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0006.asdf
2026-07-28 17:37:21,144 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:37:21,573 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:37:21,577 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:37:21,692 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:37:21,693 - jwst.extract_1d.ifu - INFO - Using x_center = 26.3118, y_center = 28.4667
2026-07-28 17:37:26,336 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:37:27,371 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:37:29,389 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:37:30,127 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:37:30,137 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0006.asdf
2026-07-28 17:37:30,146 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:37:30,582 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:37:30,588 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:37:30,719 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:37:30,720 - jwst.extract_1d.ifu - INFO - Using x_center = 26.0272, y_center = 28.7845
2026-07-28 17:37:36,057 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:37:37,129 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:37:38,318 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:37:39,123 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:37:39,130 - CRDS - INFO - Syncing 1 files
2026-07-28 17:37:39,131 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0004.asdf 810.2 K bytes (1 / 1 files) (0 / 810.2 K bytes)
2026-07-28 17:37:39,781 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0004.asdf
2026-07-28 17:37:39,789 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:37:40,215 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:37:40,217 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:37:40,252 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:37:40,253 - jwst.extract_1d.ifu - INFO - Using x_center = 16.41, y_center = 20.1682
2026-07-28 17:37:42,937 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:37:43,731 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:37:44,937 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:37:45,489 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:37:45,496 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0004.asdf
2026-07-28 17:37:45,502 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:37:45,930 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:37:45,932 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:37:45,974 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:37:45,974 - jwst.extract_1d.ifu - INFO - Using x_center = 16.4181, y_center = 20.2903
2026-07-28 17:37:49,111 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:37:49,967 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:37:51,155 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:37:51,760 - jwst.extract_1d.extract_1d_step - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2026-07-28 17:37:51,769 - jwst.extract_1d.extract_1d_step - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0004.asdf
2026-07-28 17:37:51,778 - jwst.extract_1d.ifu - INFO - Source type = POINT
2026-07-28 17:37:52,213 - jwst.extract_1d.ifu - INFO - Input model does not break out variance information. Passing only generalized errors.
2026-07-28 17:37:52,215 - jwst.extract_1d.ifu - INFO - Using auto source detection.
2026-07-28 17:37:52,233 - jwst.extract_1d.ifu - INFO - Auto source detection success.
2026-07-28 17:37:52,234 - jwst.extract_1d.ifu - INFO - Using x_center = 15.9159, y_center = 20.1744
2026-07-28 17:37:55,850 - jwst.extract_1d.ifu - INFO - Applying 1d residual fringe correction.
2026-07-28 17:37:56,637 - jwst.extract_1d.ifu - INFO - Applying ERR covariance prefactor of 1.8
2026-07-28 17:37:58,672 - jwst.extract_1d.ifu - INFO - Applying Aperture correction.
2026-07-28 17:37:59,452 - stpipe.step - INFO - Step extract_1d done
2026-07-28 17:38:00,321 - stpipe.step - INFO - Step spectral_leak running with args (<jwst.datamodels.container.ModelContainer object at 0x7fa7e618d5d0>,).
2026-07-28 17:38:00,389 - jwst.spectral_leak.spectral_leak_step - INFO - Found CH 1B in input data
2026-07-28 17:38:00,390 - jwst.spectral_leak.spectral_leak_step - INFO - Found CH 3A in the input data
2026-07-28 17:38:00,653 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-short_x1d.fits
2026-07-28 17:38:00,749 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-medium_x1d.fits
2026-07-28 17:38:00,849 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-long_x1d.fits
2026-07-28 17:38:00,945 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-short_x1d.fits
2026-07-28 17:38:01,041 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-medium_x1d.fits
2026-07-28 17:38:01,138 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-long_x1d.fits
2026-07-28 17:38:01,241 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-short_x1d.fits
2026-07-28 17:38:01,338 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-medium_x1d.fits
2026-07-28 17:38:01,452 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-long_x1d.fits
2026-07-28 17:38:01,548 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-short_x1d.fits
2026-07-28 17:38:01,649 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-medium_x1d.fits
2026-07-28 17:38:01,763 - stpipe.step - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-long_x1d.fits
2026-07-28 17:38:01,763 - stpipe.step - INFO - Step spectral_leak done
2026-07-28 17:38:01,768 - jwst.pipeline.calwebb_spec3 - INFO - Ending calwebb_spec3
2026-07-28 17:38:01,787 - stpipe.step - INFO - Step Spec3Pipeline done
2026-07-28 17:38:01,788 - jwst.stpipe.core - INFO - Results used jwst version: 3.0.0
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime so far: {time1 - time0:0.4f} seconds")
print(f"Runtime for Spec3: {time1 - time_spec3} seconds")
Runtime so far: 3830.0870 seconds
Runtime for Spec3: 429.06484107000006 seconds
8.-Plot the spectra#
Here we’ll plot the spectra to see what our source looks like.
if doviz:
# Find and sort all of the input files
# Science Files
# Use the final extracted spectra (x1d.fits)
sstring = sorted(glob.glob(os.path.join(spec3_dir, '*x1d.fits')))
x1dfiles = np.array(sorted(sstring))
if doviz:
# Make normal plots
%matplotlib inline
# Interactive plots
#%matplotlib notebook
rc('axes', linewidth=2)
fig, ax = plt.subplots(1, 1, figsize=(10, 3), dpi=150)
if (len(x1dfiles) > 0):
hdu = fits.open(x1dfiles[0])
objname = hdu[0].header['TARGPROP']
hdu.close()
else:
objname = 'Unknown'
ymin, ymax = np.nan, np.nan
for file in x1dfiles:
x1d = fits.open(file)
x1ddata = x1d[1].data
wave = x1ddata['WAVELENGTH']
# MRS x1d files have both regular ('flux') and residual-fringe (RF) corrected ('rf_flux') spectra.
# The RF-corrected spectra will have NaN values if RF correction was disabled or failed to converge.
# Plot the RF corrected spectrum if available, otherwise plot the regular spectrum.
if (np.nansum(x1ddata['RF_FLUX']) != 0):
flux = x1ddata['RF_FLUX']
else:
flux = x1ddata['FLUX']
ymin = np.nanmin([ymin, np.nanpercentile(flux, 2)])
ymax = np.nanmax([ymax, np.nanpercentile(flux, 99.5)])
# labels
label = x1d[0].header['CHANNEL'] + x1d[0].header['BAND']
plt.plot(wave, flux, label=label)
x1d.close()
plt.xlabel(r'Wavelength ($\mu$m)')
plt.ylabel('Flux (Jy)')
plt.title(objname)
plt.ylim(ymin, ymax)
plt.legend(fontsize=8, loc='center left', bbox_to_anchor=(1, 0.5))
plt.grid()
plt.tight_layout()
plt.savefig('mrs_example_plot.png')
