MIRI MRS Pipeline Notebook#
Authors: David Law, Kirsten Larson; MIRI branch
Last Updated: May 22, 2025
Pipeline Version: 1.18.1 (Build 11.3)
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 31 2024: Update to 1.13.4 pipeline, enabling spectral leak
correction
Jul 1 2024: Migrate from MRS_FlightNB1 notebook, adapt to .call()
format, add post-hook example, add demo mode capability.
Oct 11 2024: Update to Build 11.0 (jwst 1.15.1); move pixel_replacement to spec3 and enable by default, add option for bad pixel self-calibration in spec2.
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.
Table of Contents#
Configuration
Package Imports
Demo Mode Setup
Directory Setup
Detector1 Pipeline
Spec2 Pipeline
Spec3 Pipeline
Plot the spectra
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
# 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 = 1.18.1
CRDS - INFO - Calibration SW Found: jwst 1.18.1 (/usr/share/miniconda/lib/python3.13/site-packages/jwst-1.18.1.dist-info)
Using CRDS Context = jwst_1364.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: 82.9037 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 = {}
det1dict['group_scale'], det1dict['dq_init'], det1dict['emicorr'], det1dict['saturation'], det1dict['ipc'] = {}, {}, {}, {}, {}
det1dict['firstframe'], det1dict['lastframe'], det1dict['reset'], det1dict['linearity'], det1dict['rscd'] = {}, {}, {}, {}, {}
det1dict['dark_current'], det1dict['refpix'], det1dict['charge_migration'], det1dict['jump'], det1dict['ramp_fit'] = {}, {}, {}, {}, {}
det1dict['gain_scale'] = {}
# 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')
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2025-06-17 11:59:15,025 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_wavelengthrange_0024.rmap 1.4 K bytes (4 / 204 files) (6.4 K / 741.0 K bytes)
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2025-06-17 11:59:15,802 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_refpix_0015.rmap 1.6 K bytes (10 / 204 files) (67.9 K / 741.0 K bytes)
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2025-06-17 11:59:22,866 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-darkpipeline_0002.rmap 868 bytes (74 / 204 files) (230.8 K / 741.0 K bytes)
2025-06-17 11:59:22,978 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-darkcurrentstep_0001.rmap 591 bytes (75 / 204 files) (231.7 K / 741.0 K bytes)
2025-06-17 11:59:23,104 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-chargemigrationstep_0004.rmap 5.7 K bytes (76 / 204 files) (232.3 K / 741.0 K bytes)
2025-06-17 11:59:23,207 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_nrm_0005.rmap 663 bytes (77 / 204 files) (237.9 K / 741.0 K bytes)
2025-06-17 11:59:23,309 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_mask_0022.rmap 1.3 K bytes (78 / 204 files) (238.6 K / 741.0 K bytes)
2025-06-17 11:59:23,412 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_linearity_0022.rmap 961 bytes (79 / 204 files) (239.9 K / 741.0 K bytes)
2025-06-17 11:59:23,516 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_ipc_0007.rmap 651 bytes (80 / 204 files) (240.9 K / 741.0 K bytes)
2025-06-17 11:59:23,626 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_gain_0011.rmap 797 bytes (81 / 204 files) (241.5 K / 741.0 K bytes)
2025-06-17 11:59:23,738 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_flat_0023.rmap 5.9 K bytes (82 / 204 files) (242.3 K / 741.0 K bytes)
2025-06-17 11:59:23,854 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_filteroffset_0010.rmap 853 bytes (83 / 204 files) (248.2 K / 741.0 K bytes)
2025-06-17 11:59:23,968 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_extract1d_0007.rmap 905 bytes (84 / 204 files) (249.0 K / 741.0 K bytes)
2025-06-17 11:59:24,075 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_drizpars_0004.rmap 519 bytes (85 / 204 files) (249.9 K / 741.0 K bytes)
2025-06-17 11:59:24,188 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_distortion_0025.rmap 3.4 K bytes (86 / 204 files) (250.4 K / 741.0 K bytes)
2025-06-17 11:59:24,298 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_dark_0034.rmap 7.5 K bytes (87 / 204 files) (253.9 K / 741.0 K bytes)
2025-06-17 11:59:24,405 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_bkg_0002.rmap 2.9 K bytes (88 / 204 files) (261.4 K / 741.0 K bytes)
2025-06-17 11:59:24,515 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_area_0014.rmap 2.7 K bytes (89 / 204 files) (264.3 K / 741.0 K bytes)
2025-06-17 11:59:24,619 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_apcorr_0010.rmap 4.3 K bytes (90 / 204 files) (267.0 K / 741.0 K bytes)
2025-06-17 11:59:24,722 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_abvegaoffset_0004.rmap 1.4 K bytes (91 / 204 files) (271.3 K / 741.0 K bytes)
2025-06-17 11:59:24,825 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_0272.imap 5.8 K bytes (92 / 204 files) (272.7 K / 741.0 K bytes)
2025-06-17 11:59:24,930 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_wfssbkg_0004.rmap 7.2 K bytes (93 / 204 files) (278.5 K / 741.0 K bytes)
2025-06-17 11:59:25,032 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_wavelengthrange_0010.rmap 996 bytes (94 / 204 files) (285.7 K / 741.0 K bytes)
2025-06-17 11:59:25,135 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_tsophot_0003.rmap 896 bytes (95 / 204 files) (286.7 K / 741.0 K bytes)
2025-06-17 11:59:25,240 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_trappars_0003.rmap 1.6 K bytes (96 / 204 files) (287.6 K / 741.0 K bytes)
2025-06-17 11:59:25,343 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_trapdensity_0003.rmap 1.6 K bytes (97 / 204 files) (289.2 K / 741.0 K bytes)
2025-06-17 11:59:25,447 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_superbias_0019.rmap 18.9 K bytes (98 / 204 files) (290.8 K / 741.0 K bytes)
2025-06-17 11:59:25,580 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_specwcs_0022.rmap 7.1 K bytes (99 / 204 files) (309.7 K / 741.0 K bytes)
2025-06-17 11:59:25,692 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_sirskernel_0002.rmap 671 bytes (100 / 204 files) (316.8 K / 741.0 K bytes)
2025-06-17 11:59:25,796 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_saturation_0011.rmap 2.8 K bytes (101 / 204 files) (317.5 K / 741.0 K bytes)
2025-06-17 11:59:25,902 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_readnoise_0026.rmap 25.9 K bytes (102 / 204 files) (320.3 K / 741.0 K bytes)
2025-06-17 11:59:26,035 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_psfmask_0008.rmap 28.4 K bytes (103 / 204 files) (346.2 K / 741.0 K bytes)
2025-06-17 11:59:26,168 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_photom_0028.rmap 3.4 K bytes (104 / 204 files) (374.6 K / 741.0 K bytes)
2025-06-17 11:59:26,274 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_persat_0005.rmap 1.6 K bytes (105 / 204 files) (377.9 K / 741.0 K bytes)
2025-06-17 11:59:26,390 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-whitelightstep_0004.rmap 2.0 K bytes (106 / 204 files) (379.5 K / 741.0 K bytes)
2025-06-17 11:59:26,501 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-tweakregstep_0003.rmap 4.5 K bytes (107 / 204 files) (381.5 K / 741.0 K bytes)
2025-06-17 11:59:26,605 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-spec2pipeline_0008.rmap 984 bytes (108 / 204 files) (386.0 K / 741.0 K bytes)
2025-06-17 11:59:26,711 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-sourcecatalogstep_0002.rmap 4.6 K bytes (109 / 204 files) (387.0 K / 741.0 K bytes)
2025-06-17 11:59:26,821 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-resamplestep_0002.rmap 687 bytes (110 / 204 files) (391.6 K / 741.0 K bytes)
2025-06-17 11:59:26,931 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-outlierdetectionstep_0003.rmap 940 bytes (111 / 204 files) (392.3 K / 741.0 K bytes)
2025-06-17 11:59:27,037 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-jumpstep_0005.rmap 806 bytes (112 / 204 files) (393.2 K / 741.0 K bytes)
2025-06-17 11:59:27,152 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-image2pipeline_0004.rmap 1.1 K bytes (113 / 204 files) (394.0 K / 741.0 K bytes)
2025-06-17 11:59:27,256 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-detector1pipeline_0005.rmap 1.3 K bytes (114 / 204 files) (395.2 K / 741.0 K bytes)
2025-06-17 11:59:27,362 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-darkpipeline_0002.rmap 868 bytes (115 / 204 files) (396.4 K / 741.0 K bytes)
2025-06-17 11:59:27,467 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_pars-darkcurrentstep_0001.rmap 618 bytes (116 / 204 files) (397.3 K / 741.0 K bytes)
2025-06-17 11:59:27,568 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_mask_0012.rmap 4.1 K bytes (117 / 204 files) (397.9 K / 741.0 K bytes)
2025-06-17 11:59:27,679 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_linearity_0011.rmap 2.4 K bytes (118 / 204 files) (402.1 K / 741.0 K bytes)
2025-06-17 11:59:27,791 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_ipc_0003.rmap 2.0 K bytes (119 / 204 files) (404.5 K / 741.0 K bytes)
2025-06-17 11:59:27,895 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_gain_0016.rmap 2.1 K bytes (120 / 204 files) (406.4 K / 741.0 K bytes)
2025-06-17 11:59:28,003 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_flat_0028.rmap 51.7 K bytes (121 / 204 files) (408.6 K / 741.0 K bytes)
2025-06-17 11:59:28,159 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_filteroffset_0004.rmap 1.4 K bytes (122 / 204 files) (460.2 K / 741.0 K bytes)
2025-06-17 11:59:28,271 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_extract1d_0005.rmap 1.2 K bytes (123 / 204 files) (461.7 K / 741.0 K bytes)
2025-06-17 11:59:28,376 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_drizpars_0001.rmap 519 bytes (124 / 204 files) (462.9 K / 741.0 K bytes)
2025-06-17 11:59:28,480 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_distortion_0033.rmap 53.4 K bytes (125 / 204 files) (463.4 K / 741.0 K bytes)
2025-06-17 11:59:28,646 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_dark_0047.rmap 29.0 K bytes (126 / 204 files) (516.7 K / 741.0 K bytes)
2025-06-17 11:59:28,787 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_area_0012.rmap 33.5 K bytes (127 / 204 files) (545.7 K / 741.0 K bytes)
2025-06-17 11:59:28,928 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_apcorr_0008.rmap 4.3 K bytes (128 / 204 files) (579.2 K / 741.0 K bytes)
2025-06-17 11:59:29,036 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_abvegaoffset_0003.rmap 1.3 K bytes (129 / 204 files) (583.5 K / 741.0 K bytes)
2025-06-17 11:59:29,141 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nircam_0314.imap 5.6 K bytes (130 / 204 files) (584.8 K / 741.0 K bytes)
2025-06-17 11:59:29,248 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_wavelengthrange_0027.rmap 929 bytes (131 / 204 files) (590.4 K / 741.0 K bytes)
2025-06-17 11:59:29,356 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_tsophot_0004.rmap 882 bytes (132 / 204 files) (591.3 K / 741.0 K bytes)
2025-06-17 11:59:29,483 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_straymask_0009.rmap 987 bytes (133 / 204 files) (592.2 K / 741.0 K bytes)
2025-06-17 11:59:29,587 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_specwcs_0043.rmap 5.8 K bytes (134 / 204 files) (593.2 K / 741.0 K bytes)
2025-06-17 11:59:29,703 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_saturation_0015.rmap 1.2 K bytes (135 / 204 files) (599.0 K / 741.0 K bytes)
2025-06-17 11:59:29,816 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_rscd_0008.rmap 1.0 K bytes (136 / 204 files) (600.1 K / 741.0 K bytes)
2025-06-17 11:59:29,924 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_resol_0006.rmap 790 bytes (137 / 204 files) (601.2 K / 741.0 K bytes)
2025-06-17 11:59:30,029 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_reset_0026.rmap 3.9 K bytes (138 / 204 files) (602.0 K / 741.0 K bytes)
2025-06-17 11:59:30,138 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_regions_0034.rmap 5.2 K bytes (139 / 204 files) (605.8 K / 741.0 K bytes)
2025-06-17 11:59:30,245 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_readnoise_0023.rmap 1.6 K bytes (140 / 204 files) (611.0 K / 741.0 K bytes)
2025-06-17 11:59:30,349 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_psfmask_0009.rmap 2.1 K bytes (141 / 204 files) (612.7 K / 741.0 K bytes)
2025-06-17 11:59:30,451 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_psf_0003.rmap 839 bytes (142 / 204 files) (614.8 K / 741.0 K bytes)
2025-06-17 11:59:30,564 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_photom_0056.rmap 3.7 K bytes (143 / 204 files) (615.6 K / 741.0 K bytes)
2025-06-17 11:59:30,667 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pathloss_0005.rmap 866 bytes (144 / 204 files) (619.4 K / 741.0 K bytes)
2025-06-17 11:59:30,776 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-whitelightstep_0003.rmap 912 bytes (145 / 204 files) (620.2 K / 741.0 K bytes)
2025-06-17 11:59:30,886 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-tweakregstep_0003.rmap 1.8 K bytes (146 / 204 files) (621.2 K / 741.0 K bytes)
2025-06-17 11:59:31,000 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-spec3pipeline_0009.rmap 816 bytes (147 / 204 files) (623.0 K / 741.0 K bytes)
2025-06-17 11:59:31,106 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-spec2pipeline_0012.rmap 1.3 K bytes (148 / 204 files) (623.8 K / 741.0 K bytes)
2025-06-17 11:59:31,219 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-sourcecatalogstep_0003.rmap 1.9 K bytes (149 / 204 files) (625.1 K / 741.0 K bytes)
2025-06-17 11:59:31,327 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-resamplestep_0002.rmap 677 bytes (150 / 204 files) (627.0 K / 741.0 K bytes)
2025-06-17 11:59:31,440 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-resamplespecstep_0002.rmap 706 bytes (151 / 204 files) (627.7 K / 741.0 K bytes)
2025-06-17 11:59:31,544 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-outlierdetectionstep_0020.rmap 3.4 K bytes (152 / 204 files) (628.4 K / 741.0 K bytes)
2025-06-17 11:59:31,656 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-jumpstep_0011.rmap 1.6 K bytes (153 / 204 files) (631.8 K / 741.0 K bytes)
2025-06-17 11:59:31,762 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-image2pipeline_0010.rmap 1.1 K bytes (154 / 204 files) (633.4 K / 741.0 K bytes)
2025-06-17 11:59:31,868 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-extract1dstep_0003.rmap 807 bytes (155 / 204 files) (634.5 K / 741.0 K bytes)
2025-06-17 11:59:31,970 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-emicorrstep_0003.rmap 796 bytes (156 / 204 files) (635.3 K / 741.0 K bytes)
2025-06-17 11:59:32,073 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-detector1pipeline_0010.rmap 1.6 K bytes (157 / 204 files) (636.1 K / 741.0 K bytes)
2025-06-17 11:59:32,177 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-darkpipeline_0002.rmap 860 bytes (158 / 204 files) (637.7 K / 741.0 K bytes)
2025-06-17 11:59:32,278 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_pars-darkcurrentstep_0002.rmap 683 bytes (159 / 204 files) (638.5 K / 741.0 K bytes)
2025-06-17 11:59:32,390 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_mrsxartcorr_0002.rmap 2.2 K bytes (160 / 204 files) (639.2 K / 741.0 K bytes)
2025-06-17 11:59:32,494 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_mrsptcorr_0005.rmap 2.0 K bytes (161 / 204 files) (641.4 K / 741.0 K bytes)
2025-06-17 11:59:32,605 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_mask_0026.rmap 4.3 K bytes (162 / 204 files) (643.3 K / 741.0 K bytes)
2025-06-17 11:59:32,709 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_linearity_0018.rmap 2.8 K bytes (163 / 204 files) (647.6 K / 741.0 K bytes)
2025-06-17 11:59:32,816 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_ipc_0008.rmap 700 bytes (164 / 204 files) (650.4 K / 741.0 K bytes)
2025-06-17 11:59:32,920 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_gain_0013.rmap 3.9 K bytes (165 / 204 files) (651.1 K / 741.0 K bytes)
2025-06-17 11:59:33,022 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_fringefreq_0003.rmap 1.4 K bytes (166 / 204 files) (655.0 K / 741.0 K bytes)
2025-06-17 11:59:33,124 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_fringe_0019.rmap 3.9 K bytes (167 / 204 files) (656.5 K / 741.0 K bytes)
2025-06-17 11:59:33,232 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_flat_0066.rmap 15.7 K bytes (168 / 204 files) (660.4 K / 741.0 K bytes)
2025-06-17 11:59:33,366 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_filteroffset_0025.rmap 2.5 K bytes (169 / 204 files) (676.1 K / 741.0 K bytes)
2025-06-17 11:59:33,478 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_extract1d_0020.rmap 1.4 K bytes (170 / 204 files) (678.6 K / 741.0 K bytes)
2025-06-17 11:59:33,579 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_emicorr_0003.rmap 663 bytes (171 / 204 files) (679.9 K / 741.0 K bytes)
2025-06-17 11:59:33,691 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_drizpars_0002.rmap 511 bytes (172 / 204 files) (680.6 K / 741.0 K bytes)
2025-06-17 11:59:33,807 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_distortion_0040.rmap 4.9 K bytes (173 / 204 files) (681.1 K / 741.0 K bytes)
2025-06-17 11:59:33,909 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_dark_0036.rmap 4.4 K bytes (174 / 204 files) (686.0 K / 741.0 K bytes)
2025-06-17 11:59:34,021 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_cubepar_0017.rmap 800 bytes (175 / 204 files) (690.4 K / 741.0 K bytes)
2025-06-17 11:59:34,123 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_area_0015.rmap 866 bytes (176 / 204 files) (691.2 K / 741.0 K bytes)
2025-06-17 11:59:34,232 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_apcorr_0019.rmap 5.0 K bytes (177 / 204 files) (692.0 K / 741.0 K bytes)
2025-06-17 11:59:34,335 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_abvegaoffset_0003.rmap 1.3 K bytes (178 / 204 files) (697.0 K / 741.0 K bytes)
2025-06-17 11:59:34,436 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_miri_0437.imap 5.8 K bytes (179 / 204 files) (698.3 K / 741.0 K bytes)
2025-06-17 11:59:34,543 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_trappars_0004.rmap 903 bytes (180 / 204 files) (704.1 K / 741.0 K bytes)
2025-06-17 11:59:34,650 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_trapdensity_0006.rmap 930 bytes (181 / 204 files) (705.0 K / 741.0 K bytes)
2025-06-17 11:59:34,753 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_superbias_0017.rmap 3.8 K bytes (182 / 204 files) (706.0 K / 741.0 K bytes)
2025-06-17 11:59:34,856 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_saturation_0009.rmap 779 bytes (183 / 204 files) (709.7 K / 741.0 K bytes)
2025-06-17 11:59:34,959 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_readnoise_0014.rmap 1.3 K bytes (184 / 204 files) (710.5 K / 741.0 K bytes)
2025-06-17 11:59:35,063 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_photom_0014.rmap 1.1 K bytes (185 / 204 files) (711.8 K / 741.0 K bytes)
2025-06-17 11:59:35,182 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_persat_0006.rmap 884 bytes (186 / 204 files) (712.9 K / 741.0 K bytes)
2025-06-17 11:59:35,290 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-tweakregstep_0002.rmap 850 bytes (187 / 204 files) (713.8 K / 741.0 K bytes)
2025-06-17 11:59:35,391 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-sourcecatalogstep_0001.rmap 636 bytes (188 / 204 files) (714.6 K / 741.0 K bytes)
2025-06-17 11:59:35,495 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-outlierdetectionstep_0001.rmap 654 bytes (189 / 204 files) (715.3 K / 741.0 K bytes)
2025-06-17 11:59:35,598 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-image2pipeline_0005.rmap 974 bytes (190 / 204 files) (715.9 K / 741.0 K bytes)
2025-06-17 11:59:35,701 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-detector1pipeline_0002.rmap 1.0 K bytes (191 / 204 files) (716.9 K / 741.0 K bytes)
2025-06-17 11:59:35,811 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_pars-darkpipeline_0002.rmap 856 bytes (192 / 204 files) (717.9 K / 741.0 K bytes)
2025-06-17 11:59:35,918 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_mask_0023.rmap 1.1 K bytes (193 / 204 files) (718.8 K / 741.0 K bytes)
2025-06-17 11:59:36,022 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_linearity_0015.rmap 925 bytes (194 / 204 files) (719.8 K / 741.0 K bytes)
2025-06-17 11:59:36,127 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_ipc_0003.rmap 614 bytes (195 / 204 files) (720.8 K / 741.0 K bytes)
2025-06-17 11:59:36,243 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_gain_0010.rmap 890 bytes (196 / 204 files) (721.4 K / 741.0 K bytes)
2025-06-17 11:59:36,350 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_flat_0009.rmap 1.1 K bytes (197 / 204 files) (722.3 K / 741.0 K bytes)
2025-06-17 11:59:36,462 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_distortion_0011.rmap 1.2 K bytes (198 / 204 files) (723.4 K / 741.0 K bytes)
2025-06-17 11:59:36,565 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_dark_0017.rmap 4.3 K bytes (199 / 204 files) (724.6 K / 741.0 K bytes)
2025-06-17 11:59:36,673 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_area_0010.rmap 1.2 K bytes (200 / 204 files) (728.9 K / 741.0 K bytes)
2025-06-17 11:59:36,779 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_apcorr_0004.rmap 4.0 K bytes (201 / 204 files) (730.1 K / 741.0 K bytes)
2025-06-17 11:59:36,883 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_abvegaoffset_0002.rmap 1.3 K bytes (202 / 204 files) (734.0 K / 741.0 K bytes)
2025-06-17 11:59:36,989 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_fgs_0123.imap 5.1 K bytes (203 / 204 files) (735.3 K / 741.0 K bytes)
2025-06-17 11:59:37,091 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_1364.pmap 580 bytes (204 / 204 files) (740.4 K / 741.0 K bytes)
2025-06-17 11:59:37,357 - 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)
2025-06-17 11:59:37,466 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 11:59:37,483 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf 936 bytes (1 / 1 files) (0 / 936 bytes)
2025-06-17 11:59:37,593 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 11:59:37,603 - 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)
2025-06-17 11:59:37,717 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 11:59:37,729 - 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)
2025-06-17 11:59:37,834 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 11:59:37,853 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 11:59:37,854 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 11:59:37,855 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 11:59:37,856 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 11:59:37,857 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 11:59:37,858 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 11:59:37,859 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 11:59:37,860 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 11:59:37,861 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 11:59:37,862 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 11:59:37,863 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 11:59:37,863 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 11:59:37,864 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 11:59:37,865 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 11:59:37,866 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 11:59:37,867 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 11:59:37,868 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 11:59:37,869 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 11:59:37,870 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 11:59:37,871 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 11:59:37,874 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 11:59:37,977 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00001_mirifulong_uncal.fits'),).
2025-06-17 11:59:37,997 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 11:59:38,123 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 11:59:38,127 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits 6.1 G bytes (1 / 8 files) (0 / 6.3 G bytes)
2025-06-17 12:04:01,023 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits 8.5 M bytes (2 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:04:01,464 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits 21.2 M bytes (3 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:04:01,998 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits 4.2 M bytes (4 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:04:02,347 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits 4.2 M bytes (5 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:04:02,703 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits 173.3 M bytes (6 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:04:04,922 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits 37.4 K bytes (7 / 8 files) (6.3 G / 6.3 G bytes)
2025-06-17 12:04:05,076 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits 8.5 M bytes (8 / 8 files) (6.3 G / 6.3 G bytes)
2025-06-17 12:04:05,497 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:04:05,498 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2025-06-17 12:04:05,499 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2025-06-17 12:04:05,499 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:04:05,500 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:04:05,500 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:04:05,501 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:04:05,501 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:04:05,502 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:04:05,503 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:04:05,503 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:04:05,504 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:04:05,506 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:04:05,907 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:05,915 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:04:05,915 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:04:05,917 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:04:06,020 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:06,037 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:04:06,283 - CRDS - INFO - Calibration SW Found: jwst 1.18.1 (/usr/share/miniconda/lib/python3.13/site-packages/jwst-1.18.1.dist-info)
2025-06-17 12:04:06,411 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:04:06,523 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:06,524 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:04:06,624 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:06,643 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:04:06,666 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:04:06,675 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:04:06,727 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:04:06,982 - stpipe.Detector1Pipeline.saturation - INFO - Detected 373 saturated pixels
2025-06-17 12:04:07,004 - stpipe.Detector1Pipeline.saturation - INFO - Detected 23 A/D floor pixels
2025-06-17 12:04:07,008 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:04:07,124 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:07,125 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:04:07,238 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:07,294 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:04:07,415 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:07,472 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:04:07,584 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:07,608 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:04:07,660 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:04:07,669 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:04:07,743 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:04:07,859 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:07,877 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2025-06-17 12:04:07,902 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:04:07,911 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:04:08,142 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:04:08,248 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:08,267 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:04:08,349 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:04:08,351 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:04:08,454 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:08,473 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:04:10,974 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:04:10,975 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:04:10,975 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:04:11,829 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:04:11,984 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:11,985 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:04:12,091 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:12,092 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:04:12,191 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:12,198 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:04:12,199 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:04:12,262 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:04:12,271 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:04:12,333 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:04:12,333 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:04:15,187 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:04:20,501 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:04:20,502 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.16822 sec
2025-06-17 12:04:20,518 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.319879
2025-06-17 12:04:20,522 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:04:20,640 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:20,641 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:04:20,757 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:20,837 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:04:20,838 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:04:20,862 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:04:20,862 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:04:21,234 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:04:21,240 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:04:21,240 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:04:24,910 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.668964385986328
2025-06-17 12:04:24,982 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:04:25,102 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:25,136 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:04:25,136 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:04:25,257 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:25,275 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:04:25,277 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:04:25,278 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:04:25,400 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:25,428 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:04:25,428 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:04:25,546 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00001_mirifulong_uncal.fits>,).
2025-06-17 12:04:25,565 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:04:25,566 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:04:25,568 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:04:25,640 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rateints.fits
2025-06-17 12:04:25,641 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:04:25,642 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:04:25,708 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong_rate.fits
2025-06-17 12:04:25,709 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:04:25,709 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:04:25,892 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:04:25,905 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:04:25,914 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:04:25,925 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:04:25,943 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:04:25,944 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:04:25,945 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:04:25,945 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:04:25,946 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:04:25,947 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:04:25,948 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:04:25,949 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:04:25,950 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:04:25,951 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:04:25,952 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:04:25,953 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:04:25,954 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:04:25,955 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:04:25,956 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:04:25,957 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:04:25,959 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:04:25,960 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:04:25,961 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:04:25,962 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:04:25,963 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:04:26,085 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00001_mirifushort_uncal.fits'),).
2025-06-17 12:04:26,105 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:04:26,224 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:04:26,227 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits 6.1 G bytes (1 / 8 files) (0 / 6.3 G bytes)
2025-06-17 12:07:02,574 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits 4.2 M bytes (2 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:07:06,741 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits 21.2 M bytes (3 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:07:07,382 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits 4.2 M bytes (4 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:07:07,753 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits 4.2 M bytes (5 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:07:08,094 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits 173.3 M bytes (6 / 8 files) (6.1 G / 6.3 G bytes)
2025-06-17 12:07:10,077 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits 37.4 K bytes (7 / 8 files) (6.3 G / 6.3 G bytes)
2025-06-17 12:07:10,252 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits 8.5 M bytes (8 / 8 files) (6.3 G / 6.3 G bytes)
2025-06-17 12:07:10,703 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:07:10,704 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:07:10,704 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:07:10,705 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:07:10,705 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:07:10,705 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:07:10,706 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:07:10,707 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:07:10,707 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:07:10,708 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:07:10,708 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:07:10,708 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:07:10,710 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:07:11,011 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:11,019 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:07:11,020 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:07:11,021 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:07:11,133 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:11,149 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:07:11,325 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:07:11,437 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:11,438 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:07:11,542 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:11,557 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:07:11,578 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:11,587 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:11,639 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:07:11,899 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1739 saturated pixels
2025-06-17 12:07:11,920 - stpipe.Detector1Pipeline.saturation - INFO - Detected 16 A/D floor pixels
2025-06-17 12:07:11,924 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:07:12,030 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:12,031 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:07:12,143 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:12,199 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:07:12,317 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:12,374 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:07:12,492 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:12,508 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:07:12,559 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:12,568 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:12,639 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:07:12,752 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:12,767 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:07:12,790 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:12,799 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:13,029 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:07:13,145 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:13,160 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:07:13,242 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:07:13,244 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:07:13,360 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:13,376 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:07:16,394 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:07:16,395 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:07:16,396 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:07:17,154 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:07:17,338 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:17,339 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:07:17,451 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:17,452 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:07:17,559 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:17,566 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:07:17,567 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:07:17,622 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:07:17,630 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:07:17,703 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:07:17,704 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:07:20,446 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:07:25,610 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:07:25,611 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 7.90741 sec
2025-06-17 12:07:25,644 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.077790
2025-06-17 12:07:25,648 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:07:25,760 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:25,760 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:07:25,874 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:25,944 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:07:25,945 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:07:25,967 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:07:25,967 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:07:26,343 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:07:26,348 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:07:26,349 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:07:29,898 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5474557876586914
2025-06-17 12:07:29,955 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:07:30,067 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:30,092 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:07:30,092 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:07:30,201 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:30,218 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:07:30,220 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:07:30,222 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:07:30,331 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:30,355 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:07:30,356 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:07:30,466 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00001_mirifushort_uncal.fits>,).
2025-06-17 12:07:30,483 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:07:30,485 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:07:30,487 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:07:30,553 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rateints.fits
2025-06-17 12:07:30,554 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:07:30,555 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:07:30,619 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort_rate.fits
2025-06-17 12:07:30,619 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:07:30,620 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:07:30,804 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:07:30,816 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:07:30,825 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:07:30,835 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:07:30,852 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:07:30,853 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:07:30,854 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:07:30,855 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:07:30,855 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:07:30,856 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:07:30,857 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:07:30,858 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:07:30,859 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:07:30,860 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:07:30,861 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:07:30,861 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:07:30,862 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:07:30,863 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:07:30,864 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:07:30,865 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:07:30,866 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:07:30,867 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:07:30,869 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:07:30,870 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:07:30,871 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:07:30,973 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00002_mirifulong_uncal.fits'),).
2025-06-17 12:07:30,993 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:07:31,112 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:07:31,115 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:07:31,115 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2025-06-17 12:07:31,116 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2025-06-17 12:07:31,116 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:07:31,116 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:07:31,117 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:07:31,117 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:07:31,118 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:07:31,118 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:07:31,118 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:07:31,119 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:07:31,119 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:07:31,121 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:07:31,432 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:31,439 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:07:31,440 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:07:31,442 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:07:31,544 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:31,560 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:07:31,694 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:07:31,804 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:31,804 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:07:31,901 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:31,917 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:07:31,945 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:31,955 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:32,004 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:07:32,258 - stpipe.Detector1Pipeline.saturation - INFO - Detected 354 saturated pixels
2025-06-17 12:07:32,279 - stpipe.Detector1Pipeline.saturation - INFO - Detected 25 A/D floor pixels
2025-06-17 12:07:32,283 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:07:32,393 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:32,394 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:07:32,508 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:32,564 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:07:32,679 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:32,734 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:07:32,849 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:32,864 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:07:33,025 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:33,034 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:33,106 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:07:33,224 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:33,239 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2025-06-17 12:07:33,275 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:33,284 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:07:33,512 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:07:33,627 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:33,642 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:07:33,722 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:07:33,725 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:07:33,836 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:33,851 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:07:49,759 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:07:49,760 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:07:49,760 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:07:50,800 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:07:50,960 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:50,961 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:07:51,073 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:51,075 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:07:51,187 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:51,195 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:07:51,195 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:07:51,251 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:07:51,259 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:07:51,325 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:07:51,325 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:07:54,110 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:07:59,320 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 1
2025-06-17 12:07:59,320 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 7.9948 sec
2025-06-17 12:07:59,337 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.141932
2025-06-17 12:07:59,340 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:07:59,450 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:59,451 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:07:59,547 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:07:59,618 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:07:59,619 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:07:59,643 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:07:59,643 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:08:00,010 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:08:00,016 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:08:00,017 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:08:03,685 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.667402982711792
2025-06-17 12:08:03,742 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:08:03,853 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:08:03,880 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:08:03,880 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:08:03,993 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:08:04,011 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:08:04,012 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:08:04,014 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:08:04,128 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:08:04,155 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:08:04,155 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:08:04,272 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00002_mirifulong_uncal.fits>,).
2025-06-17 12:08:04,290 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:08:04,291 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:08:04,293 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:08:04,361 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rateints.fits
2025-06-17 12:08:04,362 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:08:04,362 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:08:04,427 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong_rate.fits
2025-06-17 12:08:04,428 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:08:04,428 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:08:04,617 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:08:04,629 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:08:04,638 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:08:04,648 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:08:04,665 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:08:04,666 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:08:04,667 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:08:04,668 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:08:04,669 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:08:04,669 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:08:04,670 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:08:04,671 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:08:04,672 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:08:04,673 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:08:04,674 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:08:04,674 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:08:04,675 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:08:04,676 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:08:04,677 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:08:04,678 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:08:04,680 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:08:04,681 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:08:04,681 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:08:04,682 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:08:04,683 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:08:04,797 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00002_mirifushort_uncal.fits'),).
2025-06-17 12:08:04,818 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:08:04,939 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:08:04,942 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:08:04,943 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:08:04,943 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:08:04,943 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:08:04,944 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:08:04,944 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:08:04,944 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:08:04,945 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:08:04,945 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:08:04,946 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:08:04,946 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:08:04,946 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:08:04,948 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:08:05,265 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:05,272 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:08:05,273 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:08:05,275 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:08:05,385 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:05,400 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:08:05,531 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:08:05,644 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:05,645 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:08:05,746 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:05,762 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:08:05,790 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:05,800 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:05,849 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:08:06,097 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1638 saturated pixels
2025-06-17 12:08:06,118 - stpipe.Detector1Pipeline.saturation - INFO - Detected 6 A/D floor pixels
2025-06-17 12:08:06,122 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:08:06,231 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:06,232 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:08:06,332 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:06,389 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:08:06,501 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:06,556 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:08:06,658 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:06,673 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:08:06,814 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:06,823 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:06,894 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:08:06,998 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:07,014 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:08:07,051 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:07,061 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:07,289 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:08:07,403 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:07,418 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:08:07,497 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:08:07,500 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:08:07,613 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:07,629 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:08:21,659 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:08:21,660 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:08:21,661 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:08:22,530 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:08:22,749 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:22,750 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:08:22,856 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:22,857 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:08:22,950 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:22,958 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:08:22,958 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:08:23,014 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:08:23,022 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:08:23,098 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:08:23,098 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:08:25,835 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:08:30,938 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 1
2025-06-17 12:08:30,939 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 7.84013 sec
2025-06-17 12:08:30,971 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.013382
2025-06-17 12:08:30,975 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:08:31,081 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:31,082 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:08:31,173 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:31,243 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:08:31,244 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:08:31,266 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:08:31,266 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:08:31,637 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:08:31,643 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:08:31,643 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:08:35,189 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.543912172317505
2025-06-17 12:08:35,245 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:08:35,359 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:35,384 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:08:35,385 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:08:35,488 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:35,507 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:08:35,508 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:08:35,510 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:08:35,611 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:35,636 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:08:35,636 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:08:35,737 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00002_mirifushort_uncal.fits>,).
2025-06-17 12:08:35,755 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:08:35,756 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:08:35,758 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:08:35,825 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rateints.fits
2025-06-17 12:08:35,825 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:08:35,826 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:08:35,890 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort_rate.fits
2025-06-17 12:08:35,890 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:08:35,891 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:08:36,075 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:08:36,087 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:08:36,097 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:08:36,106 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:08:36,123 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:08:36,124 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:08:36,125 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:08:36,126 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:08:36,127 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:08:36,127 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:08:36,128 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:08:36,129 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:08:36,130 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:08:36,131 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:08:36,131 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:08:36,132 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:08:36,133 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:08:36,134 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:08:36,135 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:08:36,135 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:08:36,137 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:08:36,138 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:08:36,139 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:08:36,140 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:08:36,141 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:08:36,242 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00003_mirifulong_uncal.fits'),).
2025-06-17 12:08:36,263 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:08:36,379 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00003_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:08:36,382 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:08:36,383 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2025-06-17 12:08:36,383 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2025-06-17 12:08:36,384 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:08:36,385 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:08:36,385 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:08:36,385 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:08:36,386 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:08:36,387 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:08:36,387 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:08:36,388 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:08:36,388 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:08:36,390 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:08:36,680 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:36,688 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:08:36,689 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:08:36,690 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:08:36,780 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:36,795 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:08:36,931 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:08:37,034 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:37,035 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:08:37,128 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:37,143 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:08:37,171 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:37,180 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:37,230 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:08:37,478 - stpipe.Detector1Pipeline.saturation - INFO - Detected 358 saturated pixels
2025-06-17 12:08:37,498 - stpipe.Detector1Pipeline.saturation - INFO - Detected 26 A/D floor pixels
2025-06-17 12:08:37,502 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:08:37,611 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:37,611 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:08:37,704 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:37,761 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:08:37,865 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:37,920 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:08:38,027 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:38,043 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:08:38,215 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:38,224 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:38,297 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:08:38,410 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:38,426 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2025-06-17 12:08:38,461 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:38,471 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:08:38,707 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:08:38,807 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:38,823 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:08:38,902 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:08:38,905 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:08:39,004 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:39,020 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:08:52,311 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:08:52,312 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:08:52,312 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:08:53,479 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:08:53,690 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:53,691 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:08:53,810 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:53,811 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:08:53,924 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:08:53,932 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:08:53,933 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:08:53,990 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:08:53,998 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:08:54,065 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:08:54,066 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:08:56,821 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:09:02,169 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:09:02,170 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.10415 sec
2025-06-17 12:09:02,187 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.254508
2025-06-17 12:09:02,190 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:09:02,299 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:09:02,300 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:09:02,406 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:09:02,478 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:09:02,478 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:09:02,502 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:09:02,503 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:09:02,875 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:09:02,880 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:09:02,881 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:09:06,539 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6569697856903076
2025-06-17 12:09:06,595 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:09:06,700 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:09:06,727 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:09:06,728 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:09:06,828 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:09:06,846 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:09:06,847 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:09:06,849 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:09:06,944 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:09:06,972 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:09:06,972 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:09:07,075 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00003_mirifulong_uncal.fits>,).
2025-06-17 12:09:07,094 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:09:07,095 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:09:07,097 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:09:07,165 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rateints.fits
2025-06-17 12:09:07,165 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:09:07,166 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:09:07,231 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong_rate.fits
2025-06-17 12:09:07,232 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:09:07,232 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:09:07,409 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:09:07,422 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:09:07,430 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:09:07,441 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:09:07,458 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:09:07,459 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:09:07,460 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:09:07,461 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:09:07,462 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:09:07,463 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:09:07,463 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:09:07,464 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:09:07,465 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:09:07,466 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:09:07,467 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:09:07,468 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:09:07,469 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:09:07,469 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:09:07,470 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:09:07,471 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:09:07,473 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:09:07,474 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:09:07,475 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:09:07,476 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:09:07,477 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:09:07,586 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00003_mirifushort_uncal.fits'),).
2025-06-17 12:09:07,608 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:09:07,724 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00003_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:09:07,727 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:09:07,727 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:09:07,728 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:09:07,728 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:09:07,729 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:09:07,729 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:09:07,729 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:09:07,730 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:09:07,731 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:09:07,731 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:09:07,732 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:09:07,732 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:09:07,734 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:09:08,027 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:08,035 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:09:08,035 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:09:08,037 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:09:08,133 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:08,149 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:09:08,285 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:09:08,403 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:08,404 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:09:08,518 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:08,534 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:09:08,561 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:08,571 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:08,621 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:09:08,900 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1594 saturated pixels
2025-06-17 12:09:08,922 - stpipe.Detector1Pipeline.saturation - INFO - Detected 8 A/D floor pixels
2025-06-17 12:09:08,926 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:09:09,062 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:09,063 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:09:09,195 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:09,257 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:09:09,387 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:09,445 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:09:09,552 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:09,568 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:09:09,726 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:09,735 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:09,808 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:09:09,924 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:09,939 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:09:09,975 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:09,984 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:10,214 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:09:10,329 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:10,344 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:09:10,425 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:09:10,428 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:09:10,543 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:10,558 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:09:24,348 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:09:24,348 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:09:24,349 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:09:25,286 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:09:25,533 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:25,534 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:09:25,653 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:25,654 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:09:25,771 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:25,778 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:09:25,779 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:09:25,836 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:09:25,844 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:09:25,920 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:09:25,921 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:09:28,791 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:09:34,030 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 1
2025-06-17 12:09:34,031 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.10942 sec
2025-06-17 12:09:34,064 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.286119
2025-06-17 12:09:34,068 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:09:34,178 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:34,178 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:09:34,298 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:34,370 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:09:34,370 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:09:34,393 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:09:34,393 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:09:34,767 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:09:34,772 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:09:34,773 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:09:38,344 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.569288730621338
2025-06-17 12:09:38,401 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:09:38,528 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:38,553 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:09:38,554 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:09:38,675 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:38,693 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:09:38,695 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:09:38,697 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:09:38,824 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:38,852 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:09:38,852 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:09:38,978 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00003_mirifushort_uncal.fits>,).
2025-06-17 12:09:38,997 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:09:38,999 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:09:39,001 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:09:39,069 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rateints.fits
2025-06-17 12:09:39,070 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:09:39,071 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:09:39,137 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort_rate.fits
2025-06-17 12:09:39,138 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:09:39,138 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:09:39,341 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:09:39,354 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:09:39,363 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:09:39,373 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:09:39,391 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:09:39,392 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:09:39,392 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:09:39,394 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:09:39,395 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:09:39,395 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:09:39,396 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:09:39,397 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:09:39,398 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:09:39,399 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:09:39,400 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:09:39,401 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:09:39,401 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:09:39,402 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:09:39,403 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:09:39,405 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:09:39,407 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:09:39,408 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:09:39,409 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:09:39,410 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:09:39,411 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:09:39,538 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00004_mirifulong_uncal.fits'),).
2025-06-17 12:09:39,558 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:09:39,683 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00004_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:09:39,687 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:09:39,687 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2025-06-17 12:09:39,688 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2025-06-17 12:09:39,688 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:09:39,689 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:09:39,689 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:09:39,689 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:09:39,690 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:09:39,690 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:09:39,691 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:09:39,691 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:09:39,691 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:09:39,693 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:09:40,027 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:40,035 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:09:40,035 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:09:40,037 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:09:40,166 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:40,182 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:09:40,322 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:09:40,447 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:40,447 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:09:40,564 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:40,579 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:09:40,607 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:40,617 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:40,670 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:09:40,931 - stpipe.Detector1Pipeline.saturation - INFO - Detected 359 saturated pixels
2025-06-17 12:09:40,951 - stpipe.Detector1Pipeline.saturation - INFO - Detected 21 A/D floor pixels
2025-06-17 12:09:40,955 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:09:41,073 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:41,073 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:09:41,194 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:41,256 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:09:41,376 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:41,432 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:09:41,549 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:41,565 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:09:41,730 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:41,739 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:41,815 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:09:41,945 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:41,961 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2025-06-17 12:09:42,002 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:42,011 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:09:42,249 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:09:42,374 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:42,390 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:09:42,474 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:09:42,477 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:09:42,606 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:42,622 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:09:55,660 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:09:55,661 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:09:55,662 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:09:56,848 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:09:57,083 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:57,084 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:09:57,198 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:57,199 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:09:57,310 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:09:57,319 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:09:57,319 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:09:57,378 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:09:57,387 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:09:57,450 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:09:57,451 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:10:00,272 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:10:05,547 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 2
2025-06-17 12:10:05,548 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.09692 sec
2025-06-17 12:10:05,567 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.248103
2025-06-17 12:10:05,570 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:10:05,693 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:10:05,694 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:10:05,803 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:10:05,875 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:10:05,876 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:10:05,900 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:10:05,901 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:10:06,274 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:10:06,279 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:10:06,280 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:10:09,961 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6798319816589355
2025-06-17 12:10:10,018 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:10:10,129 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:10:10,158 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:10:10,158 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:10:10,276 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:10:10,293 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:10:10,295 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:10:10,297 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:10:10,409 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:10:10,437 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:10:10,438 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:10:10,552 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00004_mirifulong_uncal.fits>,).
2025-06-17 12:10:10,570 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:10:10,571 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:10:10,573 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:10:10,640 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rateints.fits
2025-06-17 12:10:10,641 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:10:10,641 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:10:10,707 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong_rate.fits
2025-06-17 12:10:10,708 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:10:10,708 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:10:10,898 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:10:10,911 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:10:10,920 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:10:10,930 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:10:10,947 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:10:10,948 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:10:10,949 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:10:10,951 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:10:10,952 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:10:10,953 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:10:10,953 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:10:10,955 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:10:10,956 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:10:10,957 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:10:10,957 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:10:10,958 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:10:10,959 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:10:10,960 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:10:10,961 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:10:10,962 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:10:10,964 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:10:10,965 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:10:10,966 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:10:10,967 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:10:10,968 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:10:11,083 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03102_00004_mirifushort_uncal.fits'),).
2025-06-17 12:10:11,105 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:10:11,233 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00004_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:10:11,236 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:10:11,236 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:10:11,237 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:10:11,237 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:10:11,238 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:10:11,238 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:10:11,239 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:10:11,239 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:10:11,240 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:10:11,241 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:10:11,241 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:10:11,242 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:10:11,244 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:10:11,572 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:11,580 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:10:11,581 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:10:11,582 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:10:11,706 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:11,721 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:10:11,858 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:10:11,981 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:11,981 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:10:12,100 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:12,117 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:10:12,144 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:12,154 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:12,206 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:10:12,465 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1515 saturated pixels
2025-06-17 12:10:12,487 - stpipe.Detector1Pipeline.saturation - INFO - Detected 10 A/D floor pixels
2025-06-17 12:10:12,491 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:10:12,608 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:12,609 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:10:12,739 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:12,798 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:10:12,920 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:12,981 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:10:13,108 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:13,124 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:10:13,279 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:13,288 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:13,363 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:10:13,490 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:13,507 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:10:13,543 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:13,552 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:13,787 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:10:13,913 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:13,929 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:10:14,015 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:10:14,018 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:10:14,144 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:14,160 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:10:27,871 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:10:27,872 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:10:27,872 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:10:28,832 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:10:29,097 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:29,098 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:10:29,221 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:29,222 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:10:29,343 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:29,351 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:10:29,352 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:10:29,410 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:10:29,419 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:10:29,496 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:10:29,497 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:10:32,247 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:10:37,504 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:10:37,505 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.00768 sec
2025-06-17 12:10:37,538 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.186935
2025-06-17 12:10:37,541 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:10:37,655 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:37,655 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:10:37,762 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:37,833 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:10:37,833 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:10:37,855 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:10:37,856 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:10:38,231 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:10:38,236 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:10:38,237 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:10:41,793 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5548956394195557
2025-06-17 12:10:41,850 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:10:41,971 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:41,996 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:10:41,996 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:10:42,110 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:42,128 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:10:42,130 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:10:42,132 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:10:42,252 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:42,277 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:10:42,277 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:10:42,392 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03102_00004_mirifushort_uncal.fits>,).
2025-06-17 12:10:42,410 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:10:42,411 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:10:42,413 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:10:42,481 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rateints.fits
2025-06-17 12:10:42,482 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:10:42,483 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:10:42,548 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort_rate.fits
2025-06-17 12:10:42,548 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:10:42,549 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:10:42,740 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:10:42,752 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:10:42,761 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:10:42,771 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:10:42,789 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:10:42,789 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:10:42,790 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:10:42,791 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:10:42,792 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:10:42,793 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:10:42,794 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:10:42,795 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:10:42,796 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:10:42,797 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:10:42,798 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:10:42,799 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:10:42,799 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:10:42,800 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:10:42,801 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:10:42,802 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:10:42,805 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:10:42,806 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:10:42,806 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:10:42,807 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:10:42,808 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:10:42,932 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00001_mirifulong_uncal.fits'),).
2025-06-17 12:10:42,951 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:10:43,079 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:10:43,082 - 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)
2025-06-17 12:10:43,474 - 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)
2025-06-17 12:10:44,175 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:10:44,175 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:10:44,176 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2025-06-17 12:10:44,176 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:10:44,177 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:10:44,177 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:10:44,178 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:10:44,178 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:10:44,179 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:10:44,179 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:10:44,180 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:10:44,180 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:10:44,182 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:10:44,505 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:44,513 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:10:44,513 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:10:44,515 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:10:44,632 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:44,648 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:10:44,785 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:10:44,899 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:44,900 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:10:45,006 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:45,021 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:10:45,048 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:45,057 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:45,109 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:10:45,363 - stpipe.Detector1Pipeline.saturation - INFO - Detected 352 saturated pixels
2025-06-17 12:10:45,383 - stpipe.Detector1Pipeline.saturation - INFO - Detected 26 A/D floor pixels
2025-06-17 12:10:45,387 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:10:45,505 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:45,506 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:10:45,621 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:45,679 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:10:45,797 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:45,853 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:10:45,971 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:45,987 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:10:46,128 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:46,137 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:46,210 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:10:46,331 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:46,346 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2025-06-17 12:10:46,369 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:46,378 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:10:46,610 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:10:46,729 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:46,745 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:10:46,826 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:10:46,829 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:10:46,947 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:10:46,963 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:11:00,001 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:11:00,002 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:11:00,002 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:11:01,152 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:11:01,399 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:01,399 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:11:01,518 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:01,519 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:11:01,633 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:01,640 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:11:01,641 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:11:01,698 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:11:01,707 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:11:01,785 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:11:01,785 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:11:04,542 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:11:09,786 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 1
2025-06-17 12:11:09,787 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.0011 sec
2025-06-17 12:11:09,819 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.179004
2025-06-17 12:11:09,823 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:11:09,949 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:09,949 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:11:10,073 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:10,142 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:11:10,143 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:11:10,166 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:11:10,166 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:11:10,535 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:11:10,540 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:11:10,541 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:11:14,218 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6747686862945557
2025-06-17 12:11:14,275 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:11:14,398 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:14,423 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:11:14,423 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:11:14,544 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:14,562 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:11:14,563 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:11:14,565 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:11:14,684 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:14,710 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:11:14,711 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:11:14,831 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00001_mirifulong_uncal.fits>,).
2025-06-17 12:11:14,849 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:11:14,850 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:11:14,852 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:11:14,921 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rateints.fits
2025-06-17 12:11:14,921 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:11:14,922 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:11:14,986 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong_rate.fits
2025-06-17 12:11:14,987 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:11:14,987 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:11:15,175 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:11:15,188 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:11:15,197 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:11:15,207 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:11:15,225 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:11:15,226 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:11:15,227 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:11:15,228 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:11:15,229 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:11:15,229 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:11:15,230 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:11:15,231 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:11:15,232 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:11:15,233 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:11:15,234 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:11:15,234 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:11:15,235 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:11:15,236 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:11:15,237 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:11:15,238 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:11:15,240 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:11:15,242 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:11:15,243 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:11:15,244 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:11:15,244 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:11:15,371 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00001_mirifushort_uncal.fits'),).
2025-06-17 12:11:15,392 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:11:15,515 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:11:15,518 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:11:15,518 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:11:15,519 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:11:15,519 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:11:15,520 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:11:15,520 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:11:15,521 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:11:15,522 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:11:15,522 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:11:15,523 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:11:15,523 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:11:15,524 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:11:15,526 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:11:15,850 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:15,858 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:11:15,858 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:11:15,860 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:11:15,979 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:15,994 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:11:16,128 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:11:16,247 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:16,248 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:11:16,368 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:16,383 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:11:16,411 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:16,420 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:16,472 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:11:16,735 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1584 saturated pixels
2025-06-17 12:11:16,756 - stpipe.Detector1Pipeline.saturation - INFO - Detected 7 A/D floor pixels
2025-06-17 12:11:16,760 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:11:16,883 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:16,884 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:11:17,003 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:17,060 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:11:17,179 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:17,236 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:11:17,356 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:17,371 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:11:17,521 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:17,530 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:17,604 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:11:17,730 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:17,746 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:11:17,781 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:17,790 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:18,021 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:11:18,137 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:18,152 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:11:18,232 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:11:18,235 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:11:18,357 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:18,373 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:11:31,855 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:11:31,856 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:11:31,856 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:11:32,792 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:11:33,063 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:33,064 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:11:33,185 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:33,186 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:11:33,306 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:33,314 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:11:33,314 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:11:33,371 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:11:33,379 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:11:33,456 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:11:33,456 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:11:36,243 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:11:41,448 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:11:41,449 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 7.99232 sec
2025-06-17 12:11:41,481 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.167489
2025-06-17 12:11:41,485 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:11:41,608 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:41,609 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:11:41,727 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:41,798 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:11:41,798 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:11:41,821 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:11:41,822 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:11:42,194 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:11:42,200 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:11:42,201 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:11:45,725 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5232152938842773
2025-06-17 12:11:45,783 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:11:45,896 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:45,922 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:11:45,922 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:11:46,040 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:46,058 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:11:46,060 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:11:46,061 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:11:46,177 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:46,202 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:11:46,202 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:11:46,318 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00001_mirifushort_uncal.fits>,).
2025-06-17 12:11:46,336 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:11:46,337 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:11:46,339 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:11:46,408 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rateints.fits
2025-06-17 12:11:46,408 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:11:46,409 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:11:46,474 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort_rate.fits
2025-06-17 12:11:46,474 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:11:46,475 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:11:46,665 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:11:46,678 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:11:46,687 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:11:46,697 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:11:46,715 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:11:46,716 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:11:46,716 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:11:46,717 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:11:46,718 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:11:46,719 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:11:46,720 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:11:46,721 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:11:46,722 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:11:46,723 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:11:46,723 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:11:46,724 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:11:46,725 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:11:46,726 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:11:46,727 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:11:46,727 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:11:46,729 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:11:46,730 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:11:46,731 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:11:46,732 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:11:46,733 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:11:46,852 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00002_mirifulong_uncal.fits'),).
2025-06-17 12:11:46,873 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:11:46,998 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:11:47,001 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:11:47,001 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:11:47,002 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2025-06-17 12:11:47,002 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:11:47,003 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:11:47,003 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:11:47,004 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:11:47,004 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:11:47,005 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:11:47,005 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:11:47,006 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:11:47,006 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:11:47,008 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:11:47,325 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:47,333 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:11:47,334 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:11:47,335 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:11:47,451 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:47,471 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:11:47,608 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:11:47,727 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:47,728 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:11:47,833 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:47,848 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:11:47,875 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:47,884 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:47,935 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:11:48,190 - stpipe.Detector1Pipeline.saturation - INFO - Detected 343 saturated pixels
2025-06-17 12:11:48,211 - stpipe.Detector1Pipeline.saturation - INFO - Detected 25 A/D floor pixels
2025-06-17 12:11:48,215 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:11:48,333 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:48,334 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:11:48,464 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:48,526 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:11:48,647 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:48,704 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:11:48,822 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:48,838 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:11:49,026 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:49,035 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:49,106 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:11:49,229 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:49,244 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2025-06-17 12:11:49,281 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:49,290 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:11:49,522 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:11:49,646 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:49,662 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:11:49,743 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:11:49,746 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:11:49,866 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:11:49,882 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:12:02,807 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:12:02,808 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:12:02,808 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:12:03,984 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:12:04,242 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:04,243 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:12:04,367 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:04,368 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:12:04,488 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:04,495 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:12:04,497 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:12:04,555 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:12:04,563 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:12:04,641 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:12:04,642 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:12:07,455 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:12:12,795 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 2
2025-06-17 12:12:12,796 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.15403 sec
2025-06-17 12:12:12,829 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.333385
2025-06-17 12:12:12,832 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:12:12,957 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:12,958 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:12:13,079 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:13,151 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:12:13,151 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:12:13,174 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:12:13,175 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:12:13,547 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:12:13,552 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:12:13,553 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:12:17,248 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6932179927825928
2025-06-17 12:12:17,305 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:12:17,429 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:17,454 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:12:17,455 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:12:17,580 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:17,598 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:12:17,600 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:12:17,602 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:12:17,724 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:17,748 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:12:17,749 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:12:17,867 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00002_mirifulong_uncal.fits>,).
2025-06-17 12:12:17,885 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:12:17,886 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:12:17,888 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:12:17,956 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rateints.fits
2025-06-17 12:12:17,957 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:12:17,958 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:12:18,023 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong_rate.fits
2025-06-17 12:12:18,024 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:12:18,024 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:12:18,205 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:12:18,217 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:12:18,226 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:12:18,236 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:12:18,254 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:12:18,255 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:12:18,256 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:12:18,257 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:12:18,258 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:12:18,259 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:12:18,259 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:12:18,260 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:12:18,261 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:12:18,262 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:12:18,263 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:12:18,264 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:12:18,264 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:12:18,265 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:12:18,266 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:12:18,267 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:12:18,269 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:12:18,270 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:12:18,271 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:12:18,272 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:12:18,273 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:12:18,401 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00002_mirifushort_uncal.fits'),).
2025-06-17 12:12:18,422 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:12:18,540 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:12:18,543 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:12:18,544 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:12:18,544 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:12:18,545 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:12:18,545 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:12:18,546 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:12:18,546 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:12:18,547 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:12:18,547 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:12:18,548 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:12:18,548 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:12:18,549 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:12:18,551 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:12:18,870 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:18,877 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:12:18,878 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:12:18,879 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:12:18,994 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:19,010 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:12:19,145 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:12:19,268 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:19,268 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:12:19,386 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:19,402 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:12:19,430 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:19,439 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:19,491 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:12:19,748 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1534 saturated pixels
2025-06-17 12:12:19,770 - stpipe.Detector1Pipeline.saturation - INFO - Detected 7 A/D floor pixels
2025-06-17 12:12:19,774 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:12:19,898 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:19,899 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:12:20,018 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:20,076 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:12:20,200 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:20,256 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:12:20,379 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:20,394 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:12:20,530 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:20,539 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:20,613 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:12:20,732 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:20,748 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:12:20,783 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:20,793 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:21,026 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:12:21,142 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:21,157 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:12:21,239 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:12:21,242 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:12:21,370 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:21,387 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:12:34,803 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:12:34,804 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:12:34,804 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:12:35,716 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:12:35,978 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:35,979 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:12:36,098 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:36,098 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:12:36,221 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:36,228 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:12:36,229 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:12:36,285 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:12:36,293 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:12:36,370 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:12:36,370 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:12:39,201 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:12:44,491 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 2
2025-06-17 12:12:44,492 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.12176 sec
2025-06-17 12:12:44,526 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.297480
2025-06-17 12:12:44,529 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:12:44,653 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:44,654 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:12:44,777 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:44,850 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:12:44,850 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:12:44,873 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:12:44,873 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:12:45,250 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:12:45,255 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:12:45,256 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:12:48,808 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5504674911499023
2025-06-17 12:12:48,865 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:12:48,988 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:49,013 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:12:49,013 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:12:49,139 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:49,156 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:12:49,158 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:12:49,160 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:12:49,283 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:49,308 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:12:49,309 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:12:49,431 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00002_mirifushort_uncal.fits>,).
2025-06-17 12:12:49,449 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:12:49,450 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:12:49,452 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:12:49,520 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rateints.fits
2025-06-17 12:12:49,521 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:12:49,522 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:12:49,587 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort_rate.fits
2025-06-17 12:12:49,587 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:12:49,588 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:12:49,770 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:12:49,783 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:12:49,793 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:12:49,803 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:12:49,821 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:12:49,822 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:12:49,823 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:12:49,824 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:12:49,825 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:12:49,826 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:12:49,827 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:12:49,828 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:12:49,829 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:12:49,830 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:12:49,831 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:12:49,832 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:12:49,832 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:12:49,833 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:12:49,834 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:12:49,835 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:12:49,837 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:12:49,838 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:12:49,839 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:12:49,840 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:12:49,841 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:12:49,967 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00003_mirifulong_uncal.fits'),).
2025-06-17 12:12:49,988 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:12:50,107 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00003_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:12:50,111 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:12:50,111 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:12:50,112 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2025-06-17 12:12:50,112 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:12:50,113 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:12:50,113 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:12:50,114 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:12:50,114 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:12:50,115 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:12:50,115 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:12:50,115 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:12:50,116 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:12:50,118 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:12:50,441 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:50,448 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:12:50,449 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:12:50,450 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:12:50,568 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:50,584 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:12:50,724 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:12:50,851 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:50,852 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:12:50,978 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:50,993 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:12:51,020 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:51,030 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:51,082 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:12:51,338 - stpipe.Detector1Pipeline.saturation - INFO - Detected 347 saturated pixels
2025-06-17 12:12:51,360 - stpipe.Detector1Pipeline.saturation - INFO - Detected 21 A/D floor pixels
2025-06-17 12:12:51,364 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:12:51,481 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:51,481 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:12:51,586 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:51,645 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:12:51,766 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:51,823 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:12:51,950 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:51,965 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:12:52,130 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:52,140 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:52,215 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:12:52,335 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:52,350 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2025-06-17 12:12:52,387 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:52,397 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:12:52,634 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:12:52,760 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:52,775 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:12:52,857 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:12:52,860 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:12:52,979 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:12:52,995 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:13:05,905 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:13:05,906 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:13:05,907 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:13:07,081 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:13:07,346 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:07,347 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:13:07,469 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:07,470 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:13:07,592 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:07,600 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:13:07,600 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:13:07,657 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:13:07,665 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:13:07,744 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:13:07,744 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:13:10,530 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:13:15,804 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 4
2025-06-17 12:13:15,804 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.06008 sec
2025-06-17 12:13:15,838 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.238045
2025-06-17 12:13:15,842 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:13:15,965 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:15,966 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:13:16,086 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:16,160 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:13:16,160 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:13:16,184 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:13:16,184 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:13:16,563 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:13:16,569 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:13:16,570 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:13:20,237 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6657509803771973
2025-06-17 12:13:20,305 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:13:20,439 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:20,465 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:13:20,466 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:13:20,597 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:20,617 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:13:20,619 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:13:20,621 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:13:20,748 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:20,774 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:13:20,775 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:13:20,907 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00003_mirifulong_uncal.fits>,).
2025-06-17 12:13:20,925 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:13:20,927 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:13:20,929 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:13:21,000 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rateints.fits
2025-06-17 12:13:21,000 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:13:21,001 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:13:21,066 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong_rate.fits
2025-06-17 12:13:21,067 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:13:21,067 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:13:21,254 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:13:21,267 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:13:21,276 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:13:21,286 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:13:21,304 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:13:21,305 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:13:21,306 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:13:21,307 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:13:21,308 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:13:21,309 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:13:21,310 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:13:21,311 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:13:21,312 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:13:21,313 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:13:21,313 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:13:21,314 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:13:21,315 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:13:21,316 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:13:21,317 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:13:21,318 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:13:21,320 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:13:21,321 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:13:21,322 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:13:21,323 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:13:21,323 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:13:21,446 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00003_mirifushort_uncal.fits'),).
2025-06-17 12:13:21,468 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:13:21,597 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00003_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:13:21,600 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:13:21,600 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:13:21,601 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:13:21,601 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:13:21,602 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:13:21,602 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:13:21,603 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:13:21,603 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:13:21,604 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:13:21,605 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:13:21,606 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:13:21,606 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:13:21,608 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:13:21,945 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:21,953 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:13:21,954 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:13:21,956 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:13:22,086 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:22,102 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:13:22,240 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:13:22,373 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:22,374 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:13:22,501 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:22,516 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:13:22,544 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:22,553 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:22,604 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:13:22,883 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1466 saturated pixels
2025-06-17 12:13:22,906 - stpipe.Detector1Pipeline.saturation - INFO - Detected 6 A/D floor pixels
2025-06-17 12:13:22,910 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:13:23,043 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:23,043 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:13:23,170 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:23,229 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:13:23,365 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:23,424 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:13:23,557 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:23,573 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:13:23,723 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:23,731 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:23,805 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:13:23,939 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:23,954 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:13:23,991 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:24,000 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:24,237 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:13:24,367 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:24,383 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:13:24,466 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:13:24,469 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:13:24,598 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:24,614 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:13:38,005 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:13:38,006 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:13:38,006 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:13:38,949 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:13:39,234 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:39,235 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:13:39,367 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:39,367 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:13:39,503 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:39,511 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:13:39,511 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:13:39,571 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:13:39,580 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:13:39,658 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:13:39,658 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:13:42,487 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:13:48,017 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:13:48,017 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.35906 sec
2025-06-17 12:13:48,051 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.540447
2025-06-17 12:13:48,056 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:13:48,195 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:48,196 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:13:48,327 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:48,404 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:13:48,404 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:13:48,428 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:13:48,429 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:13:48,813 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:13:48,819 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:13:48,820 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:13:52,373 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.55214786529541
2025-06-17 12:13:52,433 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:13:52,565 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:52,590 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:13:52,591 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:13:52,719 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:52,739 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:13:52,740 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:13:52,742 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:13:52,873 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:52,898 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:13:52,899 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:13:53,028 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00003_mirifushort_uncal.fits>,).
2025-06-17 12:13:53,047 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:13:53,049 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:13:53,051 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:13:53,125 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rateints.fits
2025-06-17 12:13:53,126 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:13:53,126 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:13:53,193 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort_rate.fits
2025-06-17 12:13:53,194 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:13:53,195 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:13:53,389 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:13:53,402 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:13:53,412 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:13:53,422 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:13:53,440 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:13:53,442 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:13:53,442 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:13:53,443 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:13:53,444 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:13:53,445 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:13:53,446 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:13:53,448 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:13:53,449 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:13:53,449 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:13:53,450 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:13:53,452 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:13:53,453 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:13:53,454 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:13:53,455 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:13:53,456 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:13:53,458 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:13:53,460 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:13:53,461 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:13:53,462 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:13:53,463 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:13:53,592 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00004_mirifulong_uncal.fits'),).
2025-06-17 12:13:53,614 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:13:53,741 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00004_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:13:53,744 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:13:53,745 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:13:53,745 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2025-06-17 12:13:53,746 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:13:53,746 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:13:53,747 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:13:53,748 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:13:53,748 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:13:53,749 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:13:53,749 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:13:53,750 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:13:53,750 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:13:53,752 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:13:54,080 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:54,088 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:13:54,088 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:13:54,090 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:13:54,220 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:54,236 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:13:54,373 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:13:54,504 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:54,505 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:13:54,632 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:54,648 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:13:54,676 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:54,685 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:54,736 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:13:55,012 - stpipe.Detector1Pipeline.saturation - INFO - Detected 352 saturated pixels
2025-06-17 12:13:55,033 - stpipe.Detector1Pipeline.saturation - INFO - Detected 26 A/D floor pixels
2025-06-17 12:13:55,037 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:13:55,171 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:55,172 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:13:55,304 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:55,364 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:13:55,497 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:55,555 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:13:55,687 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:55,703 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:13:55,879 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:55,887 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:55,959 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:13:56,090 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:56,106 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2025-06-17 12:13:56,143 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:56,152 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:13:56,393 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:13:56,529 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:56,546 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:13:56,632 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:13:56,635 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:13:56,767 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:13:56,784 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:14:09,609 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:14:09,610 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:14:09,611 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:14:10,795 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:14:11,070 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:11,070 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:14:11,200 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:11,201 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:14:11,329 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:11,337 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:14:11,338 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:14:11,398 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:14:11,407 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:14:11,487 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:14:11,488 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:14:14,348 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:14:19,800 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 1
2025-06-17 12:14:19,801 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.31282 sec
2025-06-17 12:14:19,835 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.497927
2025-06-17 12:14:19,839 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:14:19,973 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:19,974 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:14:20,106 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:20,182 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:14:20,182 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:14:20,206 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:14:20,207 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:14:20,581 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:14:20,586 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:14:20,587 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:14:24,271 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6820924282073975
2025-06-17 12:14:24,331 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:14:24,461 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:24,487 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:14:24,488 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:14:24,617 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:24,635 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:14:24,636 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:14:24,638 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:14:24,766 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:24,791 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:14:24,792 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:14:24,921 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00004_mirifulong_uncal.fits>,).
2025-06-17 12:14:24,939 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:14:24,941 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:14:24,943 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:14:25,013 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rateints.fits
2025-06-17 12:14:25,013 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:14:25,014 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:14:25,081 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong_rate.fits
2025-06-17 12:14:25,081 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:14:25,082 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:14:25,268 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:14:25,281 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:14:25,291 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:14:25,302 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:14:25,321 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:14:25,322 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:14:25,323 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:14:25,324 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:14:25,325 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:14:25,326 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:14:25,326 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:14:25,328 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:14:25,328 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:14:25,329 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:14:25,330 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:14:25,331 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:14:25,332 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:14:25,333 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:14:25,334 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:14:25,335 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:14:25,337 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:14:25,338 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:14:25,339 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:14:25,340 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:14:25,341 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:14:25,473 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03104_00004_mirifushort_uncal.fits'),).
2025-06-17 12:14:25,495 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:14:25,612 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00004_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:14:25,616 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:14:25,616 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:14:25,617 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:14:25,617 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:14:25,618 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:14:25,618 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:14:25,619 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:14:25,619 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:14:25,620 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:14:25,620 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:14:25,620 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:14:25,621 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:14:25,623 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:14:25,951 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:25,958 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:14:25,959 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:14:25,960 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:14:26,087 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:26,103 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:14:26,237 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:14:26,369 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:26,370 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:14:26,499 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:26,515 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:14:26,544 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:14:26,552 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:14:26,605 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:14:26,878 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1451 saturated pixels
2025-06-17 12:14:26,899 - stpipe.Detector1Pipeline.saturation - INFO - Detected 8 A/D floor pixels
2025-06-17 12:14:26,904 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:14:27,039 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:27,039 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:14:27,166 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:27,225 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:14:27,361 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:27,420 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:14:27,555 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:27,572 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:14:27,723 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:14:27,731 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:14:27,806 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:14:27,938 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:27,955 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:14:27,994 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:14:28,002 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:14:28,242 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:14:28,377 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:28,394 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:14:28,479 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:14:28,482 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:14:28,615 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:28,633 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:14:42,152 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:14:42,153 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:14:42,154 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:14:43,088 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:14:43,377 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:43,378 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:14:43,509 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:43,510 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:14:43,640 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:43,648 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:14:43,649 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:14:43,708 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:14:43,718 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:14:43,798 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:14:43,799 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:14:46,671 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:14:52,149 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:14:52,150 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.35072 sec
2025-06-17 12:14:52,184 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.535489
2025-06-17 12:14:52,187 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:14:52,319 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:52,320 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:14:52,448 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:52,519 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:14:52,520 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:14:52,543 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:14:52,543 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:14:52,921 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:14:52,926 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:14:52,927 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:14:56,464 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5349960327148438
2025-06-17 12:14:56,527 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:14:56,661 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:56,688 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:14:56,688 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:14:56,819 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:56,838 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:14:56,839 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:14:56,841 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:14:56,971 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:56,997 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:14:56,998 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:14:57,129 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03104_00004_mirifushort_uncal.fits>,).
2025-06-17 12:14:57,148 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:14:57,150 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:14:57,152 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:14:57,224 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rateints.fits
2025-06-17 12:14:57,225 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:14:57,225 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:14:57,295 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort_rate.fits
2025-06-17 12:14:57,296 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:14:57,297 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:14:57,487 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:14:57,500 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:14:57,510 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:14:57,520 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:14:57,539 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:14:57,540 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:14:57,541 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:14:57,542 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:14:57,544 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:14:57,545 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:14:57,546 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:14:57,547 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:14:57,548 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:14:57,550 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:14:57,550 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:14:57,551 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:14:57,552 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:14:57,553 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:14:57,554 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:14:57,555 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:14:57,558 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:14:57,559 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:14:57,560 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:14:57,561 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:14:57,562 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:14:57,696 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00001_mirifulong_uncal.fits'),).
2025-06-17 12:14:57,717 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:14:57,838 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:14:57,842 - 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)
2025-06-17 12:14:58,408 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:14:58,408 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:14:58,409 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2025-06-17 12:14:58,410 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:14:58,410 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:14:58,411 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:14:58,411 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:14:58,412 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:14:58,412 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:14:58,413 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:14:58,413 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:14:58,414 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:14:58,416 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:14:58,761 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:14:58,769 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:14:58,769 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:14:58,771 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:14:58,901 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:14:58,917 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:14:59,054 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:14:59,187 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:14:59,188 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:14:59,337 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:14:59,354 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:14:59,385 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:14:59,394 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:14:59,451 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:14:59,726 - stpipe.Detector1Pipeline.saturation - INFO - Detected 316 saturated pixels
2025-06-17 12:14:59,748 - stpipe.Detector1Pipeline.saturation - INFO - Detected 28 A/D floor pixels
2025-06-17 12:14:59,752 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:14:59,884 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:14:59,885 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:15:00,013 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:00,074 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:15:00,206 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:00,263 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:15:00,395 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:00,411 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:15:00,617 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:00,625 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:00,700 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:15:00,835 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:00,851 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2025-06-17 12:15:00,875 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:00,884 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:01,131 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:15:01,264 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:01,282 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:15:01,371 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:15:01,374 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:15:01,507 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:01,522 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:15:14,389 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:15:14,390 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:15:14,391 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:15:15,536 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:15:15,806 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:15,807 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:15:15,932 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:15,933 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:15:16,063 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:16,072 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:15:16,072 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:15:16,134 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:15:16,144 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:15:16,227 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:15:16,228 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:15:19,094 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:15:24,626 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 2
2025-06-17 12:15:24,626 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.39841 sec
2025-06-17 12:15:24,660 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.588657
2025-06-17 12:15:24,664 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:15:24,796 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:24,797 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:15:24,929 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:25,003 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:15:25,003 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:15:25,027 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:15:25,029 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:15:25,409 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:15:25,414 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:15:25,415 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:15:29,055 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.638849973678589
2025-06-17 12:15:29,118 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:15:29,251 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:29,277 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:15:29,277 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:15:29,411 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:29,429 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:15:29,431 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:15:29,433 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:15:29,558 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:29,584 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:15:29,585 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:15:29,714 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00001_mirifulong_uncal.fits>,).
2025-06-17 12:15:29,732 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:15:29,734 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:15:29,735 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:15:29,806 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rateints.fits
2025-06-17 12:15:29,806 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:15:29,807 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:15:29,874 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong_rate.fits
2025-06-17 12:15:29,875 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:15:29,875 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:15:30,069 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:15:30,082 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:15:30,092 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:15:30,103 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:15:30,121 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:15:30,123 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:15:30,123 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:15:30,125 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:15:30,125 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:15:30,126 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:15:30,127 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:15:30,128 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:15:30,129 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:15:30,130 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:15:30,131 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:15:30,131 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:15:30,132 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:15:30,133 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:15:30,134 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:15:30,135 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:15:30,138 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:15:30,139 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:15:30,140 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:15:30,141 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:15:30,141 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:15:30,271 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00001_mirifushort_uncal.fits'),).
2025-06-17 12:15:30,292 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:15:30,416 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:15:30,420 - 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)
2025-06-17 12:15:30,816 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:15:30,817 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2025-06-17 12:15:30,817 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:15:30,818 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:15:30,818 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:15:30,819 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:15:30,819 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:15:30,819 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:15:30,820 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:15:30,821 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:15:30,821 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:15:30,822 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:15:30,824 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:15:31,171 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:31,179 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:15:31,179 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:15:31,181 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:15:31,308 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:31,323 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:15:31,457 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:15:31,590 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:31,591 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:15:31,721 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:31,738 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:15:31,765 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:31,773 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:31,825 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:15:32,094 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1585 saturated pixels
2025-06-17 12:15:32,119 - stpipe.Detector1Pipeline.saturation - INFO - Detected 9 A/D floor pixels
2025-06-17 12:15:32,124 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:15:32,264 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:32,265 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:15:32,397 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:32,455 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:15:32,589 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:32,649 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:15:32,783 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:32,799 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:15:32,981 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:32,990 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:33,066 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:15:33,207 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:33,224 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:15:33,261 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:33,270 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:15:33,518 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:15:33,651 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:33,667 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:15:33,751 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:15:33,755 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:15:33,890 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:33,906 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:15:47,370 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:15:47,370 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:15:47,371 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:15:48,335 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:15:48,623 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:48,623 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:15:48,757 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:48,757 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:15:48,887 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:48,895 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:15:48,895 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:15:48,955 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:15:48,964 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:15:49,033 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:15:49,034 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:15:51,872 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:15:57,419 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 2
2025-06-17 12:15:57,419 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.38512 sec
2025-06-17 12:15:57,436 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.541435
2025-06-17 12:15:57,440 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:15:57,572 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:57,573 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:15:57,701 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:15:57,776 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:15:57,776 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:15:57,803 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:15:57,804 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:15:58,182 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:15:58,187 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:15:58,188 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:16:01,709 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5189194679260254
2025-06-17 12:16:01,768 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:16:01,896 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:16:01,924 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:16:01,924 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:16:02,052 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:16:02,071 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:16:02,073 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:16:02,074 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:16:02,200 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:16:02,229 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:16:02,230 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:16:02,359 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00001_mirifushort_uncal.fits>,).
2025-06-17 12:16:02,378 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:16:02,379 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:16:02,381 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:16:02,450 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rateints.fits
2025-06-17 12:16:02,451 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:16:02,452 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:16:02,519 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort_rate.fits
2025-06-17 12:16:02,520 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:16:02,520 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:16:02,720 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:16:02,733 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:16:02,743 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:16:02,753 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:16:02,771 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:16:02,772 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:16:02,773 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:16:02,775 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:16:02,775 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:16:02,776 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:16:02,778 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:16:02,779 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:16:02,780 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:16:02,781 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:16:02,782 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:16:02,783 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:16:02,784 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:16:02,785 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:16:02,786 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:16:02,787 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:16:02,789 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:16:02,790 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:16:02,791 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:16:02,792 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:16:02,792 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:16:02,926 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00002_mirifulong_uncal.fits'),).
2025-06-17 12:16:02,947 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:16:03,078 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:16:03,081 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:16:03,082 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:16:03,082 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2025-06-17 12:16:03,083 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:16:03,083 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:16:03,084 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:16:03,084 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:16:03,085 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:16:03,086 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:16:03,086 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:16:03,087 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:16:03,087 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:16:03,089 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:16:03,428 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:03,436 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:16:03,437 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:16:03,438 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:16:03,568 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:03,584 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:16:03,720 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:16:03,845 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:03,846 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:16:03,973 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:03,989 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:16:04,018 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:04,027 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:04,078 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:16:04,342 - stpipe.Detector1Pipeline.saturation - INFO - Detected 315 saturated pixels
2025-06-17 12:16:04,365 - stpipe.Detector1Pipeline.saturation - INFO - Detected 23 A/D floor pixels
2025-06-17 12:16:04,370 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:16:04,502 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:04,502 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:16:04,629 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:04,687 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:16:04,820 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:04,878 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:16:05,011 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:05,028 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:16:05,182 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:05,191 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:05,266 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:16:05,404 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:05,420 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2025-06-17 12:16:05,458 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:05,468 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:05,713 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:16:05,846 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:05,862 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:16:05,946 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:16:05,949 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:16:06,085 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:06,102 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:16:18,961 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:16:18,961 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:16:18,962 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:16:20,128 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:16:20,405 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:20,406 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:16:20,532 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:20,533 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:16:20,662 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:20,670 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:16:20,671 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:16:20,732 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:16:20,742 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:16:20,824 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:16:20,825 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:16:23,668 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:16:29,211 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 4
2025-06-17 12:16:29,212 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.38721 sec
2025-06-17 12:16:29,246 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.575469
2025-06-17 12:16:29,250 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:16:29,382 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:29,383 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:16:29,511 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:29,585 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:16:29,586 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:16:29,610 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:16:29,611 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:16:29,994 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:16:30,000 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:16:30,001 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:16:33,653 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6511104106903076
2025-06-17 12:16:33,714 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:16:33,849 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:33,875 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:16:33,876 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:16:34,002 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:34,021 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:16:34,023 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:16:34,025 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:16:34,152 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:34,178 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:16:34,178 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:16:34,306 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00002_mirifulong_uncal.fits>,).
2025-06-17 12:16:34,324 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:16:34,326 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:16:34,328 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:16:34,400 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rateints.fits
2025-06-17 12:16:34,401 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:16:34,402 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:16:34,469 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong_rate.fits
2025-06-17 12:16:34,470 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:16:34,471 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:16:34,665 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:16:34,678 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:16:34,688 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:16:34,698 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:16:34,716 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:16:34,717 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:16:34,718 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:16:34,719 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:16:34,720 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:16:34,721 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:16:34,722 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:16:34,723 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:16:34,724 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:16:34,725 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:16:34,726 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:16:34,727 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:16:34,728 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:16:34,729 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:16:34,730 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:16:34,731 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:16:34,733 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:16:34,734 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:16:34,735 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:16:34,736 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:16:34,737 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:16:34,866 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00002_mirifushort_uncal.fits'),).
2025-06-17 12:16:34,891 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:16:35,018 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:16:35,021 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:16:35,021 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2025-06-17 12:16:35,022 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:16:35,023 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:16:35,023 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:16:35,024 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:16:35,024 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:16:35,025 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:16:35,026 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:16:35,026 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:16:35,027 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:16:35,027 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:16:35,029 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:16:35,376 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:35,384 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:16:35,384 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:16:35,386 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:16:35,520 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:35,536 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:16:35,675 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:16:35,810 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:35,811 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:16:35,940 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:35,956 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:16:35,984 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:35,993 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:36,045 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:16:36,329 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1516 saturated pixels
2025-06-17 12:16:36,353 - stpipe.Detector1Pipeline.saturation - INFO - Detected 7 A/D floor pixels
2025-06-17 12:16:36,357 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:16:36,488 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:36,488 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:16:36,616 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:36,675 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:16:36,807 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:36,865 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:16:37,005 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:37,021 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:16:37,175 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:37,184 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:37,256 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:16:37,388 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:37,404 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:16:37,444 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:37,453 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:16:37,718 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:16:37,852 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:37,867 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:16:37,949 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:16:37,952 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:16:38,084 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:38,101 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:16:51,524 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:16:51,525 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:16:51,526 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:16:52,455 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:16:52,745 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:52,746 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:16:52,874 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:52,875 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:16:53,003 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:16:53,010 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:16:53,011 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:16:53,068 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:16:53,077 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:16:53,146 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:16:53,147 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:16:55,958 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:17:01,385 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:17:01,386 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.23884 sec
2025-06-17 12:17:01,403 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.392261
2025-06-17 12:17:01,407 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:17:01,542 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:17:01,543 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:17:01,673 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:17:01,746 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:17:01,747 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:17:01,773 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:17:01,773 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:17:02,159 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:17:02,165 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:17:02,166 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:17:05,676 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5096395015716553
2025-06-17 12:17:05,738 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:17:05,869 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:17:05,897 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:17:05,898 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:17:06,028 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:17:06,047 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:17:06,048 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:17:06,050 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:17:06,182 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:17:06,211 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:17:06,211 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:17:06,341 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00002_mirifushort_uncal.fits>,).
2025-06-17 12:17:06,359 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:17:06,361 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:17:06,363 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:17:06,433 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rateints.fits
2025-06-17 12:17:06,434 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:17:06,435 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:17:06,505 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort_rate.fits
2025-06-17 12:17:06,506 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:17:06,506 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:17:06,699 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:17:06,712 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:17:06,722 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:17:06,733 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:17:06,752 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:17:06,753 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:17:06,754 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:17:06,755 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:17:06,756 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:17:06,757 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:17:06,758 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:17:06,759 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:17:06,760 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:17:06,760 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:17:06,761 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:17:06,762 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:17:06,763 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:17:06,764 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:17:06,765 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:17:06,766 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:17:06,768 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:17:06,769 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:17:06,770 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:17:06,771 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:17:06,772 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:17:06,907 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00003_mirifulong_uncal.fits'),).
2025-06-17 12:17:06,930 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:17:07,058 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00003_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:17:07,061 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:17:07,062 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:17:07,062 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2025-06-17 12:17:07,063 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:17:07,063 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:17:07,064 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:17:07,065 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:17:07,065 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:17:07,066 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:17:07,066 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:17:07,067 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:17:07,067 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:17:07,069 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:17:07,409 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:07,417 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:17:07,417 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:17:07,419 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:17:07,551 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:07,567 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:17:07,710 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:17:07,842 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:07,843 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:17:07,972 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:07,988 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:17:08,016 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:08,025 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:08,079 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:17:08,351 - stpipe.Detector1Pipeline.saturation - INFO - Detected 317 saturated pixels
2025-06-17 12:17:08,373 - stpipe.Detector1Pipeline.saturation - INFO - Detected 22 A/D floor pixels
2025-06-17 12:17:08,378 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:17:08,512 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:08,513 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:17:08,642 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:08,700 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:17:08,834 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:08,892 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:17:09,028 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:09,044 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:17:09,224 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:09,232 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:09,307 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:17:09,440 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:09,456 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2025-06-17 12:17:09,494 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:09,503 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:09,739 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:17:09,872 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:09,887 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:17:09,969 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:17:09,972 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:17:10,104 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:10,121 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:17:22,970 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:17:22,971 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:17:22,972 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:17:24,140 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:17:24,417 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:24,418 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:17:24,549 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:24,550 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:17:24,681 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:24,689 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:17:24,690 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:17:24,751 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:17:24,760 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:17:24,841 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:17:24,842 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:17:27,608 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:17:32,846 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 4
2025-06-17 12:17:32,846 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.00427 sec
2025-06-17 12:17:32,880 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.190452
2025-06-17 12:17:32,884 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:17:33,015 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:33,015 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:17:33,144 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:33,218 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:17:33,218 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:17:33,241 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:17:33,242 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:17:33,622 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:17:33,628 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:17:33,629 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:17:37,244 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6136233806610107
2025-06-17 12:17:37,305 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:17:37,440 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:37,466 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:17:37,467 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:17:37,602 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:37,621 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:17:37,623 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:17:37,625 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:17:37,755 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:37,781 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:17:37,782 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:17:37,914 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00003_mirifulong_uncal.fits>,).
2025-06-17 12:17:37,933 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:17:37,935 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:17:37,937 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:17:38,007 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rateints.fits
2025-06-17 12:17:38,008 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:17:38,009 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:17:38,076 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong_rate.fits
2025-06-17 12:17:38,077 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:17:38,077 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:17:38,271 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:17:38,284 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:17:38,293 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:17:38,304 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:17:38,322 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:17:38,323 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:17:38,324 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:17:38,325 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:17:38,326 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:17:38,327 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:17:38,328 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:17:38,330 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:17:38,330 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:17:38,331 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:17:38,332 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:17:38,333 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:17:38,334 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:17:38,335 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:17:38,336 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:17:38,337 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:17:38,339 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:17:38,340 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:17:38,341 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:17:38,341 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:17:38,342 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:17:38,478 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00003_mirifushort_uncal.fits'),).
2025-06-17 12:17:38,500 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:17:38,631 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00003_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:17:38,634 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:17:38,635 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2025-06-17 12:17:38,636 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:17:38,636 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:17:38,637 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:17:38,637 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:17:38,638 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:17:38,639 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:17:38,639 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:17:38,640 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:17:38,640 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:17:38,641 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:17:38,642 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:17:38,985 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:38,993 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:17:38,994 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:17:38,995 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:17:39,125 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:39,141 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:17:39,277 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:17:39,411 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:39,412 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:17:39,544 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:39,560 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:17:39,590 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:39,598 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:39,650 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:17:39,920 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1446 saturated pixels
2025-06-17 12:17:39,942 - stpipe.Detector1Pipeline.saturation - INFO - Detected 9 A/D floor pixels
2025-06-17 12:17:39,946 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:17:40,080 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:40,081 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:17:40,210 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:40,267 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:17:40,398 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:40,456 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:17:40,596 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:40,612 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:17:40,767 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:40,776 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:40,851 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:17:40,985 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:41,002 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:17:41,039 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:41,049 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:17:41,299 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:17:41,430 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:41,446 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:17:41,531 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:17:41,534 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:17:41,668 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:41,685 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:17:55,223 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:17:55,224 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:17:55,224 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:17:56,160 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:17:56,457 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:56,458 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:17:56,589 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:56,590 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:17:56,719 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:17:56,726 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:17:56,727 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:17:56,785 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:17:56,793 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:17:56,859 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:17:56,860 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:17:59,707 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:18:05,192 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:18:05,193 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.33318 sec
2025-06-17 12:18:05,210 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.483828
2025-06-17 12:18:05,214 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:18:05,349 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:18:05,350 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:18:05,483 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:18:05,557 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:18:05,558 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:18:05,583 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:18:05,584 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:18:05,964 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:18:05,970 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:18:05,971 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:18:09,473 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5010480880737305
2025-06-17 12:18:09,533 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:18:09,668 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:18:09,696 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:18:09,697 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:18:09,829 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:18:09,848 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:18:09,850 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:18:09,852 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:18:09,985 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:18:10,013 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:18:10,014 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:18:10,146 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00003_mirifushort_uncal.fits>,).
2025-06-17 12:18:10,165 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:18:10,167 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:18:10,168 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:18:10,239 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rateints.fits
2025-06-17 12:18:10,240 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:18:10,241 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:18:10,308 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort_rate.fits
2025-06-17 12:18:10,309 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:18:10,309 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:18:10,510 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:18:10,523 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:18:10,534 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:18:10,545 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:18:10,563 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:18:10,565 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:18:10,566 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:18:10,567 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:18:10,568 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:18:10,569 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:18:10,570 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:18:10,571 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:18:10,572 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:18:10,573 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:18:10,574 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:18:10,576 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:18:10,577 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:18:10,577 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:18:10,578 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:18:10,579 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:18:10,581 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:18:10,583 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:18:10,584 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:18:10,585 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:18:10,586 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:18:10,720 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00004_mirifulong_uncal.fits'),).
2025-06-17 12:18:10,741 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:18:10,874 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00004_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:18:10,878 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:18:10,878 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:18:10,879 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2025-06-17 12:18:10,879 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:18:10,880 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:18:10,880 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:18:10,881 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:18:10,881 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:18:10,882 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:18:10,882 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:18:10,883 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:18:10,883 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:18:10,886 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:18:11,229 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:11,237 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:18:11,238 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:18:11,240 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:18:11,370 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:11,386 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:18:11,529 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:18:11,663 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:11,664 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:18:11,795 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:11,811 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:18:11,839 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:11,848 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:11,902 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:18:12,178 - stpipe.Detector1Pipeline.saturation - INFO - Detected 315 saturated pixels
2025-06-17 12:18:12,201 - stpipe.Detector1Pipeline.saturation - INFO - Detected 28 A/D floor pixels
2025-06-17 12:18:12,205 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:18:12,338 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:12,339 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:18:12,472 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:12,530 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:18:12,664 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:12,722 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:18:12,856 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:12,872 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:18:13,024 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:13,033 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:13,107 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:18:13,240 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:13,256 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2025-06-17 12:18:13,292 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:13,301 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:13,547 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:18:13,679 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:13,695 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:18:13,778 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:18:13,781 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:18:13,917 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:13,935 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:18:26,765 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:18:26,766 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:18:26,766 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:18:27,953 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:18:28,227 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:28,228 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:18:28,358 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:28,359 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:18:28,489 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:28,496 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:18:28,497 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:18:28,555 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:18:28,564 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:18:28,644 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:18:28,645 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:18:31,395 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:18:36,723 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 5
2025-06-17 12:18:36,724 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.07911 sec
2025-06-17 12:18:36,757 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.260468
2025-06-17 12:18:36,761 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:18:36,897 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:36,897 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:18:37,026 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:37,098 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:18:37,099 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:18:37,123 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:18:37,123 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:18:37,500 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:18:37,505 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:18:37,506 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:18:41,150 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.642460823059082
2025-06-17 12:18:41,211 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:18:41,344 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:41,370 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:18:41,371 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:18:41,499 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:41,518 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:18:41,519 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:18:41,521 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:18:41,650 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:41,677 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:18:41,678 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:18:41,806 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00004_mirifulong_uncal.fits>,).
2025-06-17 12:18:41,825 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:18:41,827 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:18:41,828 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:18:41,898 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rateints.fits
2025-06-17 12:18:41,899 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:18:41,899 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:18:41,966 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong_rate.fits
2025-06-17 12:18:41,967 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:18:41,968 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:18:42,163 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:18:42,177 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:18:42,187 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:18:42,198 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:18:42,216 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:18:42,217 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:18:42,218 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:18:42,219 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:18:42,220 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:18:42,221 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:18:42,222 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:18:42,223 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:18:42,224 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:18:42,225 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:18:42,226 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:18:42,227 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:18:42,227 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:18:42,228 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:18:42,229 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:18:42,230 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:18:42,232 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:18:42,233 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:18:42,236 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:18:42,237 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:18:42,238 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:18:42,373 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs003/uncal/jw01523003001_03106_00004_mirifushort_uncal.fits'),).
2025-06-17 12:18:42,394 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:18:42,525 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00004_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:18:42,529 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:18:42,529 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2025-06-17 12:18:42,530 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:18:42,530 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:18:42,531 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:18:42,531 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:18:42,532 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:18:42,532 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:18:42,533 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:18:42,533 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:18:42,534 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:18:42,534 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:18:42,536 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:18:42,881 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:42,889 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:18:42,890 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:18:42,891 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:18:43,023 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:43,040 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:18:43,181 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:18:43,314 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:43,315 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:18:43,448 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:43,463 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:18:43,492 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:43,501 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:43,555 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:18:43,827 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1408 saturated pixels
2025-06-17 12:18:43,850 - stpipe.Detector1Pipeline.saturation - INFO - Detected 5 A/D floor pixels
2025-06-17 12:18:43,854 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:18:43,989 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:43,990 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:18:44,122 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:44,182 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:18:44,316 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:44,374 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:18:44,507 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:44,524 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:18:44,666 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:44,675 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:44,751 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:18:44,888 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:44,904 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:18:44,945 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:44,954 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:18:45,194 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:18:45,329 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:45,344 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:18:45,428 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:18:45,431 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:18:45,569 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:18:45,585 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:18:58,914 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:18:58,915 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:18:58,915 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:18:59,877 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:19:00,173 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:00,174 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:19:00,306 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:00,306 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:19:00,437 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:00,445 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:19:00,445 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:19:00,504 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:19:00,513 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:19:00,579 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:19:00,580 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:19:03,412 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:19:08,803 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:19:08,803 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.22373 sec
2025-06-17 12:19:08,820 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.375681
2025-06-17 12:19:08,825 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:19:08,956 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:08,957 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:19:09,085 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:09,158 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:19:09,158 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:19:09,184 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:19:09,185 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:19:09,564 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:19:09,569 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:19:09,570 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:19:13,064 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.4931867122650146
2025-06-17 12:19:13,125 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:19:13,257 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:13,285 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:19:13,286 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:19:13,415 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:13,433 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:19:13,435 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:19:13,438 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:19:13,566 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:13,594 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:19:13,595 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:19:13,724 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523003001_03106_00004_mirifushort_uncal.fits>,).
2025-06-17 12:19:13,743 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:19:13,745 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:19:13,747 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:19:13,817 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rateints.fits
2025-06-17 12:19:13,817 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:19:13,818 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:19:13,886 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort_rate.fits
2025-06-17 12:19:13,886 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:19:13,887 - stpipe - INFO - Results used jwst version: 1.18.1
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')
2025-06-17 12:19:14,093 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:19:14,107 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:19:14,117 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:19:14,127 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:19:14,146 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:19:14,147 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:19:14,148 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:19:14,149 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:19:14,150 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:19:14,151 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:19:14,151 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:19:14,152 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:19:14,153 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:19:14,154 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:19:14,155 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:19:14,156 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:19:14,156 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:19:14,157 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:19:14,158 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:19:14,159 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:19:14,161 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:19:14,162 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:19:14,163 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:19:14,164 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:19:14,165 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:19:14,298 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00001_mirifulong_uncal.fits'),).
2025-06-17 12:19:14,321 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:19:14,452 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:19:14,455 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:19:14,456 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2025-06-17 12:19:14,457 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2025-06-17 12:19:14,457 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:19:14,457 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:19:14,458 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:19:14,458 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:19:14,459 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:19:14,460 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:19:14,460 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:19:14,460 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:19:14,461 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:19:14,463 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:19:14,804 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:14,812 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:19:14,813 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:19:14,814 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:19:14,944 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:14,960 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:19:15,101 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:19:15,235 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:15,236 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:19:15,367 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:15,383 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:19:15,411 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:15,420 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:15,474 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:19:15,745 - stpipe.Detector1Pipeline.saturation - INFO - Detected 326 saturated pixels
2025-06-17 12:19:15,767 - stpipe.Detector1Pipeline.saturation - INFO - Detected 26 A/D floor pixels
2025-06-17 12:19:15,772 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:19:15,905 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:15,906 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:19:16,037 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:16,096 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:19:16,229 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:16,287 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:19:16,422 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:16,438 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:19:16,626 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:16,635 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:16,710 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:19:16,844 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:16,861 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2025-06-17 12:19:16,904 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:16,913 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:17,155 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:19:17,293 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:17,310 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:19:17,397 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:19:17,401 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:19:17,536 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:17,552 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:19:30,402 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:19:30,403 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:19:30,403 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:19:31,572 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:19:31,846 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:31,846 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:19:31,979 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:31,980 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:19:32,115 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:32,124 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:19:32,125 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:19:32,185 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:19:32,195 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:19:32,262 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:19:32,263 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:19:35,142 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:19:40,742 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 7
2025-06-17 12:19:40,743 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.48013 sec
2025-06-17 12:19:40,760 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.636233
2025-06-17 12:19:40,764 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:19:40,902 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:40,902 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:19:41,034 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:41,110 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:19:41,111 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:19:41,137 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:19:41,137 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:19:41,523 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:19:41,528 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:19:41,528 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:19:45,179 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.649446487426758
2025-06-17 12:19:45,240 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:19:45,374 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:45,402 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:19:45,402 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:19:45,535 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:45,553 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:19:45,555 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:19:45,556 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:19:45,691 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:45,719 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:19:45,719 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:19:45,854 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00001_mirifulong_uncal.fits>,).
2025-06-17 12:19:45,873 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:19:45,874 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:19:45,876 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:19:45,948 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rateints.fits
2025-06-17 12:19:45,949 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:19:45,950 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:19:46,018 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong_rate.fits
2025-06-17 12:19:46,018 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:19:46,019 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:19:46,217 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:19:46,230 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:19:46,240 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:19:46,250 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:19:46,268 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:19:46,269 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:19:46,270 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:19:46,271 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:19:46,272 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:19:46,273 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:19:46,274 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:19:46,275 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:19:46,275 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:19:46,276 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:19:46,277 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:19:46,278 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:19:46,278 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:19:46,279 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:19:46,280 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:19:46,281 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:19:46,283 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:19:46,284 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:19:46,285 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:19:46,286 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:19:46,287 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:19:46,419 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00001_mirifushort_uncal.fits'),).
2025-06-17 12:19:46,442 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:19:46,572 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:19:46,575 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:19:46,576 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:19:46,576 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:19:46,577 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:19:46,577 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:19:46,578 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:19:46,578 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:19:46,579 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:19:46,579 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:19:46,580 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:19:46,580 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:19:46,581 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:19:46,583 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:19:46,927 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:46,935 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:19:46,936 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:19:46,938 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:19:47,071 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:47,087 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:19:47,222 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:19:47,356 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:47,357 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:19:47,490 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:47,505 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:19:47,534 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:47,543 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:47,599 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:19:47,870 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1697 saturated pixels
2025-06-17 12:19:47,893 - stpipe.Detector1Pipeline.saturation - INFO - Detected 9 A/D floor pixels
2025-06-17 12:19:47,897 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:19:48,032 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:48,033 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:19:48,167 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:48,227 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:19:48,362 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:48,421 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:19:48,561 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:48,577 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:19:48,736 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:48,745 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:48,821 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:19:48,954 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:48,970 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:19:49,009 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:49,019 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:19:49,265 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:19:49,402 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:49,417 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:19:49,501 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:19:49,505 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:19:49,637 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:19:49,653 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:20:03,056 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:20:03,057 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:20:03,058 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:20:04,008 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:20:04,310 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:04,311 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:20:04,443 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:04,444 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:20:04,578 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:04,586 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:20:04,586 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:20:04,649 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:20:04,658 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:20:04,741 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:20:04,742 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:20:07,515 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:20:12,881 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:20:12,882 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.13924 sec
2025-06-17 12:20:12,915 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.329648
2025-06-17 12:20:12,919 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:20:13,052 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:13,052 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:20:13,182 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:13,256 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:20:13,256 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:20:13,280 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:20:13,280 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:20:13,658 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:20:13,663 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:20:13,664 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:20:17,173 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5078399181365967
2025-06-17 12:20:17,232 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:20:17,365 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:17,392 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:20:17,393 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:20:17,521 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:17,539 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:20:17,541 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:20:17,543 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:20:17,673 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:17,701 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:20:17,701 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:20:17,832 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00001_mirifushort_uncal.fits>,).
2025-06-17 12:20:17,851 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:20:17,853 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:20:17,854 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:20:17,924 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rateints.fits
2025-06-17 12:20:17,925 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:20:17,925 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:20:17,992 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort_rate.fits
2025-06-17 12:20:17,992 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:20:17,993 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:20:18,177 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:20:18,190 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:20:18,200 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:20:18,210 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:20:18,229 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:20:18,230 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:20:18,231 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:20:18,232 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:20:18,233 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:20:18,234 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:20:18,235 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:20:18,236 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:20:18,236 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:20:18,237 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:20:18,238 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:20:18,239 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:20:18,240 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:20:18,240 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:20:18,241 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:20:18,242 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:20:18,244 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:20:18,245 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:20:18,247 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:20:18,248 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:20:18,250 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:20:18,383 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00002_mirifulong_uncal.fits'),).
2025-06-17 12:20:18,404 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:20:18,535 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:20:18,539 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:20:18,539 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits'.
2025-06-17 12:20:18,540 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits'.
2025-06-17 12:20:18,540 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:20:18,541 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:20:18,541 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:20:18,542 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:20:18,542 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:20:18,543 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:20:18,543 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:20:18,544 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:20:18,544 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:20:18,547 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:20:18,888 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:18,896 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:20:18,897 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:20:18,898 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:20:19,030 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:19,047 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:20:19,187 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:20:19,319 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:19,320 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:20:19,449 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:19,465 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:20:19,494 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:19,502 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:19,555 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:20:19,828 - stpipe.Detector1Pipeline.saturation - INFO - Detected 316 saturated pixels
2025-06-17 12:20:19,850 - stpipe.Detector1Pipeline.saturation - INFO - Detected 27 A/D floor pixels
2025-06-17 12:20:19,854 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:20:19,988 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:19,989 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:20:20,121 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:20,178 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:20:20,311 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:20,368 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:20:20,498 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:20,514 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:20:20,680 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:20,689 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:20,766 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:20:20,901 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:20,918 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0035.fits
2025-06-17 12:20:20,957 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:20,965 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:21,207 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:20:21,339 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:21,356 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:20:21,439 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:20:21,442 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:20:21,573 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:21,589 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:20:34,409 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:20:34,409 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:20:34,410 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:20:35,593 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:20:35,864 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:35,865 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:20:35,995 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:35,995 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:20:36,124 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:36,132 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:20:36,132 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:20:36,189 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:20:36,198 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:20:36,261 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:20:36,262 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:20:39,140 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:20:44,603 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:20:44,604 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.34278 sec
2025-06-17 12:20:44,621 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.489543
2025-06-17 12:20:44,625 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:20:44,756 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:44,757 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:20:44,886 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:44,959 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:20:44,960 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0033.fits
2025-06-17 12:20:44,986 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:20:44,986 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:20:45,366 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:20:45,371 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:20:45,372 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:20:49,019 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.646395206451416
2025-06-17 12:20:49,080 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:20:49,214 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:49,242 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:20:49,243 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:20:49,372 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:49,390 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:20:49,391 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:20:49,393 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:20:49,521 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:49,549 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:20:49,550 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:20:49,679 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00002_mirifulong_uncal.fits>,).
2025-06-17 12:20:49,698 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:20:49,700 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:20:49,702 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:20:49,773 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rateints.fits
2025-06-17 12:20:49,774 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:20:49,775 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:20:49,841 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong_rate.fits
2025-06-17 12:20:49,842 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:20:49,842 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:20:50,029 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:20:50,042 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:20:50,052 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:20:50,062 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:20:50,081 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:20:50,082 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:20:50,083 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:20:50,084 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:20:50,085 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:20:50,085 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:20:50,086 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:20:50,087 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:20:50,088 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:20:50,089 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:20:50,090 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:20:50,091 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:20:50,092 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:20:50,092 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:20:50,093 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:20:50,094 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:20:50,096 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:20:50,097 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:20:50,098 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:20:50,099 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:20:50,100 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:20:50,230 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02101_00002_mirifushort_uncal.fits'),).
2025-06-17 12:20:50,252 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:20:50,378 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:20:50,382 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:20:50,382 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:20:50,383 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:20:50,383 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:20:50,384 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:20:50,384 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:20:50,385 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:20:50,386 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:20:50,386 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:20:50,386 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:20:50,387 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:20:50,387 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:20:50,390 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:20:50,720 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:50,728 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:20:50,728 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:20:50,730 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:20:50,857 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:50,874 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:20:51,015 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:20:51,144 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:51,145 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:20:51,272 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:51,288 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:20:51,316 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:51,326 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:51,378 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:20:51,641 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1608 saturated pixels
2025-06-17 12:20:51,663 - stpipe.Detector1Pipeline.saturation - INFO - Detected 10 A/D floor pixels
2025-06-17 12:20:51,667 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:20:51,797 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:51,798 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:20:51,927 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:51,986 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:20:52,119 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:52,175 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:20:52,306 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:52,322 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:20:52,466 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:52,474 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:52,548 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:20:52,679 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:52,695 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:20:52,736 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:52,744 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:20:52,988 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:20:53,119 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:53,135 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:20:53,218 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:20:53,221 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:20:53,351 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:20:53,367 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:21:06,875 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:21:06,876 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:21:06,876 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:21:07,815 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:21:08,098 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:08,099 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:21:08,209 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:08,210 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:21:08,325 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:08,333 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:21:08,334 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:21:08,391 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:21:08,399 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:21:08,476 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:21:08,477 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:21:11,264 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:21:16,542 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:21:16,543 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.06569 sec
2025-06-17 12:21:16,576 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.243024
2025-06-17 12:21:16,580 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:21:16,710 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:16,711 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:21:16,842 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:16,914 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:21:16,915 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:21:16,939 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:21:16,940 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:21:17,323 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:21:17,328 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:21:17,329 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:21:20,840 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.509716033935547
2025-06-17 12:21:20,900 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:21:21,029 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:21,056 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:21:21,057 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:21:21,183 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:21,201 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:21:21,203 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:21:21,204 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:21:21,329 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:21,355 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:21:21,356 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:21:21,480 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02101_00002_mirifushort_uncal.fits>,).
2025-06-17 12:21:21,498 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:21:21,500 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:21:21,501 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:21:21,571 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rateints.fits
2025-06-17 12:21:21,572 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:21:21,573 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:21:21,639 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort_rate.fits
2025-06-17 12:21:21,640 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:21:21,640 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:21:21,838 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:21:21,851 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:21:21,862 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:21:21,873 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:21:21,892 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:21:21,893 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:21:21,894 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:21:21,895 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:21:21,896 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:21:21,897 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:21:21,898 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:21:21,899 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:21:21,900 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:21:21,901 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:21:21,902 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:21:21,903 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:21:21,904 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:21:21,905 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:21:21,906 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:21:21,907 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:21:21,909 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:21:21,910 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:21:21,911 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:21:21,912 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:21:21,913 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:21:22,040 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00001_mirifulong_uncal.fits'),).
2025-06-17 12:21:22,062 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:21:22,182 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:21:22,185 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:21:22,186 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:21:22,186 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2025-06-17 12:21:22,187 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:21:22,187 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:21:22,188 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:21:22,188 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:21:22,189 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:21:22,189 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:21:22,190 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:21:22,190 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:21:22,191 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:21:22,193 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:21:22,525 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:22,532 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:21:22,533 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:21:22,534 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:21:22,660 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:22,676 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:21:22,812 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:21:22,941 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:22,941 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:21:23,068 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:23,083 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:21:23,111 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:23,119 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:23,171 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:21:23,438 - stpipe.Detector1Pipeline.saturation - INFO - Detected 329 saturated pixels
2025-06-17 12:21:23,461 - stpipe.Detector1Pipeline.saturation - INFO - Detected 25 A/D floor pixels
2025-06-17 12:21:23,465 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:21:23,602 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:23,603 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:21:23,731 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:23,788 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:21:23,921 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:23,977 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:21:24,106 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:24,122 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:21:24,273 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:24,281 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:24,355 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:21:24,482 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:24,499 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2025-06-17 12:21:24,538 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:24,546 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:24,782 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:21:24,911 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:24,927 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:21:25,008 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:21:25,011 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:21:25,139 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:25,155 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:21:37,965 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:21:37,965 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:21:37,966 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:21:39,158 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:21:39,435 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:39,436 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:21:39,566 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:39,567 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:21:39,696 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:39,704 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:21:39,705 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:21:39,762 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:21:39,771 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:21:39,851 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:21:39,851 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:21:42,637 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:21:47,871 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:21:47,871 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.02007 sec
2025-06-17 12:21:47,904 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.200280
2025-06-17 12:21:47,908 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:21:48,035 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:48,036 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:21:48,163 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:48,235 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:21:48,236 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:21:48,259 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:21:48,260 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:21:48,638 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:21:48,644 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:21:48,644 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:21:52,286 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.640087127685547
2025-06-17 12:21:52,345 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:21:52,473 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:52,500 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:21:52,501 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:21:52,625 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:52,643 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:21:52,645 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:21:52,647 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:21:52,772 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:52,800 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:21:52,801 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:21:52,925 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00001_mirifulong_uncal.fits>,).
2025-06-17 12:21:52,944 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:21:52,945 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:21:52,947 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:21:53,015 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rateints.fits
2025-06-17 12:21:53,016 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:21:53,017 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:21:53,082 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong_rate.fits
2025-06-17 12:21:53,082 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:21:53,083 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:21:53,266 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:21:53,279 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:21:53,288 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:21:53,298 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:21:53,316 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:21:53,317 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:21:53,318 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:21:53,319 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:21:53,320 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:21:53,321 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:21:53,321 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:21:53,322 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:21:53,323 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:21:53,324 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:21:53,325 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:21:53,327 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:21:53,328 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:21:53,328 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:21:53,329 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:21:53,330 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:21:53,332 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:21:53,333 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:21:53,334 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:21:53,335 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:21:53,335 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:21:53,461 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00001_mirifushort_uncal.fits'),).
2025-06-17 12:21:53,482 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:21:53,599 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:21:53,602 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:21:53,602 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:21:53,603 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:21:53,604 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:21:53,604 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:21:53,605 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:21:53,606 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:21:53,606 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:21:53,606 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:21:53,607 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:21:53,607 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:21:53,608 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:21:53,610 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:21:53,941 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:53,949 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:21:53,949 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:21:53,951 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:21:54,077 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:54,092 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:21:54,228 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:21:54,356 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:54,357 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:21:54,477 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:54,492 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:21:54,520 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:54,530 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:54,580 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:21:54,846 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1607 saturated pixels
2025-06-17 12:21:54,868 - stpipe.Detector1Pipeline.saturation - INFO - Detected 2 A/D floor pixels
2025-06-17 12:21:54,872 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:21:55,001 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:55,002 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:21:55,128 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:55,186 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:21:55,314 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:55,371 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:21:55,501 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:55,516 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:21:55,667 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:55,676 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:55,748 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:21:55,881 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:55,897 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:21:55,938 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:55,947 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:21:56,181 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:21:56,308 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:56,324 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:21:56,405 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:21:56,408 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:21:56,537 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:21:56,553 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:22:10,151 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:22:10,152 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:22:10,152 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:22:11,108 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:22:11,402 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:11,403 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:22:11,531 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:11,532 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:22:11,662 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:11,670 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:22:11,671 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:22:11,729 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:22:11,737 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:22:11,816 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:22:11,816 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:22:14,652 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:22:20,027 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:22:20,027 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.21097 sec
2025-06-17 12:22:20,062 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.391440
2025-06-17 12:22:20,066 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:22:20,202 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:20,202 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:22:20,334 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:20,410 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:22:20,411 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:22:20,435 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:22:20,436 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:22:20,821 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:22:20,826 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:22:20,827 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:22:24,328 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.4996237754821777
2025-06-17 12:22:24,389 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:22:24,522 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:24,550 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:22:24,551 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:22:24,680 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:24,699 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:22:24,700 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:22:24,702 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:22:24,832 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:24,860 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:22:24,860 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:22:24,990 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00001_mirifushort_uncal.fits>,).
2025-06-17 12:22:25,009 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:22:25,011 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:22:25,014 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:22:25,088 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rateints.fits
2025-06-17 12:22:25,089 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:22:25,090 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:22:25,157 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort_rate.fits
2025-06-17 12:22:25,158 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:22:25,159 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:22:25,344 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:22:25,357 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:22:25,368 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:22:25,379 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:22:25,398 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:22:25,399 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:22:25,400 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:22:25,401 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:22:25,402 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:22:25,403 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:22:25,404 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:22:25,406 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:22:25,407 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:22:25,407 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:22:25,408 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:22:25,409 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:22:25,410 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:22:25,411 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:22:25,412 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:22:25,413 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:22:25,416 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:22:25,417 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:22:25,419 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:22:25,420 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:22:25,421 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:22:25,555 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00002_mirifulong_uncal.fits'),).
2025-06-17 12:22:25,577 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:22:25,698 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:22:25,702 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:22:25,702 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:22:25,703 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits'.
2025-06-17 12:22:25,703 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:22:25,704 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:22:25,704 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:22:25,705 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:22:25,705 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:22:25,705 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:22:25,706 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:22:25,706 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:22:25,707 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:22:25,709 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:22:26,037 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:26,045 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:22:26,045 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:22:26,047 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:22:26,175 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:26,192 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:22:26,330 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:22:26,460 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:26,461 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:22:26,588 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:26,604 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:22:26,631 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:26,640 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:26,690 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:22:26,950 - stpipe.Detector1Pipeline.saturation - INFO - Detected 319 saturated pixels
2025-06-17 12:22:26,972 - stpipe.Detector1Pipeline.saturation - INFO - Detected 25 A/D floor pixels
2025-06-17 12:22:26,976 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:22:27,106 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:27,107 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:22:27,237 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:27,296 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:22:27,426 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:27,482 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:22:27,613 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:27,628 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:22:27,770 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:27,778 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:27,851 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:22:27,981 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:27,996 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0036.fits
2025-06-17 12:22:28,035 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:28,044 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:28,281 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:22:28,415 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:28,431 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:22:28,514 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:22:28,518 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:22:28,650 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:28,666 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:22:41,464 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:22:41,465 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:22:41,465 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:22:42,628 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:22:42,898 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:42,899 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:22:43,025 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:43,026 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:22:43,154 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:43,162 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:22:43,163 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:22:43,220 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:22:43,229 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:22:43,308 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:22:43,309 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:22:46,116 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:22:51,349 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 4
2025-06-17 12:22:51,349 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.04092 sec
2025-06-17 12:22:51,383 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.220983
2025-06-17 12:22:51,387 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:22:51,517 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:51,518 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:22:51,647 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:51,721 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:22:51,722 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:22:51,745 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:22:51,746 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:22:52,123 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:22:52,129 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:22:52,129 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:22:55,768 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6370584964752197
2025-06-17 12:22:55,832 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:22:55,963 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:55,990 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:22:55,991 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:22:56,118 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:56,136 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:22:56,137 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:22:56,140 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:22:56,267 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:56,295 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:22:56,295 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:22:56,427 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00002_mirifulong_uncal.fits>,).
2025-06-17 12:22:56,446 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:22:56,447 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:22:56,449 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:22:56,522 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rateints.fits
2025-06-17 12:22:56,522 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:22:56,523 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:22:56,590 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong_rate.fits
2025-06-17 12:22:56,590 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:22:56,591 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:22:56,808 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:22:56,820 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:22:56,830 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:22:56,841 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:22:56,859 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:22:56,861 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:22:56,861 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:22:56,863 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:22:56,863 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:22:56,864 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:22:56,865 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:22:56,866 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:22:56,867 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:22:56,868 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:22:56,869 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:22:56,870 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:22:56,871 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:22:56,872 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:22:56,873 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:22:56,874 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:22:56,876 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:22:56,878 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:22:56,878 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:22:56,879 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:22:56,880 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:22:57,007 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02103_00002_mirifushort_uncal.fits'),).
2025-06-17 12:22:57,029 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:22:57,148 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:22:57,152 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:22:57,152 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits'.
2025-06-17 12:22:57,153 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:22:57,153 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:22:57,154 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:22:57,154 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:22:57,155 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:22:57,155 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:22:57,156 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:22:57,156 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:22:57,156 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:22:57,157 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:22:57,159 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:22:57,487 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:57,494 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:22:57,495 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:22:57,497 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:22:57,624 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:57,640 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:22:57,777 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:22:57,909 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:57,909 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:22:58,036 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:58,053 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:22:58,083 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:58,091 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:58,142 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:22:58,406 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1472 saturated pixels
2025-06-17 12:22:58,427 - stpipe.Detector1Pipeline.saturation - INFO - Detected 9 A/D floor pixels
2025-06-17 12:22:58,432 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:22:58,560 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:58,561 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:22:58,688 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:58,744 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:22:58,873 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:58,929 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:22:59,056 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:59,072 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:22:59,226 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:59,234 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:59,307 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:22:59,436 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:59,452 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:22:59,492 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:59,502 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:22:59,739 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:22:59,867 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:22:59,882 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:22:59,964 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:22:59,967 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:23:00,098 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:00,114 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:23:13,553 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:23:13,554 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:23:13,554 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:23:14,506 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:23:14,801 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:14,801 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:23:14,930 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:14,931 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:23:15,057 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:15,066 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:23:15,066 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:23:15,122 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:23:15,131 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:23:15,209 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:23:15,209 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:23:17,934 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:23:23,209 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:23:23,210 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.00016 sec
2025-06-17 12:23:23,242 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.176828
2025-06-17 12:23:23,246 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:23:23,379 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:23,379 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:23:23,508 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:23,580 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:23:23,581 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0007.fits
2025-06-17 12:23:23,604 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:23:23,605 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:23:23,979 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:23:23,984 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:23:23,985 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:23:27,447 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.4607441425323486
2025-06-17 12:23:27,509 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:23:27,641 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:27,668 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:23:27,668 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:23:27,801 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:27,819 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:23:27,821 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:23:27,822 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:23:27,948 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:27,975 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:23:27,976 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:23:28,102 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02103_00002_mirifushort_uncal.fits>,).
2025-06-17 12:23:28,120 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:23:28,121 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:23:28,123 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:23:28,192 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rateints.fits
2025-06-17 12:23:28,193 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:23:28,194 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:23:28,260 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort_rate.fits
2025-06-17 12:23:28,261 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:23:28,262 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:23:28,446 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:23:28,459 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:23:28,469 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:23:28,479 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:23:28,498 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:23:28,499 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:23:28,500 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:23:28,501 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:23:28,502 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:23:28,502 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:23:28,504 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:23:28,505 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:23:28,506 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:23:28,506 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:23:28,507 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:23:28,508 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:23:28,509 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:23:28,510 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:23:28,511 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:23:28,511 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:23:28,513 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:23:28,515 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:23:28,516 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:23:28,517 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:23:28,518 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:23:28,646 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00001_mirifulong_uncal.fits'),).
2025-06-17 12:23:28,667 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:23:28,785 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00001_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:23:28,788 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:23:28,789 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:23:28,789 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2025-06-17 12:23:28,790 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:23:28,790 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:23:28,790 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:23:28,791 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:23:28,792 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:23:28,792 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:23:28,793 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:23:28,793 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:23:28,793 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:23:28,795 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:23:29,126 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:29,135 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:23:29,135 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:23:29,137 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:23:29,267 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:29,282 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:23:29,421 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:23:29,553 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:29,554 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:23:29,684 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:29,699 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:23:29,727 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:23:29,737 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:23:29,788 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:23:30,045 - stpipe.Detector1Pipeline.saturation - INFO - Detected 320 saturated pixels
2025-06-17 12:23:30,067 - stpipe.Detector1Pipeline.saturation - INFO - Detected 25 A/D floor pixels
2025-06-17 12:23:30,072 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:23:30,201 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:30,202 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:23:30,327 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:30,385 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:23:30,514 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:30,569 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:23:30,698 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:30,714 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:23:30,875 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:23:30,884 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:23:30,959 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:23:31,093 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:31,109 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2025-06-17 12:23:31,148 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:23:31,158 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:23:31,397 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:23:31,528 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:31,543 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:23:31,627 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:23:31,630 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:23:31,762 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:31,777 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:23:44,703 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:23:44,704 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:23:44,704 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:23:45,879 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:23:46,153 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:46,154 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:23:46,287 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:46,288 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:23:46,418 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:46,426 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:23:46,427 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:23:46,485 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:23:46,494 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:23:46,573 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:23:46,573 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:23:49,367 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:23:54,513 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 3
2025-06-17 12:23:54,514 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 7.94032 sec
2025-06-17 12:23:54,562 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.136341
2025-06-17 12:23:54,566 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:23:54,698 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:54,699 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:23:54,825 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:54,896 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:23:54,896 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:23:54,919 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:23:54,920 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:23:55,292 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:23:55,297 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:23:55,298 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:23:58,921 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.621782064437866
2025-06-17 12:23:58,981 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:23:59,112 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:59,139 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:23:59,139 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:23:59,266 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:59,284 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:23:59,285 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:23:59,287 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:23:59,416 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:59,446 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:23:59,446 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:23:59,575 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00001_mirifulong_uncal.fits>,).
2025-06-17 12:23:59,594 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:23:59,596 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:23:59,598 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:23:59,667 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rateints.fits
2025-06-17 12:23:59,668 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:23:59,669 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:23:59,734 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong_rate.fits
2025-06-17 12:23:59,735 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:23:59,735 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:23:59,914 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:23:59,927 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:23:59,937 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:23:59,948 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:23:59,966 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:23:59,967 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:23:59,968 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:23:59,969 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:23:59,970 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:23:59,970 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:23:59,971 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:23:59,972 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:23:59,973 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:23:59,974 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:23:59,975 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:23:59,976 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:23:59,976 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:23:59,977 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:23:59,978 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:23:59,979 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:23:59,981 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:23:59,984 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:23:59,985 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:23:59,986 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:23:59,987 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:24:00,116 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00001_mirifushort_uncal.fits'),).
2025-06-17 12:24:00,136 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:24:00,255 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00001_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:24:00,258 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:24:00,259 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2025-06-17 12:24:00,260 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:24:00,260 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:24:00,261 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:24:00,261 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:24:00,262 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:24:00,262 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:24:00,262 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:24:00,263 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:24:00,263 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:24:00,264 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:24:00,266 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:24:00,594 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:00,601 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:24:00,602 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:24:00,603 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:24:00,733 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:00,749 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:24:00,889 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:24:01,036 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:01,036 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:24:01,168 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:01,183 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:24:01,214 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:01,223 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:01,275 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:24:01,532 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1606 saturated pixels
2025-06-17 12:24:01,553 - stpipe.Detector1Pipeline.saturation - INFO - Detected 4 A/D floor pixels
2025-06-17 12:24:01,557 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:24:01,685 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:01,686 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:24:01,813 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:01,870 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:24:02,001 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:02,057 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:24:02,187 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:02,203 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:24:02,366 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:02,374 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:02,450 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:24:02,581 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:02,597 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:24:02,637 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:02,645 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:02,880 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:24:03,007 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:03,022 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:24:03,104 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:24:03,107 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:24:03,238 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:03,253 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:24:16,816 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:24:16,817 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:24:16,818 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:24:17,755 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:24:18,045 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:18,046 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:24:18,175 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:18,177 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:24:18,304 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:18,311 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:24:18,312 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:24:18,368 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:24:18,376 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:24:18,436 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:24:18,437 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:24:21,200 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:24:26,573 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:24:26,574 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.13683 sec
2025-06-17 12:24:26,590 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.279161
2025-06-17 12:24:26,594 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:24:26,722 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:26,723 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:24:26,849 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:26,920 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:24:26,921 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:24:26,947 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:24:26,947 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:24:27,323 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:24:27,329 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:24:27,330 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:24:30,828 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.496924638748169
2025-06-17 12:24:30,889 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:24:31,024 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:31,051 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:24:31,052 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:24:31,180 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:31,199 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:24:31,201 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:24:31,203 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:24:31,332 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:31,360 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:24:31,361 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:24:31,491 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00001_mirifushort_uncal.fits>,).
2025-06-17 12:24:31,509 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:24:31,511 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:24:31,513 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:24:31,584 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rateints.fits
2025-06-17 12:24:31,584 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:24:31,585 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:24:31,652 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort_rate.fits
2025-06-17 12:24:31,652 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:24:31,653 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:24:31,840 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:24:31,853 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:24:31,863 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:24:31,874 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:24:31,893 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:24:31,894 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:24:31,895 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:24:31,896 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:24:31,897 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:24:31,897 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:24:31,898 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:24:31,900 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:24:31,901 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:24:31,901 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:24:31,902 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:24:31,903 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:24:31,904 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:24:31,905 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:24:31,906 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:24:31,906 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:24:31,908 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:24:31,909 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:24:31,911 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:24:31,911 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:24:31,912 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:24:32,040 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00002_mirifulong_uncal.fits'),).
2025-06-17 12:24:32,062 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:24:32,182 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00002_mirifulong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:24:32,185 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits'.
2025-06-17 12:24:32,186 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits'.
2025-06-17 12:24:32,186 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits'.
2025-06-17 12:24:32,187 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits'.
2025-06-17 12:24:32,187 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:24:32,188 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits'.
2025-06-17 12:24:32,188 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits'.
2025-06-17 12:24:32,189 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits'.
2025-06-17 12:24:32,189 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits'.
2025-06-17 12:24:32,190 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:24:32,190 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:24:32,191 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:24:32,193 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:24:32,523 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:32,530 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:24:32,531 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:24:32,532 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:24:32,664 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:32,679 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0052.fits
2025-06-17 12:24:32,817 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:24:32,949 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:32,950 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:24:33,083 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:33,098 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0035.fits
2025-06-17 12:24:33,130 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:33,139 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:33,189 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:24:33,458 - stpipe.Detector1Pipeline.saturation - INFO - Detected 319 saturated pixels
2025-06-17 12:24:33,480 - stpipe.Detector1Pipeline.saturation - INFO - Detected 26 A/D floor pixels
2025-06-17 12:24:33,485 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:24:33,619 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:33,619 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:24:33,751 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:33,809 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:24:33,941 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:33,998 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:24:34,131 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:34,147 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0079.fits
2025-06-17 12:24:34,320 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:34,328 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:34,401 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:24:34,533 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:34,549 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0033.fits
2025-06-17 12:24:34,590 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:34,598 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:24:34,835 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:24:34,969 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:34,985 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0016.fits
2025-06-17 12:24:35,068 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:24:35,071 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:24:35,202 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:35,218 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0108.fits
2025-06-17 12:24:48,022 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:24:48,023 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:24:48,024 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:24:49,189 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:24:49,469 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:49,470 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:24:49,603 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:49,603 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:24:49,736 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:49,744 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:24:49,745 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:24:49,803 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:24:49,812 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:24:49,892 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:24:49,893 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:24:52,700 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:24:57,936 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 2
2025-06-17 12:24:57,936 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.04356 sec
2025-06-17 12:24:57,970 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.225415
2025-06-17 12:24:57,974 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:24:58,099 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:58,100 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:24:58,224 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:24:58,295 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0086.fits
2025-06-17 12:24:58,295 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0006.fits
2025-06-17 12:24:58,318 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:24:58,319 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:24:58,689 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:24:58,694 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:24:58,695 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:25:02,299 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.6028530597686768
2025-06-17 12:25:02,360 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:25:02,494 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:25:02,521 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:25:02,522 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:25:02,652 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:25:02,671 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:25:02,673 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:25:02,675 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:25:02,802 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:25:02,828 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:25:02,829 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:25:02,955 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00002_mirifulong_uncal.fits>,).
2025-06-17 12:25:02,974 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:25:02,976 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:25:02,978 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:25:03,048 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rateints.fits
2025-06-17 12:25:03,049 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:25:03,049 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:25:03,114 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong_rate.fits
2025-06-17 12:25:03,115 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:25:03,116 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:25:03,300 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-06-17 12:25:03,313 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-06-17 12:25:03,323 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0007.asdf
2025-06-17 12:25:03,334 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0010.asdf
2025-06-17 12:25:03,352 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-06-17 12:25:03,354 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-06-17 12:25:03,354 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-06-17 12:25:03,355 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-06-17 12:25:03,356 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-06-17 12:25:03,357 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-06-17 12:25:03,358 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-06-17 12:25:03,359 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-06-17 12:25:03,360 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-06-17 12:25:03,361 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-06-17 12:25:03,361 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-06-17 12:25:03,362 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-06-17 12:25:03,363 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-06-17 12:25:03,364 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-06-17 12:25:03,365 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-06-17 12:25:03,365 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-06-17 12:25:03,367 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-06-17 12:25:03,369 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-06-17 12:25:03,370 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-06-17 12:25:03,370 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-06-17 12:25:03,371 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - XplyStep instance created.
2025-06-17 12:25:03,503 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args (np.str_('./mrs_demo_data/Obs004/uncal/jw01523004001_02105_00002_mirifushort_uncal.fits'),).
2025-06-17 12:25:03,525 - stpipe.Detector1Pipeline - 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: ''
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: sequential
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
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: ''
type: baseline
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: False
suffix: None
search_output_file: True
input_dir: ''
bright_use_group1: False
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: False
suffix: None
search_output_file: True
input_dir: ''
input_trapsfilled: ''
flag_pers_cutoff: 40.0
save_persistence: False
save_trapsfilled: True
modify_input: 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
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: ''
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: ''
2025-06-17 12:25:03,645 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00002_mirifushort_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-06-17 12:25:03,648 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits'.
2025-06-17 12:25:03,649 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits'.
2025-06-17 12:25:03,649 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits'.
2025-06-17 12:25:03,650 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits'.
2025-06-17 12:25:03,650 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-06-17 12:25:03,651 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits'.
2025-06-17 12:25:03,652 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits'.
2025-06-17 12:25:03,652 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits'.
2025-06-17 12:25:03,653 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits'.
2025-06-17 12:25:03,653 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-06-17 12:25:03,654 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-06-17 12:25:03,654 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-06-17 12:25:03,656 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-06-17 12:25:03,984 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:03,991 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-06-17 12:25:03,992 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-06-17 12:25:03,993 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-06-17 12:25:04,118 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:04,134 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0047.fits
2025-06-17 12:25:04,269 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-06-17 12:25:04,397 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:04,398 - stpipe.Detector1Pipeline.emicorr - INFO - Step skipped.
2025-06-17 12:25:04,525 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:04,541 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0033.fits
2025-06-17 12:25:04,569 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:25:04,578 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:25:04,629 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-06-17 12:25:04,894 - stpipe.Detector1Pipeline.saturation - INFO - Detected 1489 saturated pixels
2025-06-17 12:25:04,916 - stpipe.Detector1Pipeline.saturation - INFO - Detected 3 A/D floor pixels
2025-06-17 12:25:04,920 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-06-17 12:25:05,050 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:05,051 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-06-17 12:25:05,178 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:05,234 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-06-17 12:25:05,360 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:05,417 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-06-17 12:25:05,535 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:05,551 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0078.fits
2025-06-17 12:25:05,726 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:25:05,736 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:25:05,809 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-06-17 12:25:05,926 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:05,942 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0030.fits
2025-06-17 12:25:05,982 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:25:05,991 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:25:06,227 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-06-17 12:25:06,353 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:06,369 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0018.fits
2025-06-17 12:25:06,450 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-06-17 12:25:06,453 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-06-17 12:25:06,585 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:06,601 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0111.fits
2025-06-17 12:25:20,160 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-06-17 12:25:20,161 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=45, nframes=1, groupgap=0
2025-06-17 12:25:20,162 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-06-17 12:25:21,116 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-06-17 12:25:21,419 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:21,420 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-06-17 12:25:21,552 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:21,553 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-06-17 12:25:21,678 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:21,686 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-06-17 12:25:21,687 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-06-17 12:25:21,743 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:25:21,752 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:25:21,814 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-06-17 12:25:21,815 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-06-17 12:25:24,625 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-06-17 12:25:30,025 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-06-17 12:25:30,026 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.21132 sec
2025-06-17 12:25:30,043 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 8.356703
2025-06-17 12:25:30,046 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-06-17 12:25:30,180 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:30,181 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-06-17 12:25:30,314 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 45, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:30,391 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0087.fits
2025-06-17 12:25:30,392 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0054.fits
2025-06-17 12:25:30,418 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-06-17 12:25:30,419 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-06-17 12:25:30,798 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-06-17 12:25:30,803 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-06-17 12:25:30,804 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-06-17 12:25:34,324 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 3.5182652473449707
2025-06-17 12:25:34,383 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-06-17 12:25:34,509 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:34,536 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:25:34,537 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:25:34,657 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:34,675 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:25:34,676 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:25:34,678 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:25:34,802 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:34,829 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-06-17 12:25:34,830 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-06-17 12:25:34,956 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply running with args (<CubeModel(1, 1024, 1032) from jw01523004001_02105_00002_mirifushort_uncal.fits>,).
2025-06-17 12:25:34,975 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Multiplied everything by one in custom step!
2025-06-17 12:25:34,977 - stpipe.Detector1Pipeline.gain_scale.xply - INFO - Step xply done
2025-06-17 12:25:34,979 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-06-17 12:25:35,048 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rateints.fits
2025-06-17 12:25:35,049 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-06-17 12:25:35,050 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:25:35,116 - stpipe.Detector1Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort_rate.fits
2025-06-17 12:25:35,117 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-06-17 12:25:35,117 - stpipe - INFO - Results used jwst version: 1.18.1
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime so far: {time1 - time0:0.4f} seconds")
Runtime so far: 1664.1144 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 = {}
spec2dict['assign_wcs'], spec2dict['badpix_selfcal'], spec2dict['bkg_subtract'], spec2dict['flat_field'], spec2dict['srctype'] = {}, {}, {}, {}, {}
spec2dict['straylight'], spec2dict['fringe'], spec2dict['photom'], spec2dict['residual_fringe'], spec2dict['pixel_replace'] = {}, {}, {}, {}, {}
spec2dict['cube_build'], spec2dict['extract_1d'] = {}, {}
# 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')
2025-06-17 12:25:35,598 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:25:35,738 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf 965 bytes (1 / 1 files) (0 / 965 bytes)
2025-06-17 12:25:35,911 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:25:35,920 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf 987 bytes (1 / 1 files) (0 / 987 bytes)
2025-06-17 12:25:36,128 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:25:36,149 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:25:36,158 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:25:36,165 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf 2.0 K bytes (1 / 1 files) (0 / 2.0 K bytes)
2025-06-17 12:25:36,326 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:25:36,352 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:25:36,354 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:25:36,355 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:25:36,356 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:25:36,357 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:25:36,358 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:25:36,358 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:25:36,359 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:25:36,364 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:25:36,365 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:25:36,365 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:25:36,367 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:25:36,367 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:25:36,368 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:25:36,370 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:25:36,371 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:25:36,372 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:25:36,373 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:25:36,374 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:25:36,375 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:25:36,376 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:25:36,377 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:25:36,378 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:25:36,379 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:25:36,380 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:25:36,381 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:25:36,383 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:25:36,384 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:25:36,386 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:25:36,388 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:25:36,515 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:25:36,548 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:25:36,558 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:25:36,602 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00001_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:25:36,607 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf 123.8 K bytes (1 / 8 files) (0 / 106.3 M bytes)
2025-06-17 12:25:36,855 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits 21.2 M bytes (2 / 8 files) (123.8 K / 106.3 M bytes)
2025-06-17 12:25:37,749 - 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)
2025-06-17 12:25:38,235 - 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)
2025-06-17 12:25:38,459 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits 33.9 M bytes (5 / 8 files) (34.4 M / 106.3 M bytes)
2025-06-17 12:25:39,345 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf 38.0 M bytes (6 / 8 files) (68.2 M / 106.3 M bytes)
2025-06-17 12:25:40,044 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf 39.1 K bytes (7 / 8 files) (106.3 M / 106.3 M bytes)
2025-06-17 12:25:40,179 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf 2.6 K bytes (8 / 8 files) (106.3 M / 106.3 M bytes)
2025-06-17 12:25:40,386 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:25:40,386 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:25:40,387 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:25:40,387 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:25:40,387 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:25:40,388 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:25:40,388 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf'.
2025-06-17 12:25:40,389 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:25:40,389 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:25:40,389 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2025-06-17 12:25:40,390 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:25:40,390 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:25:40,391 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2025-06-17 12:25:40,391 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:25:40,392 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:25:40,392 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:25:40,392 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:25:40,394 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:25:40,394 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:25:40,394 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:25:40,395 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:25:40,395 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits'.
2025-06-17 12:25:40,396 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf'.
2025-06-17 12:25:40,396 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:25:40,397 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf'.
2025-06-17 12:25:40,397 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:25:40,398 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:25:40,399 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:25:40,405 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:25:40,406 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifulong
2025-06-17 12:25:40,406 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:25:40,574 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:25:41,193 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.00000873758768
2025-06-17 12:25:42,188 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:25:42,983 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.081781896 -70.085580813 81.089584616 -70.085580813 81.089584616 -70.082919753 81.081781896 -70.082919753
2025-06-17 12:25:42,984 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:25:42,989 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:25:43,136 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:25:43,137 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:25:43,278 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:25:43,278 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:25:43,421 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:25:43,422 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:25:43,561 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>, []).
2025-06-17 12:25:43,562 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:25:43,705 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:25:43,706 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:25:43,846 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:25:43,847 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:25:43,983 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:25:43,984 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:25:44,125 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:25:44,132 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:25:44,133 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:25:44,133 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:25:44,135 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:25:44,276 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:25:44,716 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:25:44,816 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:26:26,836 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:27:08,205 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.03718792460858822 DN/s
2025-06-17 12:27:08,206 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:27:08,208 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:27:08,388 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:27:08,481 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2025-06-17 12:27:08,481 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:27:08,482 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:27:08,482 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:27:08,944 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:27:09,133 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:27:09,153 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2025-06-17 12:27:09,177 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:27:09,178 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:27:09,178 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:27:09,590 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:27:09,593 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:27:09,782 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:27:09,783 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:27:09,955 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:27:09,956 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:27:10,129 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:27:10,157 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits
2025-06-17 12:27:10,158 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:27:10,570 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:27:10,570 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:27:10,571 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:27:10,571 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 12:27:10,626 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:27:10,628 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:27:10,628 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:27:10,639 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:27:11,172 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:27:11,373 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifulong_rate.fits>,).
2025-06-17 12:27:11,374 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:27:11,980 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits>,).
2025-06-17 12:27:11,980 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:27:12,174 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits>,).
2025-06-17 12:27:12,175 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:27:12,795 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits>,).
2025-06-17 12:27:12,796 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:27:12,797 - stpipe.Spec2Pipeline - 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
2025-06-17 12:27:12,799 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:27:12,799 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:27:13,223 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifulong_cal.fits
2025-06-17 12:27:13,224 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:27:13,224 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:27:13,584 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:27:13,666 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:27:13,675 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:27:13,695 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:27:13,705 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:27:13,713 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:27:13,736 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:27:13,738 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:27:13,739 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:27:13,740 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:27:13,741 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:27:13,742 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:27:13,743 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:27:13,744 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:27:13,749 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:27:13,750 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:27:13,751 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:27:13,752 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:27:13,753 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:27:13,754 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:27:13,755 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:27:13,757 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:27:13,759 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:27:13,760 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:27:13,761 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:27:13,762 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:27:13,763 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:27:13,763 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:27:13,765 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:27:13,766 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:27:13,767 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:27:13,767 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:27:13,769 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:27:13,770 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:27:13,771 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:27:13,773 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:27:14,052 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:27:14,088 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:27:14,098 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:27:14,137 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00001_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:27:14,141 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf 165.2 K bytes (1 / 6 files) (0 / 106.0 M bytes)
2025-06-17 12:27:14,428 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits 21.2 M bytes (2 / 6 files) (165.2 K / 106.0 M bytes)
2025-06-17 12:27:15,115 - 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)
2025-06-17 12:27:15,554 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits 33.9 M bytes (4 / 6 files) (34.0 M / 106.0 M bytes)
2025-06-17 12:27:16,340 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 106.0 M bytes)
2025-06-17 12:27:17,006 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf 52.5 K bytes (6 / 6 files) (105.9 M / 106.0 M bytes)
2025-06-17 12:27:17,169 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:27:17,170 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:27:17,170 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:27:17,170 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:27:17,171 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:27:17,171 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:27:17,172 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf'.
2025-06-17 12:27:17,172 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:27:17,173 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:27:17,173 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2025-06-17 12:27:17,174 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:27:17,174 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:27:17,175 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2025-06-17 12:27:17,176 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:27:17,177 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:27:17,177 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:27:17,178 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:27:17,179 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:27:17,179 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:27:17,179 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:27:17,180 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:27:17,180 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits'.
2025-06-17 12:27:17,181 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf'.
2025-06-17 12:27:17,182 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:27:17,182 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf'.
2025-06-17 12:27:17,183 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:27:17,183 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:27:17,184 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:27:17,191 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:27:17,191 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00001_mirifushort
2025-06-17 12:27:17,192 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:27:17,377 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:27:18,120 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.00000873758768
2025-06-17 12:27:19,417 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:27:20,316 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.083649307 -70.085039544 81.088154636 -70.085039544 81.088154636 -70.083436309 81.083649307 -70.083436309
2025-06-17 12:27:20,317 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:27:20,322 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:27:20,602 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:27:20,604 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:27:20,785 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:27:20,786 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:27:20,967 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:27:20,968 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:27:21,152 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>, []).
2025-06-17 12:27:21,152 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:27:21,333 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:27:21,334 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:27:21,516 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:27:21,517 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:27:21,701 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:27:21,702 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:27:21,886 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:27:21,894 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:27:21,894 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:27:21,895 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:27:21,897 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:27:22,079 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:27:22,656 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:27:22,755 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:27:59,378 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:28:40,727 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.023141281316234535 DN/s
2025-06-17 12:28:40,727 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:28:40,730 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:28:40,967 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:28:41,038 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2025-06-17 12:28:41,038 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:28:41,039 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:28:41,039 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:28:41,645 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:28:41,921 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:28:41,937 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2025-06-17 12:28:41,960 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:28:41,961 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:28:41,961 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:28:42,539 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:28:42,542 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:28:42,817 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:28:42,818 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:28:43,049 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:28:43,050 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:28:43,274 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:28:43,299 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits
2025-06-17 12:28:43,299 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:28:43,866 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:28:43,867 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:28:43,868 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:28:43,868 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 12:28:43,924 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:28:43,925 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:28:43,925 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:28:43,934 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:28:44,520 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:28:44,819 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00001_mirifushort_rate.fits>,).
2025-06-17 12:28:44,820 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:28:45,663 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits>,).
2025-06-17 12:28:45,664 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:28:45,925 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits>,).
2025-06-17 12:28:45,926 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:28:46,764 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits>,).
2025-06-17 12:28:46,765 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:28:46,766 - stpipe.Spec2Pipeline - 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
2025-06-17 12:28:46,768 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:28:46,768 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:28:47,294 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00001_mirifushort_cal.fits
2025-06-17 12:28:47,295 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:28:47,295 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:28:47,666 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:28:47,749 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:28:47,758 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:28:47,780 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:28:47,790 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:28:47,798 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:28:47,822 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:28:47,824 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:28:47,825 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:28:47,826 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:28:47,828 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:28:47,829 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:28:47,830 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:28:47,831 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:28:47,836 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:28:47,837 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:28:47,838 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:28:47,839 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:28:47,840 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:28:47,841 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:28:47,842 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:28:47,844 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:28:47,846 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:28:47,847 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:28:47,848 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:28:47,849 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:28:47,850 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:28:47,852 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:28:47,852 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:28:47,853 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:28:47,854 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:28:47,855 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:28:47,856 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:28:47,858 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:28:47,859 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:28:47,861 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:28:48,279 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:28:48,312 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:28:48,323 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:28:48,362 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00002_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:28:48,366 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:28:48,367 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:28:48,367 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:28:48,367 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:28:48,368 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:28:48,368 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:28:48,369 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf'.
2025-06-17 12:28:48,369 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:28:48,370 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:28:48,370 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2025-06-17 12:28:48,371 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:28:48,371 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:28:48,372 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2025-06-17 12:28:48,372 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:28:48,372 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:28:48,373 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:28:48,373 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:28:48,374 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:28:48,374 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:28:48,375 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:28:48,375 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:28:48,375 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits'.
2025-06-17 12:28:48,376 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf'.
2025-06-17 12:28:48,376 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:28:48,377 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf'.
2025-06-17 12:28:48,377 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:28:48,378 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:28:48,379 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:28:48,385 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:28:48,386 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifulong
2025-06-17 12:28:48,386 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:28:48,618 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:28:49,235 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:28:50,362 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:28:51,128 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.082515612 -70.084748017 81.090318058 -70.084748017 81.090318058 -70.082086940 81.082515612 -70.082086940
2025-06-17 12:28:51,130 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:28:51,134 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:28:51,374 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:28:51,375 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:28:51,596 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:28:51,597 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:28:51,815 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:28:51,816 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:28:52,048 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>, []).
2025-06-17 12:28:52,048 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:28:52,268 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:28:52,269 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:28:52,488 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:28:52,489 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:28:52,711 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:28:52,713 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:28:52,933 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:28:52,943 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:28:52,943 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:28:52,944 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:28:52,946 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:28:53,165 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:28:53,618 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:28:53,707 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:29:35,707 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:30:17,046 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.04422196000814438 DN/s
2025-06-17 12:30:17,046 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:30:17,049 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:30:17,311 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:30:17,382 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2025-06-17 12:30:17,383 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:30:17,383 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:30:17,383 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:30:17,847 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:30:18,151 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:30:18,167 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2025-06-17 12:30:18,190 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:30:18,191 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:30:18,192 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:30:18,632 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:30:18,635 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:30:18,936 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:30:18,937 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:30:19,189 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:30:19,190 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:30:19,443 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:30:19,468 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits
2025-06-17 12:30:19,469 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:30:19,900 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:30:19,901 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:30:19,901 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:30:19,902 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 12:30:19,955 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:30:19,956 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:30:19,957 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:30:19,966 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:30:20,495 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:30:20,809 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifulong_rate.fits>,).
2025-06-17 12:30:20,810 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:30:21,524 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits>,).
2025-06-17 12:30:21,525 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:30:21,804 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits>,).
2025-06-17 12:30:21,804 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:30:22,523 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits>,).
2025-06-17 12:30:22,524 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:30:22,525 - stpipe.Spec2Pipeline - 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
2025-06-17 12:30:22,527 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:30:22,527 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:30:22,960 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifulong_cal.fits
2025-06-17 12:30:22,961 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:30:22,962 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:30:23,334 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:30:23,421 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:30:23,430 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:30:23,451 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:30:23,462 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:30:23,471 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:30:23,495 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:30:23,497 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:30:23,498 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:30:23,499 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:30:23,500 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:30:23,501 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:30:23,502 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:30:23,503 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:30:23,508 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:30:23,509 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:30:23,510 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:30:23,510 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:30:23,511 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:30:23,512 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:30:23,513 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:30:23,515 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:30:23,517 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:30:23,518 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:30:23,519 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:30:23,520 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:30:23,521 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:30:23,522 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:30:23,523 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:30:23,524 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:30:23,525 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:30:23,526 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:30:23,526 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:30:23,528 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:30:23,529 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:30:23,531 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:30:23,944 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:30:23,980 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:30:23,990 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:30:24,029 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00002_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:30:24,034 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:30:24,035 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:30:24,035 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:30:24,035 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:30:24,036 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:30:24,036 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:30:24,037 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf'.
2025-06-17 12:30:24,037 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:30:24,038 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:30:24,038 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2025-06-17 12:30:24,039 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:30:24,039 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:30:24,039 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2025-06-17 12:30:24,040 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:30:24,040 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:30:24,041 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:30:24,041 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:30:24,041 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:30:24,042 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:30:24,042 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:30:24,043 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:30:24,043 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits'.
2025-06-17 12:30:24,044 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf'.
2025-06-17 12:30:24,044 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:30:24,045 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf'.
2025-06-17 12:30:24,045 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:30:24,046 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:30:24,047 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:30:24,053 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:30:24,054 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00002_mirifushort
2025-06-17 12:30:24,054 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:30:24,320 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:30:25,104 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.00000873758768
2025-06-17 12:30:26,524 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:30:27,442 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.084382953 -70.084206739 81.088888133 -70.084206739 81.088888133 -70.082603498 81.084382953 -70.082603498
2025-06-17 12:30:27,443 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:30:27,448 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:30:27,823 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:30:27,826 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:30:28,093 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:30:28,094 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:30:28,355 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:30:28,356 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:30:28,621 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>, []).
2025-06-17 12:30:28,622 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:30:28,885 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:30:28,886 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:30:29,150 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:30:29,151 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:30:29,411 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:30:29,412 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:30:29,673 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:30:29,681 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:30:29,682 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:30:29,683 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:30:29,684 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:30:29,945 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:30:30,533 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:30:30,629 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:31:07,334 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:31:48,860 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.026081911762333494 DN/s
2025-06-17 12:31:48,861 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:31:48,864 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:31:49,166 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:31:49,234 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2025-06-17 12:31:49,235 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:31:49,235 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:31:49,235 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:31:49,841 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:31:50,182 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:31:50,199 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2025-06-17 12:31:50,221 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:31:50,222 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:31:50,223 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:31:50,795 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:31:50,798 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:31:51,132 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:31:51,133 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:31:51,427 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:31:51,428 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:31:51,724 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:31:51,747 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits
2025-06-17 12:31:51,748 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:31:52,305 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:31:52,306 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:31:52,306 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:31:52,307 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 12:31:52,360 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:31:52,362 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:31:52,362 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:31:52,371 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:31:52,947 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:31:53,303 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00002_mirifushort_rate.fits>,).
2025-06-17 12:31:53,304 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:31:54,213 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits>,).
2025-06-17 12:31:54,214 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:31:54,542 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits>,).
2025-06-17 12:31:54,542 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:31:55,458 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits>,).
2025-06-17 12:31:55,459 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:31:55,461 - stpipe.Spec2Pipeline - 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
2025-06-17 12:31:55,462 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:31:55,463 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:31:55,981 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00002_mirifushort_cal.fits
2025-06-17 12:31:55,982 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:31:55,982 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:31:56,348 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:31:56,428 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:31:56,436 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:31:56,456 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:31:56,465 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:31:56,473 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:31:56,497 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:31:56,498 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:31:56,499 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:31:56,501 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:31:56,502 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:31:56,503 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:31:56,504 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:31:56,505 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:31:56,509 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:31:56,510 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:31:56,511 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:31:56,512 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:31:56,512 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:31:56,513 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:31:56,514 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:31:56,516 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:31:56,517 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:31:56,518 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:31:56,519 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:31:56,520 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:31:56,521 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:31:56,522 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:31:56,523 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:31:56,524 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:31:56,525 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:31:56,526 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:31:56,527 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:31:56,528 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:31:56,529 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:31:56,531 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:31:56,984 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:31:57,019 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:31:57,029 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:31:57,066 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00003_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:31:57,071 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:31:57,071 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:31:57,071 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:31:57,072 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:31:57,072 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:31:57,073 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:31:57,073 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf'.
2025-06-17 12:31:57,074 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:31:57,074 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:31:57,074 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2025-06-17 12:31:57,075 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:31:57,075 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:31:57,076 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2025-06-17 12:31:57,078 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:31:57,078 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:31:57,079 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:31:57,079 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:31:57,080 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:31:57,080 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:31:57,081 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:31:57,081 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:31:57,081 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits'.
2025-06-17 12:31:57,082 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf'.
2025-06-17 12:31:57,083 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:31:57,083 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf'.
2025-06-17 12:31:57,084 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:31:57,084 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:31:57,085 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:31:57,092 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:31:57,093 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifulong
2025-06-17 12:31:57,093 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:31:57,377 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:31:57,964 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.00000873758768
2025-06-17 12:31:59,120 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:31:59,863 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.081860054 -70.085441090 81.089662724 -70.085441090 81.089662724 -70.082780028 81.081860054 -70.082780028
2025-06-17 12:31:59,864 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:31:59,869 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:32:00,167 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:32:00,169 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:32:00,446 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:32:00,446 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:32:00,718 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:32:00,718 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:32:00,996 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>, []).
2025-06-17 12:32:00,997 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:32:01,271 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:32:01,272 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:32:01,539 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:32:01,540 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:32:01,809 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:32:01,810 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:32:02,077 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:32:02,084 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:32:02,085 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:32:02,085 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:32:02,087 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:32:02,343 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:32:02,763 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:32:02,849 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:32:44,857 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:33:26,234 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.035685233771800995 DN/s
2025-06-17 12:33:26,235 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:33:26,238 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:33:26,550 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:33:26,622 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2025-06-17 12:33:26,623 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:33:26,623 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:33:26,624 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:33:27,094 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:33:27,442 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:33:27,458 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2025-06-17 12:33:27,481 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:33:27,482 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:33:27,483 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:33:27,911 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:33:27,914 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:33:28,258 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:33:28,259 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:33:28,570 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:33:28,571 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:33:28,904 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:33:28,930 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits
2025-06-17 12:33:28,931 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:33:29,380 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:33:29,380 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:33:29,381 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:33:29,381 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 12:33:29,435 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:33:29,436 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:33:29,437 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:33:29,447 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:33:29,980 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:33:30,350 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifulong_rate.fits>,).
2025-06-17 12:33:30,352 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:33:31,138 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits>,).
2025-06-17 12:33:31,139 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:33:31,483 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits>,).
2025-06-17 12:33:31,484 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:33:32,261 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits>,).
2025-06-17 12:33:32,262 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:33:32,263 - stpipe.Spec2Pipeline - 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
2025-06-17 12:33:32,265 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:33:32,265 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:33:32,703 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifulong_cal.fits
2025-06-17 12:33:32,703 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:33:32,704 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:33:33,066 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:33:33,149 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:33:33,158 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:33:33,178 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:33:33,187 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:33:33,195 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:33:33,219 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:33:33,220 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:33:33,221 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:33:33,222 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:33:33,223 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:33:33,225 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:33:33,226 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:33:33,227 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:33:33,231 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:33:33,232 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:33:33,233 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:33:33,234 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:33:33,235 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:33:33,236 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:33:33,237 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:33:33,239 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:33:33,241 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:33:33,242 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:33:33,243 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:33:33,244 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:33:33,245 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:33:33,246 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:33:33,247 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:33:33,248 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:33:33,249 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:33:33,250 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:33:33,251 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:33:33,252 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:33:33,254 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:33:33,255 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:33:33,675 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:33:33,710 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:33:33,720 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:33:33,756 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00003_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:33:33,761 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:33:33,761 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:33:33,761 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:33:33,762 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:33:33,762 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:33:33,762 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:33:33,763 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf'.
2025-06-17 12:33:33,763 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:33:33,764 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:33:33,764 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2025-06-17 12:33:33,764 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:33:33,765 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:33:33,765 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2025-06-17 12:33:33,766 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:33:33,767 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:33:33,767 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:33:33,767 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:33:33,768 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:33:33,768 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:33:33,769 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:33:33,769 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:33:33,769 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits'.
2025-06-17 12:33:33,770 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf'.
2025-06-17 12:33:33,771 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:33:33,771 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf'.
2025-06-17 12:33:33,772 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:33:33,772 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:33:33,773 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:33:33,779 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:33:33,780 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00003_mirifushort
2025-06-17 12:33:33,780 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:33:34,092 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:33:34,838 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.00000873758768
2025-06-17 12:33:36,269 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:33:37,137 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.083727451 -70.084899819 81.088232752 -70.084899819 81.088232752 -70.083296584 81.083727451 -70.083296584
2025-06-17 12:33:37,138 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:33:37,143 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:33:37,544 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:33:37,545 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:33:37,874 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:33:37,875 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:33:38,185 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:33:38,186 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:33:38,496 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>, []).
2025-06-17 12:33:38,497 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:33:38,813 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:33:38,813 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:33:39,124 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:33:39,124 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:33:39,436 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:33:39,437 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:33:39,743 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:33:39,750 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:33:39,751 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:33:39,751 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:33:39,753 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:33:40,072 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:33:40,657 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:33:40,751 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:34:17,373 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:34:58,669 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.037794278498754524 DN/s
2025-06-17 12:34:58,669 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:34:58,673 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:34:59,059 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:34:59,131 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2025-06-17 12:34:59,131 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:34:59,132 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:34:59,132 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:34:59,740 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:35:00,151 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:35:00,167 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2025-06-17 12:35:00,190 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:35:00,190 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:35:00,191 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:35:00,777 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:35:00,779 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:35:01,194 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:35:01,195 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:35:01,563 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:35:01,564 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:35:01,941 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:35:01,965 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits
2025-06-17 12:35:01,965 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:35:02,531 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:35:02,532 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:35:02,533 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:35:02,533 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 12:35:02,588 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:35:02,589 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:35:02,590 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:35:02,599 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:35:03,190 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:35:03,625 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00003_mirifushort_rate.fits>,).
2025-06-17 12:35:03,627 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:35:04,617 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits>,).
2025-06-17 12:35:04,618 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:35:05,021 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits>,).
2025-06-17 12:35:05,022 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:35:06,013 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits>,).
2025-06-17 12:35:06,014 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:35:06,015 - stpipe.Spec2Pipeline - 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
2025-06-17 12:35:06,017 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:35:06,017 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:35:06,552 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00003_mirifushort_cal.fits
2025-06-17 12:35:06,553 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:35:06,553 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:35:06,931 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:35:07,015 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:35:07,024 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:35:07,046 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:35:07,057 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:35:07,065 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:35:07,090 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:35:07,091 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:35:07,092 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:35:07,093 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:35:07,095 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:35:07,096 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:35:07,096 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:35:07,097 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:35:07,102 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:35:07,103 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:35:07,104 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:35:07,105 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:35:07,106 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:35:07,107 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:35:07,108 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:35:07,110 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:35:07,111 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:35:07,112 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:35:07,113 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:35:07,114 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:35:07,115 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:35:07,116 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:35:07,117 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:35:07,117 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:35:07,118 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:35:07,119 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:35:07,120 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:35:07,124 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:35:07,126 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:35:07,127 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:35:07,732 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:35:07,766 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:35:07,776 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:35:07,815 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00004_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:35:07,819 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:35:07,820 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:35:07,820 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:35:07,821 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:35:07,821 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:35:07,822 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:35:07,822 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf'.
2025-06-17 12:35:07,823 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:35:07,824 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:35:07,824 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2025-06-17 12:35:07,825 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:35:07,825 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:35:07,825 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2025-06-17 12:35:07,826 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:35:07,826 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:35:07,827 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:35:07,827 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:35:07,827 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:35:07,828 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:35:07,828 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:35:07,829 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:35:07,829 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits'.
2025-06-17 12:35:07,830 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf'.
2025-06-17 12:35:07,830 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:35:07,831 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf'.
2025-06-17 12:35:07,831 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:35:07,831 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:35:07,832 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:35:07,840 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:35:07,841 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifulong
2025-06-17 12:35:07,842 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:35:08,190 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:35:08,799 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:35:10,057 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:35:10,817 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.082595083 -70.084610185 81.090397469 -70.084610185 81.090397469 -70.081949112 81.082595083 -70.081949112
2025-06-17 12:35:10,818 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:35:10,823 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:35:11,181 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:35:11,183 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:35:11,526 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:35:11,527 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:35:11,873 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:35:11,874 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:35:12,225 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>, []).
2025-06-17 12:35:12,226 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:35:12,569 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:35:12,570 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:35:12,913 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:35:12,914 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:35:13,256 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:35:13,257 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:35:13,604 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:35:13,612 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:35:13,612 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:35:13,613 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:35:13,614 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:35:13,965 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:35:14,410 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:35:14,501 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:35:56,507 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:36:37,865 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.04083895683288574 DN/s
2025-06-17 12:36:37,866 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:36:37,869 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:36:38,234 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:36:38,300 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2025-06-17 12:36:38,300 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:36:38,301 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:36:38,301 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:36:38,752 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:36:39,142 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:36:39,157 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2025-06-17 12:36:39,179 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:36:39,179 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:36:39,180 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:36:39,595 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:36:39,598 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:36:39,990 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:36:39,991 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:36:40,346 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:36:40,347 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:36:40,701 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:36:40,724 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits
2025-06-17 12:36:40,724 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:36:41,133 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:36:41,133 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:36:41,134 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:36:41,134 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 12:36:41,183 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:36:41,184 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:36:41,185 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:36:41,193 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:36:41,701 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:36:42,099 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifulong_rate.fits>,).
2025-06-17 12:36:42,100 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:36:42,917 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits>,).
2025-06-17 12:36:42,918 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:36:43,303 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits>,).
2025-06-17 12:36:43,304 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:36:44,108 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits>,).
2025-06-17 12:36:44,108 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:36:44,110 - stpipe.Spec2Pipeline - 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
2025-06-17 12:36:44,111 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:36:44,112 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:36:44,523 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifulong_cal.fits
2025-06-17 12:36:44,524 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:36:44,524 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:36:44,880 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:36:44,959 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:36:44,967 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:36:44,987 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:36:44,996 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:36:45,004 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:36:45,027 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:36:45,028 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:36:45,029 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:36:45,030 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:36:45,031 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:36:45,032 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:36:45,033 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:36:45,034 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:36:45,038 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:36:45,039 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:36:45,040 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:36:45,041 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:36:45,041 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:36:45,042 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:36:45,043 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:36:45,045 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:36:45,047 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:36:45,047 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:36:45,048 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:36:45,049 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:36:45,050 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:36:45,051 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:36:45,052 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:36:45,052 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:36:45,056 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:36:45,056 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:36:45,057 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:36:45,058 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:36:45,060 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:36:45,061 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:36:45,511 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:36:45,544 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:36:45,554 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:36:45,590 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00004_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:36:45,594 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:36:45,595 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:36:45,595 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:36:45,596 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:36:45,596 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:36:45,597 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:36:45,597 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf'.
2025-06-17 12:36:45,597 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:36:45,598 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:36:45,598 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2025-06-17 12:36:45,599 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:36:45,599 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:36:45,600 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2025-06-17 12:36:45,600 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:36:45,601 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:36:45,601 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:36:45,601 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:36:45,602 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:36:45,602 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:36:45,603 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:36:45,603 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:36:45,604 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits'.
2025-06-17 12:36:45,604 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf'.
2025-06-17 12:36:45,604 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:36:45,605 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf'.
2025-06-17 12:36:45,605 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:36:45,606 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:36:45,609 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:36:45,615 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:36:45,615 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03102_00004_mirifushort
2025-06-17 12:36:45,616 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:36:45,975 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:36:46,699 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:36:48,239 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:36:49,093 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.084462411 -70.084068909 81.088967554 -70.084068909 81.088967554 -70.082465669 81.084462411 -70.082465669
2025-06-17 12:36:49,094 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:36:49,099 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:36:49,527 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:36:49,528 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:36:49,894 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:36:49,894 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:36:50,260 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:36:50,261 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:36:50,649 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>, []).
2025-06-17 12:36:50,650 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:36:51,013 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:36:51,014 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:36:51,372 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:36:51,373 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:36:51,731 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:36:51,732 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:36:52,091 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:36:52,099 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:36:52,100 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:36:52,100 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:36:52,102 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:36:52,462 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:36:53,025 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:36:53,116 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:37:29,721 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:38:11,112 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.04480464410862771 DN/s
2025-06-17 12:38:11,113 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:38:11,116 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:38:11,528 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:38:11,594 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2025-06-17 12:38:11,594 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:38:11,595 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:38:11,595 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:38:12,187 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:38:12,639 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:38:12,656 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2025-06-17 12:38:12,679 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:38:12,680 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:38:12,680 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:38:13,243 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:38:13,245 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:38:13,693 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:38:13,694 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:38:14,104 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:38:14,105 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:38:14,516 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:38:14,539 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits
2025-06-17 12:38:14,539 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:38:15,083 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:38:15,084 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:38:15,084 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:38:15,085 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 12:38:15,136 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:38:15,138 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:38:15,139 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:38:15,147 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:38:15,201 - stpipe.Spec2Pipeline.photom - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/selector.py:634: RuntimeWarning: invalid value encountered in add
np.empty(inputs[0].shape) + self._undefined_transform_value
2025-06-17 12:38:15,737 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:38:16,207 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03102_00004_mirifushort_rate.fits>,).
2025-06-17 12:38:16,208 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:38:17,233 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits>,).
2025-06-17 12:38:17,234 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:38:17,682 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits>,).
2025-06-17 12:38:17,683 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:38:18,700 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits>,).
2025-06-17 12:38:18,701 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:38:18,702 - stpipe.Spec2Pipeline - 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
2025-06-17 12:38:18,704 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:38:18,704 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:38:19,212 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03102_00004_mirifushort_cal.fits
2025-06-17 12:38:19,213 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:38:19,213 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:38:19,576 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:38:19,657 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:38:19,665 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:38:19,686 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:38:19,696 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:38:19,704 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:38:19,728 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:38:19,729 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:38:19,730 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:38:19,731 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:38:19,733 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:38:19,734 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:38:19,734 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:38:19,735 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:38:19,740 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:38:19,742 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:38:19,743 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:38:19,743 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:38:19,744 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:38:19,745 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:38:19,747 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:38:19,749 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:38:19,750 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:38:19,751 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:38:19,752 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:38:19,753 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:38:19,753 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:38:19,754 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:38:19,755 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:38:19,756 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:38:19,757 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:38:19,758 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:38:19,759 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:38:19,760 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:38:19,761 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:38:19,763 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:38:20,324 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:38:20,359 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:38:20,369 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:38:20,406 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00001_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:38:20,411 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf 123.7 K bytes (1 / 6 files) (0 / 105.9 M bytes)
2025-06-17 12:38:20,761 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits 21.2 M bytes (2 / 6 files) (123.7 K / 105.9 M bytes)
2025-06-17 12:38:21,489 - 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)
2025-06-17 12:38:22,029 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits 33.9 M bytes (4 / 6 files) (34.0 M / 105.9 M bytes)
2025-06-17 12:38:22,882 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 105.9 M bytes)
2025-06-17 12:38:23,582 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf 39.1 K bytes (6 / 6 files) (105.9 M / 105.9 M bytes)
2025-06-17 12:38:23,762 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:38:23,762 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:38:23,763 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:38:23,763 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:38:23,763 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:38:23,764 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:38:23,764 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf'.
2025-06-17 12:38:23,765 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:38:23,765 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:38:23,766 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits'.
2025-06-17 12:38:23,766 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:38:23,767 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:38:23,767 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2025-06-17 12:38:23,768 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:38:23,768 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:38:23,769 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:38:23,769 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:38:23,770 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:38:23,770 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:38:23,771 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:38:23,771 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:38:23,771 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits'.
2025-06-17 12:38:23,772 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf'.
2025-06-17 12:38:23,772 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:38:23,773 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf'.
2025-06-17 12:38:23,773 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:38:23,774 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:38:23,775 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:38:23,781 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:38:23,782 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifulong
2025-06-17 12:38:23,782 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:38:24,174 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:38:24,764 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:38:25,626 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:38:26,364 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.081929062 -70.085584310 81.089703448 -70.085584310 81.089703448 -70.082935261 81.081929062 -70.082935261
2025-06-17 12:38:26,366 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:38:26,371 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:38:26,816 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:38:26,817 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:38:27,204 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:38:27,205 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:38:27,589 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:38:27,590 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:38:27,976 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>, []).
2025-06-17 12:38:27,977 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:38:28,365 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:38:28,366 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:38:28,754 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:38:28,755 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:38:29,136 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:38:29,137 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:38:29,521 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:38:29,529 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:38:29,529 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:38:29,530 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:38:29,531 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:38:29,911 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:38:30,341 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:38:30,426 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:39:12,502 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:39:53,879 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.03665111027657986 DN/s
2025-06-17 12:39:53,880 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:39:53,883 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:39:54,297 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:39:54,364 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits
2025-06-17 12:39:54,365 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:39:54,365 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:39:54,366 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:39:54,823 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:39:55,331 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:39:55,347 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2025-06-17 12:39:55,368 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:39:55,369 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:39:55,369 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:39:55,788 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:39:55,791 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:39:56,250 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:39:56,251 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:39:56,670 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:39:56,671 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:39:57,083 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:39:57,106 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits
2025-06-17 12:39:57,106 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:39:57,522 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:39:57,523 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:39:57,523 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:39:57,523 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 12:39:57,575 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:39:57,576 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:39:57,577 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:39:57,585 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:39:58,111 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:39:58,569 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifulong_rate.fits>,).
2025-06-17 12:39:58,570 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:39:59,450 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits>,).
2025-06-17 12:39:59,451 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:39:59,900 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits>,).
2025-06-17 12:39:59,901 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:40:00,788 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits>,).
2025-06-17 12:40:00,789 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:40:00,790 - stpipe.Spec2Pipeline - 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
2025-06-17 12:40:00,792 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:40:00,792 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:40:01,218 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifulong_cal.fits
2025-06-17 12:40:01,218 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:40:01,219 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:40:01,593 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:40:01,674 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:40:01,683 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:40:01,703 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:40:01,713 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:40:01,721 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:40:01,744 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:40:01,745 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:40:01,746 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:40:01,747 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:40:01,748 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:40:01,749 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:40:01,750 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:40:01,751 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:40:01,756 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:40:01,756 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:40:01,757 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:40:01,758 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:40:01,759 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:40:01,760 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:40:01,761 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:40:01,763 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:40:01,764 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:40:01,765 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:40:01,766 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:40:01,767 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:40:01,768 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:40:01,769 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:40:01,770 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:40:01,770 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:40:01,771 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:40:01,772 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:40:01,773 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:40:01,774 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:40:01,775 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:40:01,777 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:40:02,347 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:40:02,383 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:40:02,393 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:40:02,431 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00001_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:40:02,435 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf 165.1 K bytes (1 / 6 files) (0 / 106.0 M bytes)
2025-06-17 12:40:02,654 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits 21.2 M bytes (2 / 6 files) (165.1 K / 106.0 M bytes)
2025-06-17 12:40:03,328 - 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)
2025-06-17 12:40:03,817 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits 33.9 M bytes (4 / 6 files) (34.0 M / 106.0 M bytes)
2025-06-17 12:40:04,637 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 106.0 M bytes)
2025-06-17 12:40:05,471 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf 52.4 K bytes (6 / 6 files) (105.9 M / 106.0 M bytes)
2025-06-17 12:40:05,649 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:40:05,650 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:40:05,650 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:40:05,651 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:40:05,651 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:40:05,651 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:40:05,652 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf'.
2025-06-17 12:40:05,653 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:40:05,653 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:40:05,654 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2025-06-17 12:40:05,654 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:40:05,655 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:40:05,655 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2025-06-17 12:40:05,656 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:40:05,656 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:40:05,657 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:40:05,657 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:40:05,658 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:40:05,658 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:40:05,659 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:40:05,659 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:40:05,659 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits'.
2025-06-17 12:40:05,660 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf'.
2025-06-17 12:40:05,660 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:40:05,661 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf'.
2025-06-17 12:40:05,662 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:40:05,662 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:40:05,663 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:40:05,669 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:40:05,670 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00001_mirifushort
2025-06-17 12:40:05,670 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:40:06,105 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:40:06,859 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:40:08,473 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:40:09,377 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.083792346 -70.084993222 81.088234350 -70.084993222 81.088234350 -70.083387107 81.083792346 -70.083387107
2025-06-17 12:40:09,379 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:40:09,384 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:40:09,845 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:40:09,846 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:40:10,283 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:40:10,284 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:40:10,720 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:40:10,721 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:40:11,164 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>, []).
2025-06-17 12:40:11,165 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:40:11,605 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:40:11,606 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:40:12,039 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:40:12,040 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:40:12,474 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:40:12,475 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:40:12,911 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:40:12,918 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:40:12,919 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:40:12,919 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:40:12,921 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:40:13,365 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:40:13,950 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:40:14,043 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:40:52,431 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:41:33,755 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.04852017504597484 DN/s
2025-06-17 12:41:33,756 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:41:33,759 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:41:34,232 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:41:34,298 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2025-06-17 12:41:34,299 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:41:34,300 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:41:34,300 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:41:34,899 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:41:35,386 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:41:35,403 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2025-06-17 12:41:35,425 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:41:35,426 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:41:35,426 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:41:35,983 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:41:35,986 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:41:36,491 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:41:36,492 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:41:36,970 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:41:36,971 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:41:37,468 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:41:37,492 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits
2025-06-17 12:41:37,493 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:41:38,054 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:41:38,055 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:41:38,055 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:41:38,055 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 12:41:38,111 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:41:38,112 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:41:38,113 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:41:38,122 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:41:38,711 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:41:39,263 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00001_mirifushort_rate.fits>,).
2025-06-17 12:41:39,264 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:41:40,371 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits>,).
2025-06-17 12:41:40,372 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:41:40,884 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits>,).
2025-06-17 12:41:40,885 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:41:41,946 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits>,).
2025-06-17 12:41:41,947 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:41:41,949 - stpipe.Spec2Pipeline - 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
2025-06-17 12:41:41,950 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:41:41,950 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:41:42,454 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00001_mirifushort_cal.fits
2025-06-17 12:41:42,455 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:41:42,455 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:41:42,823 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:41:42,907 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:41:42,915 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:41:42,936 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:41:42,945 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:41:42,953 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:41:42,976 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:41:42,977 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:41:42,979 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:41:42,979 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:41:42,981 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:41:42,982 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:41:42,983 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:41:42,984 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:41:42,989 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:41:42,990 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:41:42,991 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:41:42,991 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:41:42,992 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:41:42,993 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:41:42,994 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:41:42,996 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:41:42,997 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:41:42,998 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:41:42,999 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:41:43,000 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:41:43,001 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:41:43,002 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:41:43,003 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:41:43,004 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:41:43,005 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:41:43,006 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:41:43,007 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:41:43,008 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:41:43,009 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:41:43,011 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:41:43,593 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:41:43,628 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:41:43,638 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:41:43,674 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00002_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:41:43,679 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:41:43,679 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:41:43,679 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:41:43,680 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:41:43,680 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:41:43,681 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:41:43,681 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf'.
2025-06-17 12:41:43,682 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:41:43,682 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:41:43,682 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits'.
2025-06-17 12:41:43,683 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:41:43,683 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:41:43,684 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2025-06-17 12:41:43,684 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:41:43,684 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:41:43,685 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:41:43,685 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:41:43,687 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:41:43,688 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:41:43,688 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:41:43,689 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:41:43,689 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits'.
2025-06-17 12:41:43,689 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf'.
2025-06-17 12:41:43,690 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:41:43,690 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf'.
2025-06-17 12:41:43,692 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:41:43,692 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:41:43,693 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:41:43,699 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:41:43,700 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifulong
2025-06-17 12:41:43,700 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:41:44,143 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:41:44,736 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:41:45,575 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:41:46,317 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.082662691 -70.084751223 81.090436809 -70.084751223 81.090436809 -70.082102156 81.082662691 -70.082102156
2025-06-17 12:41:46,318 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:41:46,323 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:41:46,819 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:41:46,821 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:41:47,256 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:41:47,257 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:41:47,686 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:41:47,687 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:41:48,124 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>, []).
2025-06-17 12:41:48,125 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:41:48,567 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:41:48,568 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:41:49,001 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:41:49,002 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:41:49,436 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:41:49,436 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:41:49,885 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:41:49,893 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:41:49,893 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:41:49,894 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:41:49,895 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:41:50,344 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:41:50,780 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:41:50,870 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:42:33,527 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:43:14,874 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.0382488165050745 DN/s
2025-06-17 12:43:14,875 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:43:14,878 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:43:15,399 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:43:15,473 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits
2025-06-17 12:43:15,473 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:43:15,474 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:43:15,474 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:43:15,958 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:43:16,541 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:43:16,562 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2025-06-17 12:43:16,584 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:43:16,585 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:43:16,586 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:43:17,030 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:43:17,032 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:43:17,606 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:43:17,607 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:43:18,130 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:43:18,131 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:43:18,649 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:43:18,674 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits
2025-06-17 12:43:18,675 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:43:19,112 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:43:19,113 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:43:19,113 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:43:19,114 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 12:43:19,166 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:43:19,167 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:43:19,168 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:43:19,177 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:43:19,716 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:43:20,313 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifulong_rate.fits>,).
2025-06-17 12:43:20,314 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:43:21,321 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits>,).
2025-06-17 12:43:21,322 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:43:21,871 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits>,).
2025-06-17 12:43:21,872 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:43:22,886 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits>,).
2025-06-17 12:43:22,886 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:43:22,888 - stpipe.Spec2Pipeline - 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
2025-06-17 12:43:22,889 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:43:22,890 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:43:23,320 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifulong_cal.fits
2025-06-17 12:43:23,321 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:43:23,322 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:43:23,714 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:43:23,799 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:43:23,808 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:43:23,829 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:43:23,840 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:43:23,848 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:43:23,873 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:43:23,875 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:43:23,876 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:43:23,877 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:43:23,879 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:43:23,880 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:43:23,881 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:43:23,882 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:43:23,887 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:43:23,888 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:43:23,889 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:43:23,890 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:43:23,891 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:43:23,892 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:43:23,893 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:43:23,894 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:43:23,897 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:43:23,898 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:43:23,899 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:43:23,900 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:43:23,901 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:43:23,902 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:43:23,903 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:43:23,903 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:43:23,904 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:43:23,905 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:43:23,906 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:43:23,907 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:43:23,909 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:43:23,910 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:43:24,622 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:43:24,657 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:43:24,667 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:43:24,706 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00002_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:43:24,710 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:43:24,711 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:43:24,711 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:43:24,712 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:43:24,712 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:43:24,712 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:43:24,713 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf'.
2025-06-17 12:43:24,714 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:43:24,715 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:43:24,715 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2025-06-17 12:43:24,715 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:43:24,716 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:43:24,716 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2025-06-17 12:43:24,717 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:43:24,718 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:43:24,718 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:43:24,718 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:43:24,719 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:43:24,720 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:43:24,720 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:43:24,720 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:43:24,721 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits'.
2025-06-17 12:43:24,722 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf'.
2025-06-17 12:43:24,722 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:43:24,723 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf'.
2025-06-17 12:43:24,723 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:43:24,724 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:43:24,725 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:43:24,732 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:43:24,732 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00002_mirifushort
2025-06-17 12:43:24,733 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:43:25,264 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:43:26,061 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:43:27,850 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:43:28,789 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.084525904 -70.084160128 81.088967765 -70.084160128 81.088967765 -70.082554003 81.084525904 -70.082554003
2025-06-17 12:43:28,790 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:43:28,795 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:43:29,347 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:43:29,348 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:43:29,880 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:43:29,881 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:43:30,418 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:43:30,419 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:43:30,949 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>, []).
2025-06-17 12:43:30,950 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:43:31,461 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:43:31,462 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:43:31,968 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:43:31,969 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:43:32,484 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:43:32,485 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:43:33,009 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:43:33,017 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:43:33,017 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:43:33,018 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:43:33,019 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:43:33,537 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:43:34,136 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:43:34,236 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:44:12,685 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:44:54,051 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.027051021835518715 DN/s
2025-06-17 12:44:54,051 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:44:54,055 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:44:54,604 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:44:54,674 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2025-06-17 12:44:54,674 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:44:54,675 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:44:54,676 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:44:55,269 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:44:55,870 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:44:55,890 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2025-06-17 12:44:55,913 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:44:55,914 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:44:55,914 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:44:56,488 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:44:56,491 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:44:57,061 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:44:57,062 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:44:57,594 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:44:57,595 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:44:58,125 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:44:58,149 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits
2025-06-17 12:44:58,150 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:44:58,726 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:44:58,727 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:44:58,727 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:44:58,728 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 12:44:58,785 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:44:58,786 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:44:58,787 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:44:58,796 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:44:59,388 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:44:59,998 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00002_mirifushort_rate.fits>,).
2025-06-17 12:45:00,000 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:45:01,168 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits>,).
2025-06-17 12:45:01,169 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:45:01,770 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits>,).
2025-06-17 12:45:01,771 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:45:02,921 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits>,).
2025-06-17 12:45:02,922 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:45:02,923 - stpipe.Spec2Pipeline - 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
2025-06-17 12:45:02,925 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:45:02,925 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:45:03,456 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00002_mirifushort_cal.fits
2025-06-17 12:45:03,456 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:45:03,457 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:45:03,844 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:45:03,929 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:45:03,937 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:45:03,958 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:45:03,968 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:45:03,976 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:45:04,000 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:45:04,001 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:45:04,002 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:45:04,003 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:45:04,005 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:45:04,006 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:45:04,006 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:45:04,007 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:45:04,012 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:45:04,013 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:45:04,014 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:45:04,014 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:45:04,015 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:45:04,016 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:45:04,017 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:45:04,019 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:45:04,020 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:45:04,021 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:45:04,022 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:45:04,025 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:45:04,025 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:45:04,026 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:45:04,028 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:45:04,029 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:45:04,030 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:45:04,030 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:45:04,031 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:45:04,032 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:45:04,034 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:45:04,035 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:45:04,786 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:45:04,819 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:45:04,830 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:45:04,867 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00003_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:45:04,871 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:45:04,872 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:45:04,872 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:45:04,873 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:45:04,873 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:45:04,874 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:45:04,874 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf'.
2025-06-17 12:45:04,876 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:45:04,876 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:45:04,876 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits'.
2025-06-17 12:45:04,877 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:45:04,877 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:45:04,878 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2025-06-17 12:45:04,878 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:45:04,879 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:45:04,879 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:45:04,880 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:45:04,880 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:45:04,880 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:45:04,881 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:45:04,881 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:45:04,882 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits'.
2025-06-17 12:45:04,882 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf'.
2025-06-17 12:45:04,885 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:45:04,885 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf'.
2025-06-17 12:45:04,886 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:45:04,886 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:45:04,887 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:45:04,893 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:45:04,894 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifulong
2025-06-17 12:45:04,895 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:45:05,420 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:45:06,030 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:45:06,881 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:45:07,654 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.082007061 -70.085445513 81.089781386 -70.085445513 81.089781386 -70.082796467 81.082007061 -70.082796467
2025-06-17 12:45:07,655 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:45:07,660 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:45:08,283 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:45:08,285 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:45:08,825 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:45:08,826 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:45:09,376 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:45:09,377 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:45:09,965 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>, []).
2025-06-17 12:45:09,966 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:45:10,508 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:45:10,509 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:45:11,046 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:45:11,048 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:45:11,576 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:45:11,577 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:45:12,108 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:45:12,115 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:45:12,116 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:45:12,116 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:45:12,118 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:45:12,646 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:45:13,089 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:45:13,177 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:45:55,159 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:46:37,225 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.032336486503481865 DN/s
2025-06-17 12:46:37,226 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:46:37,229 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:46:37,764 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:46:37,831 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits
2025-06-17 12:46:37,832 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:46:37,832 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:46:37,833 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:46:38,292 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:46:38,864 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:46:38,880 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2025-06-17 12:46:38,901 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:46:38,902 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:46:38,903 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:46:39,324 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:46:39,327 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:46:39,894 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:46:39,895 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:46:40,416 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:46:40,417 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:46:40,947 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:46:40,970 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits
2025-06-17 12:46:40,971 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:46:41,397 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:46:41,397 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:46:41,398 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:46:41,399 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 12:46:41,450 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:46:41,452 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:46:41,452 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:46:41,461 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:46:41,974 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:46:42,545 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifulong_rate.fits>,).
2025-06-17 12:46:42,547 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:46:43,541 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits>,).
2025-06-17 12:46:43,541 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:46:44,104 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits>,).
2025-06-17 12:46:44,105 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:46:45,095 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits>,).
2025-06-17 12:46:45,096 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:46:45,097 - stpipe.Spec2Pipeline - 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
2025-06-17 12:46:45,099 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:46:45,099 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:46:45,510 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifulong_cal.fits
2025-06-17 12:46:45,511 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:46:45,512 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:46:45,876 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:46:45,957 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:46:45,965 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:46:45,986 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:46:45,995 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:46:46,003 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:46:46,026 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:46:46,027 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:46:46,028 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:46:46,029 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:46:46,031 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:46:46,032 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:46:46,033 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:46:46,033 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:46:46,038 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:46:46,039 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:46:46,040 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:46:46,041 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:46:46,042 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:46:46,042 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:46:46,043 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:46:46,045 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:46:46,047 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:46:46,048 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:46:46,049 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:46:46,050 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:46:46,050 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:46:46,051 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:46:46,052 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:46:46,053 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:46:46,054 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:46:46,055 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:46:46,056 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:46:46,057 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:46:46,058 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:46:46,060 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:46:46,707 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:46:46,743 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:46:46,753 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:46:46,790 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00003_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:46:46,794 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:46:46,794 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:46:46,795 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:46:46,795 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:46:46,796 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:46:46,796 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:46:46,796 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf'.
2025-06-17 12:46:46,797 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:46:46,798 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:46:46,798 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2025-06-17 12:46:46,799 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:46:46,799 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:46:46,799 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2025-06-17 12:46:46,800 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:46:46,800 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:46:46,800 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:46:46,801 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:46:46,802 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:46:46,803 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:46:46,803 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:46:46,804 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:46:46,804 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits'.
2025-06-17 12:46:46,804 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf'.
2025-06-17 12:46:46,805 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:46:46,806 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf'.
2025-06-17 12:46:46,807 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:46:46,807 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:46:46,808 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:46:46,814 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:46:46,815 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00003_mirifushort
2025-06-17 12:46:46,815 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:46:47,341 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:46:48,087 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:46:49,175 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:46:50,654 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.083870330 -70.084854426 81.088312297 -70.084854426 81.088312297 -70.083248312 81.083870330 -70.083248312
2025-06-17 12:46:50,655 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:46:50,660 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:46:51,227 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:46:51,228 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:46:51,780 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:46:51,781 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:46:52,329 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:46:52,330 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:46:52,891 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>, []).
2025-06-17 12:46:52,892 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:46:53,444 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:46:53,445 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:46:53,992 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:46:53,992 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:46:54,538 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:46:54,538 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:46:55,080 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:46:55,087 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:46:55,088 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:46:55,088 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:46:55,090 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:46:55,620 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:46:56,177 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:46:56,271 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:47:34,676 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:48:16,010 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.037979974139971284 DN/s
2025-06-17 12:48:16,011 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:48:16,016 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:48:16,604 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:48:16,672 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2025-06-17 12:48:16,673 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:48:16,673 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:48:16,674 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:48:17,285 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:48:17,925 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:48:17,941 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2025-06-17 12:48:17,963 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:48:17,964 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:48:17,964 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:48:18,535 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:48:18,538 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:48:19,165 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:48:19,166 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:48:19,753 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:48:19,754 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:48:20,331 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:48:20,354 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits
2025-06-17 12:48:20,355 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:48:20,910 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:48:20,911 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:48:20,911 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:48:20,912 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 12:48:20,964 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:48:20,965 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:48:20,966 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:48:20,975 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:48:21,568 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:48:22,212 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00003_mirifushort_rate.fits>,).
2025-06-17 12:48:22,213 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:48:23,403 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits>,).
2025-06-17 12:48:23,404 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:48:24,014 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits>,).
2025-06-17 12:48:24,015 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:48:25,208 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits>,).
2025-06-17 12:48:25,209 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:48:25,211 - stpipe.Spec2Pipeline - 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
2025-06-17 12:48:25,212 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:48:25,213 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:48:25,732 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00003_mirifushort_cal.fits
2025-06-17 12:48:25,732 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:48:25,733 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:48:26,095 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:48:26,176 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:48:26,185 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:48:26,205 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:48:26,215 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:48:26,223 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:48:26,247 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:48:26,248 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:48:26,249 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:48:26,250 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:48:26,252 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:48:26,253 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:48:26,254 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:48:26,255 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:48:26,260 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:48:26,261 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:48:26,262 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:48:26,263 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:48:26,264 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:48:26,265 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:48:26,266 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:48:26,268 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:48:26,269 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:48:26,270 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:48:26,272 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:48:26,273 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:48:26,274 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:48:26,275 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:48:26,276 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:48:26,277 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:48:26,278 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:48:26,279 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:48:26,280 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:48:26,281 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:48:26,282 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:48:26,285 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:48:27,082 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:48:27,117 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:48:27,127 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:48:27,164 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00004_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:48:27,168 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:48:27,169 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:48:27,170 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:48:27,170 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:48:27,170 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:48:27,171 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:48:27,171 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf'.
2025-06-17 12:48:27,172 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:48:27,172 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:48:27,173 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits'.
2025-06-17 12:48:27,173 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:48:27,174 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:48:27,174 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2025-06-17 12:48:27,175 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:48:27,175 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:48:27,175 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:48:27,176 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:48:27,176 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:48:27,177 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:48:27,177 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:48:27,177 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:48:27,178 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits'.
2025-06-17 12:48:27,178 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf'.
2025-06-17 12:48:27,179 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:48:27,179 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf'.
2025-06-17 12:48:27,180 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:48:27,181 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:48:27,182 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:48:27,188 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:48:27,189 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifulong
2025-06-17 12:48:27,189 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:48:27,772 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:48:28,360 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2025-06-17 12:48:29,197 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:48:29,945 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.082742620 -70.084612967 81.090516684 -70.084612967 81.090516684 -70.081963900 81.082742620 -70.081963900
2025-06-17 12:48:29,946 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:48:29,950 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:48:30,564 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:48:30,565 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:48:31,126 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:48:31,127 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:48:31,697 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:48:31,698 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:48:32,273 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>, []).
2025-06-17 12:48:32,274 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:48:32,858 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:48:32,859 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:48:33,435 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:48:33,435 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:48:34,012 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:48:34,013 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:48:34,579 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:48:34,587 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:48:34,588 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:48:34,589 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:48:34,590 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:48:35,148 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:48:35,581 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:48:35,666 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:49:17,680 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:49:59,006 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.03849552758038044 DN/s
2025-06-17 12:49:59,007 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:49:59,010 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:49:59,666 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:49:59,736 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits
2025-06-17 12:49:59,737 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:49:59,737 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:49:59,738 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:50:00,210 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:50:00,890 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:50:00,908 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2025-06-17 12:50:00,931 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:50:00,932 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:50:00,933 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:50:01,386 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:50:01,389 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:50:02,107 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:50:02,108 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:50:02,762 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:50:02,763 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:50:03,381 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:50:03,406 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits
2025-06-17 12:50:03,406 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:50:03,845 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:50:03,845 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:50:03,846 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:50:03,846 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 12:50:03,899 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:50:03,900 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:50:03,901 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:50:03,909 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:50:04,437 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:50:05,139 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifulong_rate.fits>,).
2025-06-17 12:50:05,141 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:50:06,253 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits>,).
2025-06-17 12:50:06,254 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:50:06,926 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits>,).
2025-06-17 12:50:06,927 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:50:08,029 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits>,).
2025-06-17 12:50:08,029 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:50:08,031 - stpipe.Spec2Pipeline - 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
2025-06-17 12:50:08,032 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:50:08,033 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:50:08,464 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifulong_cal.fits
2025-06-17 12:50:08,465 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:50:08,466 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:50:08,836 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:50:08,921 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:50:08,929 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:50:08,950 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:50:08,959 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:50:08,967 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:50:08,991 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:50:08,992 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:50:08,993 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:50:08,994 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:50:08,995 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:50:08,996 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:50:08,997 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:50:08,999 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:50:09,003 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:50:09,004 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:50:09,005 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:50:09,006 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:50:09,007 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:50:09,008 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:50:09,009 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:50:09,010 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:50:09,012 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:50:09,013 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:50:09,014 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:50:09,016 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:50:09,017 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:50:09,018 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:50:09,019 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:50:09,020 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:50:09,021 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:50:09,022 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:50:09,023 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:50:09,024 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:50:09,026 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:50:09,027 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:50:09,827 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:50:09,863 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:50:09,873 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:50:09,911 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03104_00004_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:50:09,915 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:50:09,916 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:50:09,916 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:50:09,917 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:50:09,917 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:50:09,918 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:50:09,918 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf'.
2025-06-17 12:50:09,919 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:50:09,920 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:50:09,920 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2025-06-17 12:50:09,921 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:50:09,921 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:50:09,921 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2025-06-17 12:50:09,922 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:50:09,922 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:50:09,923 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:50:09,923 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:50:09,923 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:50:09,924 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:50:09,924 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:50:09,925 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:50:09,925 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits'.
2025-06-17 12:50:09,926 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf'.
2025-06-17 12:50:09,927 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:50:09,927 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf'.
2025-06-17 12:50:09,928 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:50:09,928 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:50:09,929 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:50:09,936 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:50:09,936 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03104_00004_mirifushort
2025-06-17 12:50:09,937 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:50:10,569 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:50:11,347 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:50:12,471 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:50:13,364 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.084605821 -70.084021872 81.089047650 -70.084021872 81.089047650 -70.082415747 81.084605821 -70.082415747
2025-06-17 12:50:13,365 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:50:13,370 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:50:14,101 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:50:14,102 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:50:14,744 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:50:14,745 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:50:15,388 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:50:15,389 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:50:16,027 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>, []).
2025-06-17 12:50:16,028 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:50:16,666 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:50:16,667 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:50:17,312 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:50:17,313 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:50:17,947 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:50:17,948 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:50:18,638 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:50:18,646 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:50:18,646 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:50:18,647 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:50:18,648 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:50:19,283 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:50:19,871 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:50:19,966 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:50:58,391 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:51:39,776 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.032398187735935856 DN/s
2025-06-17 12:51:39,777 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:51:39,780 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:51:40,451 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:51:40,520 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2025-06-17 12:51:40,520 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:51:40,521 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:51:40,521 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:51:41,115 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:51:41,802 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:51:41,820 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2025-06-17 12:51:41,842 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:51:41,843 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:51:41,843 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:51:42,403 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:51:42,406 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:51:43,097 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:51:43,098 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:51:43,778 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:51:43,779 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:51:44,466 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:51:44,490 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits
2025-06-17 12:51:44,491 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:51:45,063 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:51:45,064 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:51:45,064 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:51:45,065 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 12:51:45,120 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:51:45,121 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:51:45,121 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:51:45,130 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:51:45,716 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:51:46,456 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03104_00004_mirifushort_rate.fits>,).
2025-06-17 12:51:46,457 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:51:47,748 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits>,).
2025-06-17 12:51:47,749 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:51:48,440 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits>,).
2025-06-17 12:51:48,441 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:51:49,717 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits>,).
2025-06-17 12:51:49,718 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:51:49,719 - stpipe.Spec2Pipeline - 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
2025-06-17 12:51:49,721 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:51:49,722 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:51:50,249 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03104_00004_mirifushort_cal.fits
2025-06-17 12:51:50,250 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:51:50,250 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:51:50,610 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:51:50,689 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:51:50,698 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:51:50,719 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:51:50,728 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:51:50,737 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:51:50,762 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:51:50,764 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:51:50,765 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:51:50,766 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:51:50,767 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:51:50,769 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:51:50,770 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:51:50,771 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:51:50,775 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:51:50,777 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:51:50,778 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:51:50,779 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:51:50,780 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:51:50,781 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:51:50,782 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:51:50,784 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:51:50,786 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:51:50,786 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:51:50,787 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:51:50,788 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:51:50,789 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:51:50,790 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:51:50,791 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:51:50,792 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:51:50,793 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:51:50,794 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:51:50,794 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:51:50,796 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:51:50,797 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:51:50,799 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:51:51,659 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:51:51,695 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:51:51,706 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:51:51,745 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00001_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:51:51,750 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf 123.8 K bytes (1 / 6 files) (0 / 105.9 M bytes)
2025-06-17 12:51:52,011 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits 21.2 M bytes (2 / 6 files) (123.8 K / 105.9 M bytes)
2025-06-17 12:51:52,944 - 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)
2025-06-17 12:51:53,489 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits 33.9 M bytes (4 / 6 files) (34.0 M / 105.9 M bytes)
2025-06-17 12:51:54,288 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 105.9 M bytes)
2025-06-17 12:51:55,012 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf 39.1 K bytes (6 / 6 files) (105.9 M / 105.9 M bytes)
2025-06-17 12:51:55,159 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:51:55,160 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:51:55,161 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:51:55,161 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:51:55,161 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:51:55,162 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:51:55,162 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf'.
2025-06-17 12:51:55,163 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:51:55,163 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:51:55,164 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2025-06-17 12:51:55,164 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:51:55,165 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:51:55,165 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2025-06-17 12:51:55,166 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:51:55,166 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:51:55,167 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:51:55,167 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:51:55,168 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:51:55,168 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:51:55,169 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:51:55,169 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:51:55,170 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits'.
2025-06-17 12:51:55,171 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf'.
2025-06-17 12:51:55,171 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:51:55,171 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf'.
2025-06-17 12:51:55,172 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:51:55,173 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:51:55,174 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:51:55,180 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:51:55,180 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifulong
2025-06-17 12:51:55,181 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:51:55,848 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:51:56,463 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:51:57,311 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:51:58,065 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.081854234 -70.085565346 81.089789477 -70.085565346 81.089789477 -70.082922720 81.081854234 -70.082922720
2025-06-17 12:51:58,066 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:51:58,071 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:51:58,832 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:51:58,834 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:51:59,490 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:51:59,490 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:52:00,159 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:52:00,160 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:52:00,826 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>, []).
2025-06-17 12:52:00,827 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:52:01,476 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:52:01,477 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:52:02,131 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:52:02,132 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:52:02,776 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:52:02,777 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:52:03,419 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:52:03,426 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:52:03,427 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:52:03,427 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:52:03,429 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:52:04,072 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:52:04,511 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:52:04,600 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:52:46,596 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:53:27,887 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.03679986670613289 DN/s
2025-06-17 12:53:27,887 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:53:27,891 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:53:28,580 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:53:28,647 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2025-06-17 12:53:28,648 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:53:28,648 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:53:28,649 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:53:29,115 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:53:29,871 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:53:29,888 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2025-06-17 12:53:29,910 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:53:29,911 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:53:29,912 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:53:30,352 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:53:30,355 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:53:31,090 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:53:31,091 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:53:31,767 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:53:31,768 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:53:32,435 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:53:32,460 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits
2025-06-17 12:53:32,461 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:53:32,891 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:53:32,892 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:53:32,893 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:53:32,893 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 12:53:32,942 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:53:32,943 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:53:32,943 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:53:32,953 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:53:33,476 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:53:34,196 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifulong_rate.fits>,).
2025-06-17 12:53:34,197 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:53:35,378 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits>,).
2025-06-17 12:53:35,379 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:53:36,119 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits>,).
2025-06-17 12:53:36,120 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:53:37,297 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits>,).
2025-06-17 12:53:37,298 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:53:37,299 - stpipe.Spec2Pipeline - 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
2025-06-17 12:53:37,301 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:53:37,301 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:53:37,730 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifulong_cal.fits
2025-06-17 12:53:37,730 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:53:37,731 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:53:38,102 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:53:38,186 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:53:38,194 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:53:38,216 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:53:38,225 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:53:38,234 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:53:38,258 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:53:38,259 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:53:38,260 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:53:38,261 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:53:38,263 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:53:38,264 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:53:38,265 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:53:38,266 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:53:38,272 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:53:38,273 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:53:38,274 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:53:38,275 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:53:38,276 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:53:38,277 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:53:38,278 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:53:38,280 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:53:38,283 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:53:38,284 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:53:38,285 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:53:38,286 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:53:38,286 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:53:38,287 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:53:38,288 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:53:38,289 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:53:38,290 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:53:38,291 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:53:38,292 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:53:38,293 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:53:38,294 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:53:38,296 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:53:39,168 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:53:39,202 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:53:39,212 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:53:39,251 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00001_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:53:39,255 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf 165.2 K bytes (1 / 6 files) (0 / 106.0 M bytes)
2025-06-17 12:53:39,512 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits 21.2 M bytes (2 / 6 files) (165.2 K / 106.0 M bytes)
2025-06-17 12:53:40,205 - 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)
2025-06-17 12:53:40,658 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits 33.9 M bytes (4 / 6 files) (34.0 M / 106.0 M bytes)
2025-06-17 12:53:41,364 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf 38.0 M bytes (5 / 6 files) (67.9 M / 106.0 M bytes)
2025-06-17 12:53:42,057 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf 52.4 K bytes (6 / 6 files) (105.9 M / 106.0 M bytes)
2025-06-17 12:53:42,221 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:53:42,222 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:53:42,222 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:53:42,223 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:53:42,223 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:53:42,224 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:53:42,224 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf'.
2025-06-17 12:53:42,225 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:53:42,225 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:53:42,225 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2025-06-17 12:53:42,226 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:53:42,226 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:53:42,226 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2025-06-17 12:53:42,228 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:53:42,228 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:53:42,228 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:53:42,229 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:53:42,229 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:53:42,230 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:53:42,230 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:53:42,231 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:53:42,231 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits'.
2025-06-17 12:53:42,231 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf'.
2025-06-17 12:53:42,232 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:53:42,233 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf'.
2025-06-17 12:53:42,233 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:53:42,234 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:53:42,235 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:53:42,241 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:53:42,242 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00001_mirifushort
2025-06-17 12:53:42,242 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:53:42,911 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:53:43,666 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 12:53:44,777 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:53:45,656 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.083789193 -70.085073395 81.088329898 -70.085073395 81.088329898 -70.083477127 81.083789193 -70.083477127
2025-06-17 12:53:45,657 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:53:45,662 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:53:46,444 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:53:46,446 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:53:47,139 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:53:47,140 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:53:47,820 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:53:47,821 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:53:48,502 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>, []).
2025-06-17 12:53:48,503 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:53:49,165 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:53:49,167 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:53:49,845 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:53:49,846 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:53:50,529 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:53:50,530 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:53:51,211 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:53:51,218 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:53:51,218 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:53:51,219 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:53:51,220 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:53:51,891 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:53:52,475 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:53:52,570 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:54:32,659 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:55:13,980 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.040790492038876684 DN/s
2025-06-17 12:55:13,980 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:55:13,984 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:55:14,744 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:55:14,819 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2025-06-17 12:55:14,820 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:55:14,820 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:55:14,821 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:55:15,432 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:55:16,266 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:55:16,286 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2025-06-17 12:55:16,309 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:55:16,310 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:55:16,311 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:55:16,889 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:55:16,892 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:55:17,685 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:55:17,686 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:55:18,436 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:55:18,437 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:55:19,211 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:55:19,236 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits
2025-06-17 12:55:19,236 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:55:19,808 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:55:19,808 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:55:19,809 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:55:19,809 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 12:55:19,863 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:55:19,864 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:55:19,865 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:55:19,874 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:55:20,479 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:55:21,348 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00001_mirifushort_rate.fits>,).
2025-06-17 12:55:21,349 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:55:22,731 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits>,).
2025-06-17 12:55:22,732 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:55:23,493 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits>,).
2025-06-17 12:55:23,494 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:55:24,860 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits>,).
2025-06-17 12:55:24,861 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:55:24,863 - stpipe.Spec2Pipeline - 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
2025-06-17 12:55:24,864 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:55:24,865 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:55:25,396 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00001_mirifushort_cal.fits
2025-06-17 12:55:25,396 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:55:25,397 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:55:25,764 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:55:25,847 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:55:25,858 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:55:25,880 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:55:25,890 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:55:25,898 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:55:25,922 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:55:25,923 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:55:25,924 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:55:25,925 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:55:25,927 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:55:25,928 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:55:25,928 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:55:25,930 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:55:25,934 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:55:25,935 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:55:25,936 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:55:25,937 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:55:25,938 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:55:25,939 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:55:25,941 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:55:25,942 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:55:25,944 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:55:25,945 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:55:25,946 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:55:25,947 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:55:25,948 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:55:25,949 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:55:25,949 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:55:25,950 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:55:25,952 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:55:25,953 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:55:25,954 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:55:25,955 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:55:25,956 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:55:25,958 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:55:26,929 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:55:26,964 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:55:26,975 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:55:27,013 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00002_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:55:27,017 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:55:27,018 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:55:27,018 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:55:27,019 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:55:27,019 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:55:27,019 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:55:27,020 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf'.
2025-06-17 12:55:27,021 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:55:27,021 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:55:27,022 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2025-06-17 12:55:27,022 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:55:27,023 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:55:27,023 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2025-06-17 12:55:27,024 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:55:27,024 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:55:27,025 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:55:27,025 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:55:27,026 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:55:27,026 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:55:27,027 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:55:27,027 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:55:27,028 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits'.
2025-06-17 12:55:27,028 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf'.
2025-06-17 12:55:27,030 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:55:27,030 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf'.
2025-06-17 12:55:27,031 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:55:27,031 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:55:27,033 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:55:27,039 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:55:27,040 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifulong
2025-06-17 12:55:27,040 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:55:27,781 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:55:28,404 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2025-06-17 12:55:29,269 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:55:30,036 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.082587875 -70.084732829 81.090522838 -70.084732829 81.090522838 -70.082090188 81.082587875 -70.082090188
2025-06-17 12:55:30,037 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:55:30,042 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:55:30,858 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:55:30,861 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:55:31,597 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:55:31,597 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:55:32,319 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:55:32,319 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:55:33,055 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>, []).
2025-06-17 12:55:33,057 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:55:33,795 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:55:33,796 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:55:34,536 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:55:34,536 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:55:35,275 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:55:35,276 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:55:36,016 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:55:36,023 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:55:36,024 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:55:36,024 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:55:36,026 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:55:36,758 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:55:37,222 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:55:37,323 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:56:19,265 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:57:00,677 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.00959168653935194 DN/s
2025-06-17 12:57:00,678 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:57:00,681 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:57:01,490 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:57:01,559 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2025-06-17 12:57:01,559 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:57:01,560 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:57:01,560 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:57:02,043 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:57:02,910 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:57:02,927 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2025-06-17 12:57:02,950 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:57:02,951 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:57:02,951 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:57:03,392 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:57:03,395 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:57:04,264 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:57:04,265 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:57:05,049 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:57:05,050 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:57:05,839 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:57:05,864 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits
2025-06-17 12:57:05,865 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:57:06,309 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:57:06,310 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 12:57:06,310 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:57:06,310 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 12:57:06,364 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:57:06,365 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:57:06,366 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:57:06,375 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:57:06,932 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:57:07,820 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifulong_rate.fits>,).
2025-06-17 12:57:07,822 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:57:09,101 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits>,).
2025-06-17 12:57:09,102 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:57:09,936 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits>,).
2025-06-17 12:57:09,937 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:57:11,224 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits>,).
2025-06-17 12:57:11,224 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:57:11,226 - stpipe.Spec2Pipeline - 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
2025-06-17 12:57:11,228 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:57:11,228 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:57:11,662 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifulong_cal.fits
2025-06-17 12:57:11,663 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:57:11,663 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:57:12,043 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:57:12,130 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:57:12,139 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:57:12,161 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:57:12,172 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:57:12,181 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:57:12,206 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:57:12,208 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:57:12,209 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:57:12,210 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:57:12,212 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:57:12,213 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:57:12,214 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:57:12,215 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:57:12,220 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:57:12,221 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:57:12,223 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:57:12,224 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:57:12,225 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:57:12,226 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:57:12,227 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:57:12,229 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:57:12,232 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:57:12,233 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:57:12,234 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:57:12,235 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:57:12,237 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:57:12,238 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:57:12,238 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:57:12,240 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:57:12,241 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:57:12,242 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:57:12,243 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:57:12,245 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:57:12,246 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:57:12,248 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:57:13,247 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:57:13,282 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:57:13,292 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:57:13,330 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00002_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:57:13,335 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:57:13,335 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:57:13,336 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:57:13,336 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:57:13,337 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:57:13,337 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:57:13,338 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf'.
2025-06-17 12:57:13,339 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:57:13,339 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:57:13,340 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2025-06-17 12:57:13,341 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:57:13,341 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:57:13,342 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2025-06-17 12:57:13,342 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:57:13,343 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:57:13,343 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:57:13,344 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:57:13,344 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:57:13,345 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:57:13,345 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:57:13,346 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:57:13,346 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits'.
2025-06-17 12:57:13,348 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf'.
2025-06-17 12:57:13,348 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:57:13,349 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf'.
2025-06-17 12:57:13,349 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:57:13,350 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:57:13,351 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:57:13,357 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:57:13,358 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00002_mirifushort
2025-06-17 12:57:13,358 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:57:14,139 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:57:14,918 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2025-06-17 12:57:16,053 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:57:16,948 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.084522766 -70.084240871 81.089063316 -70.084240871 81.089063316 -70.082644596 81.084522766 -70.082644596
2025-06-17 12:57:16,950 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:57:16,955 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:57:17,898 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:57:17,899 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:57:18,701 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:57:18,702 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:57:19,513 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:57:19,514 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:57:20,326 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>, []).
2025-06-17 12:57:20,327 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:57:21,128 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:57:21,129 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:57:21,917 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:57:21,918 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:57:22,703 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:57:22,704 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:57:23,485 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:57:23,492 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:57:23,493 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:57:23,493 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:57:23,495 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:57:24,292 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:57:24,891 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:57:24,991 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:58:05,129 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 12:58:46,481 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.028065568204705925 DN/s
2025-06-17 12:58:46,482 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 12:58:46,487 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 12:58:47,292 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:58:47,360 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2025-06-17 12:58:47,360 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 12:58:47,361 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 12:58:47,361 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 12:58:47,963 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 12:58:48,767 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:58:48,784 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2025-06-17 12:58:48,806 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:58:48,807 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:58:48,807 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:58:49,376 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 12:58:49,379 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 12:58:50,173 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:58:50,173 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 12:58:50,942 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:58:50,942 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 12:58:51,702 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:58:51,725 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits
2025-06-17 12:58:51,726 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 12:58:52,276 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 12:58:52,277 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 12:58:52,278 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 12:58:52,278 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 12:58:52,330 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 12:58:52,331 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 12:58:52,331 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 12:58:52,341 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 12:58:52,928 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 12:58:53,783 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00002_mirifushort_rate.fits>,).
2025-06-17 12:58:53,785 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 12:58:55,185 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits>,).
2025-06-17 12:58:55,186 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 12:58:55,995 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits>,).
2025-06-17 12:58:55,996 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 12:58:57,392 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits>,).
2025-06-17 12:58:57,393 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 12:58:57,394 - stpipe.Spec2Pipeline - 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
2025-06-17 12:58:57,396 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 12:58:57,396 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 12:58:57,911 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00002_mirifushort_cal.fits
2025-06-17 12:58:57,912 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 12:58:57,912 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 12:58:58,274 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:58:58,357 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:58:58,366 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:58:58,387 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 12:58:58,396 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 12:58:58,404 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 12:58:58,428 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 12:58:58,429 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 12:58:58,430 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 12:58:58,431 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 12:58:58,432 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 12:58:58,433 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 12:58:58,434 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 12:58:58,435 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 12:58:58,440 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 12:58:58,441 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:58:58,442 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:58:58,443 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:58:58,444 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 12:58:58,445 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:58:58,446 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:58:58,448 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:58:58,449 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 12:58:58,450 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 12:58:58,452 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 12:58:58,453 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 12:58:58,453 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 12:58:58,454 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 12:58:58,455 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 12:58:58,456 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 12:58:58,457 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 12:58:58,458 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 12:58:58,459 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 12:58:58,460 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 12:58:58,462 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 12:58:58,463 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 12:58:59,437 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 12:58:59,475 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 12:58:59,485 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:58:59,523 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00003_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 12:58:59,527 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 12:58:59,527 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 12:58:59,528 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 12:58:59,528 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 12:58:59,529 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 12:58:59,529 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 12:58:59,529 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf'.
2025-06-17 12:58:59,530 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 12:58:59,531 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 12:58:59,531 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2025-06-17 12:58:59,532 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 12:58:59,532 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 12:58:59,532 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2025-06-17 12:58:59,533 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 12:58:59,533 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 12:58:59,533 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 12:58:59,534 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 12:58:59,534 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 12:58:59,535 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 12:58:59,535 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 12:58:59,535 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 12:58:59,536 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits'.
2025-06-17 12:58:59,537 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf'.
2025-06-17 12:58:59,538 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 12:58:59,538 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf'.
2025-06-17 12:58:59,539 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 12:58:59,539 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 12:58:59,540 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 12:58:59,547 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 12:58:59,548 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifulong
2025-06-17 12:58:59,548 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 12:59:00,323 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 12:59:00,926 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2025-06-17 12:59:01,784 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 12:59:02,527 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.081932352 -70.085427022 81.089867525 -70.085427022 81.089867525 -70.082784403 81.081932352 -70.082784403
2025-06-17 12:59:02,529 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 12:59:02,533 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 12:59:03,326 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 12:59:03,327 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 12:59:04,095 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 12:59:04,095 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 12:59:04,834 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 12:59:04,835 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 12:59:05,574 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>, []).
2025-06-17 12:59:05,575 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:59:06,314 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:59:06,315 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:59:07,064 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 12:59:07,065 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 12:59:07,806 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 12:59:07,807 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 12:59:08,550 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 12:59:08,558 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 12:59:08,559 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 12:59:08,559 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 12:59:08,561 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 12:59:09,312 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 12:59:09,746 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 12:59:09,835 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 12:59:51,748 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:00:33,057 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.010717127472162247 DN/s
2025-06-17 13:00:33,057 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:00:33,060 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:00:33,845 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 13:00:33,914 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2025-06-17 13:00:33,914 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:00:33,915 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:00:33,915 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:00:34,374 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:00:35,201 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 13:00:35,218 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2025-06-17 13:00:35,240 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:00:35,241 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:00:35,242 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:00:35,674 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:00:35,677 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:00:36,504 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 13:00:36,505 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:00:37,327 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 13:00:37,328 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:00:38,133 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 13:00:38,158 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits
2025-06-17 13:00:38,158 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:00:38,582 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:00:38,583 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 13:00:38,583 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:00:38,584 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 13:00:38,633 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:00:38,635 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:00:38,635 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:00:38,644 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:00:39,181 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:00:40,032 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifulong_rate.fits>,).
2025-06-17 13:00:40,033 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:00:41,297 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits>,).
2025-06-17 13:00:41,298 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:00:42,110 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits>,).
2025-06-17 13:00:42,111 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 13:00:43,376 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits>,).
2025-06-17 13:00:43,377 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 13:00:43,379 - stpipe.Spec2Pipeline - 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
2025-06-17 13:00:43,380 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:00:43,380 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:00:43,804 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifulong_cal.fits
2025-06-17 13:00:43,804 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:00:43,805 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:00:44,176 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:00:44,257 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:00:44,265 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:00:44,286 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:00:44,295 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:00:44,303 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:00:44,326 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:00:44,327 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:00:44,328 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:00:44,329 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:00:44,331 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:00:44,332 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:00:44,333 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:00:44,333 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:00:44,338 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:00:44,339 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:00:44,340 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:00:44,341 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:00:44,341 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:00:44,342 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:00:44,343 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:00:44,345 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:00:44,347 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:00:44,348 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:00:44,349 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:00:44,350 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:00:44,351 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:00:44,352 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:00:44,353 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:00:44,354 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:00:44,355 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:00:44,356 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:00:44,357 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:00:44,358 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:00:44,359 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:00:44,361 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:00:45,299 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 13:00:45,333 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:00:45,343 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:00:45,380 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00003_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 13:00:45,384 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:00:45,385 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:00:45,385 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:00:45,386 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:00:45,386 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:00:45,387 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:00:45,387 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf'.
2025-06-17 13:00:45,388 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:00:45,389 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:00:45,389 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2025-06-17 13:00:45,390 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:00:45,390 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:00:45,391 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2025-06-17 13:00:45,391 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:00:45,392 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:00:45,392 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:00:45,393 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:00:45,394 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:00:45,394 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:00:45,395 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:00:45,395 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:00:45,395 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits'.
2025-06-17 13:00:45,396 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf'.
2025-06-17 13:00:45,397 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:00:45,397 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf'.
2025-06-17 13:00:45,398 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:00:45,398 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:00:45,399 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:00:45,406 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:00:45,407 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00003_mirifushort
2025-06-17 13:00:45,407 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:00:46,179 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:00:46,924 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 13:00:48,028 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:00:48,900 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.083867295 -70.084935073 81.088407957 -70.084935073 81.088407957 -70.083338809 81.083867295 -70.083338809
2025-06-17 13:00:48,901 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:00:48,906 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:00:49,855 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 13:00:49,857 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:00:50,690 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:00:50,691 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:00:51,519 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:00:51,520 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:00:52,355 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>, []).
2025-06-17 13:00:52,356 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:00:53,207 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 13:00:53,208 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:00:54,040 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 13:00:54,040 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:00:54,840 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 13:00:54,841 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:00:55,629 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:00:55,636 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:00:55,637 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:00:55,637 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:00:55,638 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:00:56,482 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:00:57,060 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:00:57,155 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:01:37,295 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:02:18,673 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.03930904604267174 DN/s
2025-06-17 13:02:18,673 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:02:18,676 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:02:19,556 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:02:19,624 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2025-06-17 13:02:19,625 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:02:19,625 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:02:19,626 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:02:20,241 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:02:21,167 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:02:21,183 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2025-06-17 13:02:21,205 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:02:21,206 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:02:21,207 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:02:21,781 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:02:21,784 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:02:22,668 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:02:22,669 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:02:23,535 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:02:23,536 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:02:24,411 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:02:24,435 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits
2025-06-17 13:02:24,436 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:02:24,998 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:02:24,999 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 13:02:25,000 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:02:25,000 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 13:02:25,053 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:02:25,054 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:02:25,055 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:02:25,064 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:02:25,682 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:02:26,590 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00003_mirifushort_rate.fits>,).
2025-06-17 13:02:26,592 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:02:28,037 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits>,).
2025-06-17 13:02:28,038 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:02:28,903 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits>,).
2025-06-17 13:02:28,904 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 13:02:30,368 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits>,).
2025-06-17 13:02:30,368 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 13:02:30,370 - stpipe.Spec2Pipeline - 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
2025-06-17 13:02:30,371 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:02:30,372 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:02:30,881 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00003_mirifushort_cal.fits
2025-06-17 13:02:30,882 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:02:30,883 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:02:31,240 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:02:31,321 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:02:31,330 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:02:31,352 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:02:31,361 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:02:31,369 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:02:31,392 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:02:31,393 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:02:31,394 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:02:31,395 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:02:31,396 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:02:31,397 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:02:31,398 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:02:31,399 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:02:31,404 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:02:31,405 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:02:31,405 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:02:31,406 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:02:31,407 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:02:31,408 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:02:31,411 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:02:31,412 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:02:31,413 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:02:31,414 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:02:31,415 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:02:31,416 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:02:31,417 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:02:31,418 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:02:31,419 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:02:31,420 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:02:31,421 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:02:31,421 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:02:31,422 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:02:31,423 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:02:31,425 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:02:31,426 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:02:32,371 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 13:02:32,405 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:02:32,415 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:02:32,452 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00004_mirifulong_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 13:02:32,456 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:02:32,456 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:02:32,457 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:02:32,457 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:02:32,457 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:02:32,458 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:02:32,458 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf'.
2025-06-17 13:02:32,459 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:02:32,459 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:02:32,460 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2025-06-17 13:02:32,460 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:02:32,460 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:02:32,461 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2025-06-17 13:02:32,461 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:02:32,462 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:02:32,462 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:02:32,462 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:02:32,463 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:02:32,463 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:02:32,464 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:02:32,464 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:02:32,464 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits'.
2025-06-17 13:02:32,465 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf'.
2025-06-17 13:02:32,465 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:02:32,466 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf'.
2025-06-17 13:02:32,468 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:02:32,468 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:02:32,469 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:02:32,475 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:02:32,476 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifulong
2025-06-17 13:02:32,476 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:02:33,271 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:02:33,867 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087369538972
2025-06-17 13:02:34,706 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:02:35,476 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.082667748 -70.084594178 81.090602662 -70.084594178 81.090602662 -70.081951536 81.082667748 -70.081951536
2025-06-17 13:02:35,477 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:02:35,483 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:02:36,327 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 13:02:36,329 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:02:37,126 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:02:37,127 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:02:37,911 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:02:37,912 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:02:38,703 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>, []).
2025-06-17 13:02:38,703 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:02:39,497 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 13:02:39,498 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:02:40,287 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 13:02:40,288 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:02:41,079 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 13:02:41,080 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:02:41,870 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:02:41,878 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:02:41,878 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:02:41,879 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:02:41,880 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:02:42,669 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:02:43,097 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:02:43,184 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:03:25,205 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:04:06,510 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.02789785247296095 DN/s
2025-06-17 13:04:06,511 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:04:06,514 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:04:07,376 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:04:07,444 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2025-06-17 13:04:07,444 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:04:07,445 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:04:07,445 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:04:07,910 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:04:08,804 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:04:08,819 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2025-06-17 13:04:08,841 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:04:08,842 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:04:08,842 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:04:09,268 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:04:09,271 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:04:10,161 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:04:10,162 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:04:11,014 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:04:11,014 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:04:11,872 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:04:11,896 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits
2025-06-17 13:04:11,897 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:04:12,321 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:04:12,322 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 13:04:12,322 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:04:12,323 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 13:04:12,372 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:04:12,373 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:04:12,373 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:04:12,383 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:04:12,904 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:04:13,794 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifulong_rate.fits>,).
2025-06-17 13:04:13,795 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:04:15,085 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits>,).
2025-06-17 13:04:15,086 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:04:15,941 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits>,).
2025-06-17 13:04:15,942 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 13:04:17,241 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits>,).
2025-06-17 13:04:17,242 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 13:04:17,244 - stpipe.Spec2Pipeline - 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
2025-06-17 13:04:17,245 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:04:17,245 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:04:17,664 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifulong_cal.fits
2025-06-17 13:04:17,665 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:04:17,666 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:04:18,029 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:04:18,111 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:04:18,119 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:04:18,143 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:04:18,153 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:04:18,162 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:04:18,185 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:04:18,186 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:04:18,188 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:04:18,189 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:04:18,190 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:04:18,191 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:04:18,192 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:04:18,193 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:04:18,198 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:04:18,199 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:04:18,200 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:04:18,201 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:04:18,202 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:04:18,203 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:04:18,204 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:04:18,205 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:04:18,207 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:04:18,208 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:04:18,209 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:04:18,210 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:04:18,211 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:04:18,212 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:04:18,213 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:04:18,214 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:04:18,215 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:04:18,216 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:04:18,216 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:04:18,218 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:04:18,219 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:04:18,221 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:04:19,142 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs003/l2asn.json',).
2025-06-17 13:04:19,178 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:04:19,189 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:04:19,225 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03106_00004_mirifushort_rate.fits' reftypes = ['area', 'barshadow', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pathloss', 'photom', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange']
2025-06-17 13:04:19,230 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:04:19,230 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:04:19,231 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:04:19,231 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:04:19,232 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:04:19,232 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:04:19,232 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf'.
2025-06-17 13:04:19,233 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:04:19,234 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:04:19,234 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2025-06-17 13:04:19,235 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:04:19,235 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:04:19,236 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2025-06-17 13:04:19,236 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:04:19,236 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:04:19,237 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:04:19,237 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:04:19,238 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:04:19,238 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:04:19,238 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:04:19,240 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:04:19,240 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits'.
2025-06-17 13:04:19,240 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf'.
2025-06-17 13:04:19,241 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:04:19,241 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf'.
2025-06-17 13:04:19,242 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:04:19,242 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:04:19,243 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:04:19,250 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:04:19,250 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs003/stage1/jw01523003001_03106_00004_mirifushort
2025-06-17 13:04:19,251 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:04:20,076 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:04:20,814 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087363201144
2025-06-17 13:04:21,911 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:04:22,790 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.084602624 -70.084102225 81.089143148 -70.084102225 81.089143148 -70.082505949 81.084602624 -70.082505949
2025-06-17 13:04:22,792 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:04:22,797 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:04:23,741 - stpipe.Spec2Pipeline.badpix_selfcal - 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']).
2025-06-17 13:04:23,742 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:04:24,596 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:04:24,596 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:04:25,439 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:04:25,440 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:04:26,289 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>, []).
2025-06-17 13:04:26,289 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:04:27,138 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 13:04:27,138 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:04:27,984 - stpipe.Spec2Pipeline.imprint_subtract - 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', []).
2025-06-17 13:04:27,985 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:04:28,848 - stpipe.Spec2Pipeline.bkg_subtract - 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']).
2025-06-17 13:04:28,849 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:04:29,705 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:04:29,712 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:04:29,713 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:04:29,714 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:04:29,715 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:04:30,576 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:04:31,153 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:04:31,249 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:05:11,554 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:05:52,932 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.03144222962243631 DN/s
2025-06-17 13:05:52,933 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:05:52,936 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:05:53,827 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:05:53,896 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2025-06-17 13:05:53,896 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:05:53,897 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:05:53,897 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:05:54,493 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:05:55,467 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:05:55,484 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2025-06-17 13:05:55,506 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:05:55,507 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:05:55,507 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:05:56,075 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:05:56,078 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:05:57,004 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:05:57,004 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:05:57,891 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:05:57,892 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:05:58,799 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:05:58,822 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits
2025-06-17 13:05:58,823 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:05:59,377 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:05:59,378 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 13:05:59,379 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:05:59,379 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 13:05:59,432 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:05:59,433 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:05:59,434 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:05:59,442 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:06:00,013 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:06:00,954 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523003001_03106_00004_mirifushort_rate.fits>,).
2025-06-17 13:06:00,955 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:06:02,411 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits>,).
2025-06-17 13:06:02,412 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:06:03,338 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits>,).
2025-06-17 13:06:03,339 - stpipe.Spec2Pipeline.cube_build - INFO - Step skipped.
2025-06-17 13:06:04,807 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits>,).
2025-06-17 13:06:04,808 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2025-06-17 13:06:04,809 - stpipe.Spec2Pipeline - 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
2025-06-17 13:06:04,810 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:06:04,811 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:06:05,324 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs003/stage2/jw01523003001_03106_00004_mirifushort_cal.fits
2025-06-17 13:06:05,325 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:06:05,325 - stpipe - INFO - Results used jwst version: 1.18.1
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')
2025-06-17 13:06:05,601 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:06:05,682 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:06:05,690 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:06:05,710 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:06:05,719 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:06:05,727 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:06:05,750 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:06:05,751 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:06:05,752 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:06:05,753 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:06:05,754 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:06:05,756 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:06:05,756 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:06:05,758 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:06:05,762 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:06:05,763 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:06:05,764 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:06:05,765 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:06:05,766 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:06:05,767 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:06:05,769 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:06:05,770 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:06:05,771 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:06:05,772 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:06:05,773 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:06:05,774 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:06:05,775 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:06:05,776 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:06:05,777 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:06:05,778 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:06:05,779 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:06:05,780 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:06:05,781 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:06:05,782 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:06:05,784 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:06:05,785 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:06:06,815 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:06:06,852 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:06:06,862 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:06:06,899 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00001_mirifulong_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:06:06,904 - 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)
2025-06-17 13:06:07,217 - 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)
2025-06-17 13:06:07,482 - 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)
2025-06-17 13:06:07,778 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:06:07,779 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:06:07,779 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:06:07,779 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:06:07,780 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:06:07,780 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:06:07,780 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:06:07,781 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:06:07,781 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf'.
2025-06-17 13:06:07,783 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:06:07,783 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:06:07,783 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:06:07,784 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2025-06-17 13:06:07,784 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:06:07,785 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:06:07,785 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2025-06-17 13:06:07,786 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:06:07,786 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:06:07,786 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:06:07,787 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:06:07,787 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:06:07,788 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:06:07,788 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:06:07,788 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:06:07,789 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:06:07,789 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits'.
2025-06-17 13:06:07,790 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:06:07,790 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf'.
2025-06-17 13:06:07,790 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:06:07,791 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:06:07,791 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:06:07,791 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf'.
2025-06-17 13:06:07,792 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:06:07,793 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:06:07,793 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:06:07,800 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:06:07,801 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifulong
2025-06-17 13:06:07,801 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:06:08,664 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:06:09,253 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757701947
2025-06-17 13:06:10,082 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:06:10,818 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.026348009 -70.078890360 81.034142607 -70.078890360 81.034142607 -70.076231570 81.026348009 -70.076231570
2025-06-17 13:06:10,820 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:06:10,824 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:06:11,779 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:06:11,781 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:06:12,682 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:06:12,683 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:06:13,576 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:06:13,576 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:06:14,449 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>, []).
2025-06-17 13:06:14,450 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:06:15,332 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>, []).
2025-06-17 13:06:15,333 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:06:16,218 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:06:16,225 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:06:16,226 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:06:16,226 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:06:16,227 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:06:17,089 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:06:17,527 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:06:17,615 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:06:59,571 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:07:40,908 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.037295373156666756 DN/s
2025-06-17 13:07:40,909 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:07:40,912 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:07:41,906 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:07:41,977 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2025-06-17 13:07:41,978 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:07:41,979 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:07:41,979 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:07:42,462 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:07:43,527 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:07:43,545 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2025-06-17 13:07:43,568 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:07:43,569 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:07:43,570 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:07:44,018 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:07:44,021 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:07:45,055 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:07:45,056 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:07:46,027 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:07:46,028 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:07:47,015 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:07:47,040 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits
2025-06-17 13:07:47,040 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:07:47,487 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:07:47,487 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 13:07:47,488 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:07:47,488 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 13:07:47,541 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:07:47,542 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:07:47,543 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:07:47,552 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:07:48,089 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:07:49,176 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifulong_rate.fits>,).
2025-06-17 13:07:49,178 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:07:50,630 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_cal.fits>,).
2025-06-17 13:07:50,630 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:07:51,635 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_cal.fits>,).
2025-06-17 13:07:51,636 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:07:51,637 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:07:51,637 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:07:51,645 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:07:51,672 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2025-06-17 13:07:51,673 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['long', 'long']
2025-06-17 13:07:51,673 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:07:51,978 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:07:51,979 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:07:51,982 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:07:51,986 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:07:51,986 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:07:51,987 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 51 26.00 81.03024531 0.20000000 -5.10000008 5.10000008
2025-06-17 13:07:51,987 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 51 26.00 -70.07756097 0.20000000 -5.10000008 5.10000008
2025-06-17 13:07:51,987 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:07:51,988 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:07:51,988 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 2486 1.00 15.40774059 15.40774059 28.69605064
2025-06-17 13:07:51,989 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, long
2025-06-17 13:07:51,989 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, long
2025-06-17 13:07:51,990 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_s3d.fits
2025-06-17 13:07:53,455 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 638 with wavelength below 15.404848098754883
2025-06-17 13:08:03,688 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:08:03,688 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:08:03,700 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 2
2025-06-17 13:08:03,960 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.026169032 -70.078949807 81.026169032 -70.076172030 81.034321584 -70.076172030 81.034321584 -70.078949807
2025-06-17 13:08:03,963 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:08:04,111 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_s3d.fits
2025-06-17 13:08:05,187 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdcbba41400>,).
2025-06-17 13:08:05,216 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:08:05,225 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:08:05,233 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:08:05,234 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:08:05,634 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:08:05,643 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:08:05,824 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:08:05,824 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:08:05,825 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:08:05,828 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 18, y_center = 28, based on TARG_RA and TARG_DEC
2025-06-17 13:08:16,989 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:08:18,167 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:08:19,626 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_x1d.fits
2025-06-17 13:08:19,626 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:08:19,627 - stpipe.Spec2Pipeline - 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
2025-06-17 13:08:19,630 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:08:19,631 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:08:20,057 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifulong_cal.fits
2025-06-17 13:08:20,057 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:08:20,058 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:08:20,353 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:08:20,436 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:08:20,444 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:08:20,465 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:08:20,474 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:08:20,483 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:08:20,506 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:08:20,508 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:08:20,509 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:08:20,510 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:08:20,512 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:08:20,513 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:08:20,514 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:08:20,515 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:08:20,519 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:08:20,520 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:08:20,521 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:08:20,522 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:08:20,523 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:08:20,524 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:08:20,525 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:08:20,527 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:08:20,528 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:08:20,528 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:08:20,530 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:08:20,531 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:08:20,532 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:08:20,533 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:08:20,534 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:08:20,535 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:08:20,536 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:08:20,537 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:08:20,537 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:08:20,538 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:08:20,540 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:08:20,541 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:08:21,623 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:08:21,657 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:08:21,668 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:08:21,707 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00001_mirifushort_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:08:21,712 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:08:21,712 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:08:21,713 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:08:21,713 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:08:21,714 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:08:21,714 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:08:21,714 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:08:21,715 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:08:21,715 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf'.
2025-06-17 13:08:21,716 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:08:21,716 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:08:21,717 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:08:21,717 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2025-06-17 13:08:21,718 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:08:21,718 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:08:21,718 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2025-06-17 13:08:21,719 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:08:21,719 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:08:21,719 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:08:21,720 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:08:21,720 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:08:21,720 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:08:21,721 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:08:21,721 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:08:21,721 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:08:21,722 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits'.
2025-06-17 13:08:21,723 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:08:21,724 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf'.
2025-06-17 13:08:21,724 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:08:21,724 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:08:21,725 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:08:21,725 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf'.
2025-06-17 13:08:21,726 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:08:21,726 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:08:21,727 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:08:21,734 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:08:21,734 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00001_mirifushort
2025-06-17 13:08:21,735 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:08:22,713 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:08:23,491 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757701947
2025-06-17 13:08:24,623 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:08:25,506 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.028213957 -70.078350191 81.032713404 -70.078350191 81.032713404 -70.076747879 81.028213957 -70.076747879
2025-06-17 13:08:25,507 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:08:25,512 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:08:26,647 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:08:26,649 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:08:27,638 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:08:27,639 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:08:28,624 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:08:28,625 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:08:29,692 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>, []).
2025-06-17 13:08:29,693 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:08:30,666 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>, []).
2025-06-17 13:08:30,667 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:08:31,640 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:08:31,648 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:08:31,649 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:08:31,649 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:08:31,650 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:08:32,615 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:08:33,210 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:08:33,309 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:09:09,897 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:09:51,323 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.04982371094945109 DN/s
2025-06-17 13:09:51,324 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:09:51,327 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:09:52,320 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:09:52,389 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2025-06-17 13:09:52,389 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:09:52,390 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:09:52,390 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:09:52,997 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:09:54,074 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:09:54,091 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2025-06-17 13:09:54,114 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:09:54,115 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:09:54,115 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:09:54,693 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:09:54,696 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:09:55,690 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:09:55,691 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:09:56,655 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:09:56,656 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:09:57,613 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:09:57,637 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits
2025-06-17 13:09:57,637 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:09:58,193 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:09:58,194 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 13:09:58,195 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:09:58,195 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 13:09:58,244 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:09:58,245 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:09:58,246 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:09:58,255 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:09:58,795 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:09:59,842 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00001_mirifushort_rate.fits>,).
2025-06-17 13:09:59,844 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:10:01,463 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_cal.fits>,).
2025-06-17 13:10:01,464 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:10:02,524 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_cal.fits>,).
2025-06-17 13:10:02,525 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:10:02,526 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:10:02,526 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:10:02,534 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:10:02,552 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2025-06-17 13:10:02,553 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['long', 'long']
2025-06-17 13:10:02,554 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:10:02,853 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:10:02,854 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:10:02,858 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:10:02,862 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:10:02,863 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:10:02,863 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 47 24.00 81.03046368 0.13000000 -3.05499989 3.05499989
2025-06-17 13:10:02,864 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 49 25.00 -70.07754904 0.13000000 -3.18499988 3.18499988
2025-06-17 13:10:02,864 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:10:02,865 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:10:02,865 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 4068 1.00 6.52953386 6.52953386 11.70048332
2025-06-17 13:10:02,865 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, long
2025-06-17 13:10:02,866 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, long
2025-06-17 13:10:02,866 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_s3d.fits
2025-06-17 13:10:04,516 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3145 with wavelength below 6.5286736488342285
2025-06-17 13:10:11,315 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2150 with wavelength above 11.702359199523926
2025-06-17 13:10:17,565 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:10:17,566 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:10:17,583 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 1
2025-06-17 13:10:17,913 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.028026131 -70.078415685 81.028026131 -70.076682352 81.032901230 -70.076682352 81.032901230 -70.078415685
2025-06-17 13:10:17,916 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:10:18,095 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_s3d.fits
2025-06-17 13:10:19,172 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdcb5308cb0>,).
2025-06-17 13:10:19,182 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:10:19,190 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:10:19,198 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:10:19,198 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:10:19,583 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:10:19,592 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:10:19,931 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:10:19,931 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:10:19,932 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:10:19,935 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 15, y_center = 28, based on TARG_RA and TARG_DEC
2025-06-17 13:10:38,117 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:10:39,286 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:10:41,546 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_x1d.fits
2025-06-17 13:10:41,546 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:10:41,547 - stpipe.Spec2Pipeline - 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
2025-06-17 13:10:41,550 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:10:41,550 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:10:42,073 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00001_mirifushort_cal.fits
2025-06-17 13:10:42,074 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:10:42,074 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:10:42,365 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:10:42,448 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:10:42,456 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:10:42,477 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:10:42,486 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:10:42,494 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:10:42,517 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:10:42,518 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:10:42,519 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:10:42,520 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:10:42,521 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:10:42,522 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:10:42,523 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:10:42,524 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:10:42,529 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:10:42,530 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:10:42,531 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:10:42,532 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:10:42,533 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:10:42,534 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:10:42,535 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:10:42,538 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:10:42,538 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:10:42,539 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:10:42,540 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:10:42,541 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:10:42,542 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:10:42,543 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:10:42,544 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:10:42,545 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:10:42,546 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:10:42,547 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:10:42,548 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:10:42,549 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:10:42,551 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:10:42,553 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:10:43,693 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:10:43,729 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:10:43,739 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:10:43,778 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00002_mirifulong_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:10:43,783 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:10:43,784 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:10:43,784 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:10:43,785 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:10:43,785 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:10:43,786 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:10:43,786 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:10:43,787 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:10:43,787 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf'.
2025-06-17 13:10:43,788 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:10:43,788 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:10:43,789 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:10:43,789 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits'.
2025-06-17 13:10:43,789 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:10:43,790 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:10:43,790 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits'.
2025-06-17 13:10:43,792 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:10:43,792 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:10:43,793 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:10:43,793 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:10:43,794 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:10:43,794 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:10:43,795 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:10:43,795 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:10:43,795 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:10:43,796 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits'.
2025-06-17 13:10:43,796 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:10:43,797 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf'.
2025-06-17 13:10:43,798 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:10:43,799 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:10:43,799 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:10:43,800 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf'.
2025-06-17 13:10:43,801 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:10:43,801 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:10:43,802 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:10:43,808 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:10:43,809 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifulong
2025-06-17 13:10:43,809 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:10:44,790 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:10:45,406 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757068164
2025-06-17 13:10:46,250 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0133.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0134.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0138.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:10:46,988 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.027521605 -70.078419668 81.035316054 -70.078419668 81.035316054 -70.075760867 81.027521605 -70.075760867
2025-06-17 13:10:46,989 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:10:46,994 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:10:48,023 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:10:48,024 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:10:49,006 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:10:49,007 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:10:49,987 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:10:49,988 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:10:50,950 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>, []).
2025-06-17 13:10:50,950 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:10:51,937 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>, []).
2025-06-17 13:10:51,938 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:10:52,926 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:10:52,935 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:10:52,935 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:10:52,935 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:10:52,937 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:10:53,916 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:10:54,362 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:10:54,451 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:11:36,418 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:12:17,756 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.03358255699276924 DN/s
2025-06-17 13:12:17,756 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:12:17,759 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:12:18,771 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:12:18,844 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0824.fits
2025-06-17 13:12:18,845 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:12:18,846 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:12:18,846 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:12:19,317 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:12:20,378 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:12:20,395 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0074.fits
2025-06-17 13:12:20,419 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:12:20,419 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:12:20,420 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:12:20,859 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:12:20,862 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:12:21,931 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:12:21,932 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:12:22,926 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:12:22,927 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:12:24,007 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:12:24,031 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits
2025-06-17 13:12:24,032 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:12:24,467 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:12:24,468 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 13:12:24,468 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:12:24,469 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 13:12:24,514 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:12:24,515 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:12:24,515 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:12:24,524 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:12:25,000 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:12:26,014 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifulong_rate.fits>,).
2025-06-17 13:12:26,015 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:12:27,477 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_cal.fits>,).
2025-06-17 13:12:27,478 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:12:28,486 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_cal.fits>,).
2025-06-17 13:12:28,487 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:12:28,488 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:12:28,488 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:12:28,495 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:12:28,514 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2025-06-17 13:12:28,514 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['long', 'long']
2025-06-17 13:12:28,515 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:12:28,814 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:12:28,815 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:12:28,819 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:12:28,822 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:12:28,822 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:12:28,823 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 51 26.00 81.03141883 0.20000000 -5.10000008 5.10000008
2025-06-17 13:12:28,823 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 51 26.00 -70.07709027 0.20000000 -5.10000008 5.10000008
2025-06-17 13:12:28,824 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:12:28,824 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:12:28,825 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 2486 1.00 15.40774059 15.40774059 28.69605064
2025-06-17 13:12:28,825 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, long
2025-06-17 13:12:28,826 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, long
2025-06-17 13:12:28,826 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_s3d.fits
2025-06-17 13:12:30,223 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 638 with wavelength below 15.404848098754883
2025-06-17 13:12:40,424 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:12:40,425 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:12:40,437 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 2
2025-06-17 13:12:40,704 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.027342646 -70.078479110 81.027342646 -70.075701332 81.035495013 -70.075701332 81.035495013 -70.078479110
2025-06-17 13:12:40,707 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:12:40,855 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_s3d.fits
2025-06-17 13:12:41,979 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdcafeaf380>,).
2025-06-17 13:12:41,988 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:12:41,996 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:12:42,004 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:12:42,005 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:12:42,391 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:12:42,396 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:12:42,572 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:12:42,573 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:12:42,573 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:12:42,576 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 26, y_center = 20, based on TARG_RA and TARG_DEC
2025-06-17 13:12:53,705 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:12:54,870 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:12:56,308 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_x1d.fits
2025-06-17 13:12:56,309 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:12:56,310 - stpipe.Spec2Pipeline - 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
2025-06-17 13:12:56,315 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:12:56,315 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:12:56,738 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifulong_cal.fits
2025-06-17 13:12:56,739 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:12:56,740 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:12:57,032 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:12:57,114 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:12:57,123 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:12:57,143 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:12:57,152 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:12:57,160 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:12:57,183 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:12:57,184 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:12:57,185 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:12:57,186 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:12:57,187 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:12:57,188 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:12:57,189 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:12:57,190 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:12:57,194 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:12:57,195 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:12:57,196 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:12:57,197 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:12:57,198 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:12:57,199 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:12:57,200 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:12:57,202 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:12:57,203 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:12:57,204 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:12:57,205 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:12:57,206 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:12:57,206 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:12:57,207 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:12:57,208 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:12:57,209 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:12:57,210 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:12:57,211 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:12:57,212 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:12:57,213 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:12:57,214 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:12:57,216 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:12:58,294 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:12:58,328 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:12:58,338 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:12:58,376 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02101_00002_mirifushort_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:12:58,380 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:12:58,381 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:12:58,381 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:12:58,382 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:12:58,382 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:12:58,383 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:12:58,384 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:12:58,384 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:12:58,384 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf'.
2025-06-17 13:12:58,385 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:12:58,385 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:12:58,386 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:12:58,386 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits'.
2025-06-17 13:12:58,386 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:12:58,387 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:12:58,387 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits'.
2025-06-17 13:12:58,388 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:12:58,388 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:12:58,388 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:12:58,389 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:12:58,389 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:12:58,390 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:12:58,390 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:12:58,390 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:12:58,391 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:12:58,391 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits'.
2025-06-17 13:12:58,392 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:12:58,392 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf'.
2025-06-17 13:12:58,394 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:12:58,394 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:12:58,394 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:12:58,395 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf'.
2025-06-17 13:12:58,395 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:12:58,396 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:12:58,397 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:12:58,403 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:12:58,404 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02101_00002_mirifushort
2025-06-17 13:12:58,404 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:12:59,407 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:13:00,171 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757701947
2025-06-17 13:13:01,280 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0136.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0117.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0139.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:13:02,136 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.029387513 -70.077879494 81.033886880 -70.077879494 81.033886880 -70.076277178 81.029387513 -70.076277178
2025-06-17 13:13:02,137 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:13:02,142 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:13:03,225 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:13:03,227 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:13:04,224 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:13:04,225 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:13:05,214 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:13:05,215 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:13:06,204 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>, []).
2025-06-17 13:13:06,205 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:13:07,189 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>, []).
2025-06-17 13:13:07,190 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:13:08,179 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:13:08,187 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:13:08,188 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:13:08,188 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:13:08,190 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:13:09,187 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:13:09,760 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:13:09,857 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:13:46,439 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:14:27,738 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.02941615737736708 DN/s
2025-06-17 13:14:27,739 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:14:27,742 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:14:28,788 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:14:28,855 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0819.fits
2025-06-17 13:14:28,856 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:14:28,857 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:14:28,857 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:14:29,455 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:14:30,560 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:14:30,576 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0071.fits
2025-06-17 13:14:30,599 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:14:30,600 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:14:30,601 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:14:31,177 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:14:31,179 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:14:32,263 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:14:32,264 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:14:33,303 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:14:33,304 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:14:34,331 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:14:34,356 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0212.fits
2025-06-17 13:14:34,356 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:14:34,916 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:14:34,917 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 13:14:34,917 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:14:34,918 - stpipe.Spec2Pipeline.photom - INFO - band: LONG
2025-06-17 13:14:34,965 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:14:34,966 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:14:34,966 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:14:34,975 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:14:35,505 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:14:36,589 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02101_00002_mirifushort_rate.fits>,).
2025-06-17 13:14:36,590 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:14:38,226 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_cal.fits>,).
2025-06-17 13:14:38,227 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:14:39,287 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_cal.fits>,).
2025-06-17 13:14:39,288 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:14:39,288 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:14:39,288 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:14:39,296 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:14:39,314 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2025-06-17 13:14:39,315 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['long', 'long']
2025-06-17 13:14:39,315 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:14:39,613 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:14:39,614 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:14:39,618 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:14:39,621 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:14:39,622 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:14:39,622 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 47 24.00 81.03163720 0.13000000 -3.05499989 3.05499989
2025-06-17 13:14:39,623 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 49 25.00 -70.07707834 0.13000000 -3.18499988 3.18499988
2025-06-17 13:14:39,623 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:14:39,624 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:14:39,624 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 4068 1.00 6.52953386 6.52953386 11.70048332
2025-06-17 13:14:39,625 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, long
2025-06-17 13:14:39,625 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, long
2025-06-17 13:14:39,626 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_s3d.fits
2025-06-17 13:14:41,262 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3145 with wavelength below 6.5286736488342285
2025-06-17 13:14:48,031 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2150 with wavelength above 11.702359199523926
2025-06-17 13:14:54,272 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:14:54,272 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:14:54,290 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 1
2025-06-17 13:14:54,621 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.029199702 -70.077944986 81.029199702 -70.076211653 81.034074691 -70.076211653 81.034074691 -70.077944986
2025-06-17 13:14:54,624 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:14:54,805 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_s3d.fits
2025-06-17 13:14:55,950 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdcae00d2e0>,).
2025-06-17 13:14:55,959 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:14:55,967 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:14:55,975 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:14:55,976 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:14:56,358 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:14:56,373 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:14:56,710 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:14:56,710 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:14:56,711 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:14:56,714 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 26, y_center = 15, based on TARG_RA and TARG_DEC
2025-06-17 13:15:14,710 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:15:15,877 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:15:18,202 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_x1d.fits
2025-06-17 13:15:18,202 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:15:18,203 - stpipe.Spec2Pipeline - 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
2025-06-17 13:15:18,206 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:15:18,206 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:15:18,717 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02101_00002_mirifushort_cal.fits
2025-06-17 13:15:18,718 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:15:18,718 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:15:19,012 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:15:19,092 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:15:19,101 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:15:19,121 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:15:19,130 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:15:19,138 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:15:19,161 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:15:19,162 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:15:19,163 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:15:19,164 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:15:19,166 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:15:19,167 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:15:19,168 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:15:19,169 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:15:19,173 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:15:19,174 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:15:19,175 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:15:19,176 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:15:19,177 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:15:19,178 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:15:19,179 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:15:19,181 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:15:19,182 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:15:19,183 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:15:19,183 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:15:19,184 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:15:19,185 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:15:19,186 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:15:19,187 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:15:19,188 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:15:19,189 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:15:19,189 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:15:19,190 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:15:19,191 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:15:19,193 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:15:19,195 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:15:20,319 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:15:20,352 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:15:20,362 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:15:20,400 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00001_mirifulong_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:15:20,404 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:15:20,405 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:15:20,405 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:15:20,406 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:15:20,406 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:15:20,406 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:15:20,407 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:15:20,407 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:15:20,408 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf'.
2025-06-17 13:15:20,408 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:15:20,409 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:15:20,409 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:15:20,409 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits'.
2025-06-17 13:15:20,410 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:15:20,410 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:15:20,410 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2025-06-17 13:15:20,411 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:15:20,411 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:15:20,412 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:15:20,412 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:15:20,412 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:15:20,413 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:15:20,414 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:15:20,415 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:15:20,415 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:15:20,416 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits'.
2025-06-17 13:15:20,416 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:15:20,417 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf'.
2025-06-17 13:15:20,417 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:15:20,417 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:15:20,418 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:15:20,418 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf'.
2025-06-17 13:15:20,418 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:15:20,419 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:15:20,420 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:15:20,427 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:15:20,427 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifulong
2025-06-17 13:15:20,428 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:15:21,434 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:15:22,047 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757701947
2025-06-17 13:15:22,890 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:15:23,616 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.026496010 -70.078895253 81.034262259 -70.078895253 81.034262259 -70.076248522 81.026496010 -70.076248522
2025-06-17 13:15:23,617 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:15:23,622 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:15:24,691 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:15:24,693 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:15:25,716 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:15:25,717 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:15:26,708 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:15:26,709 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:15:27,703 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>, []).
2025-06-17 13:15:27,704 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:15:28,689 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>, []).
2025-06-17 13:15:28,690 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:15:29,674 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:15:29,681 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:15:29,681 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:15:29,682 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:15:29,683 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:15:30,674 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:15:31,106 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:15:31,192 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:16:13,182 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:16:54,494 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.02839585766196251 DN/s
2025-06-17 13:16:54,495 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:16:54,498 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:16:55,526 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:16:55,594 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits
2025-06-17 13:16:55,594 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:16:55,595 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:16:55,595 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:16:56,062 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:16:57,136 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:16:57,152 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2025-06-17 13:16:57,174 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:16:57,175 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:16:57,175 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:16:57,604 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:16:57,607 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:16:58,681 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:16:58,682 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:16:59,703 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:16:59,704 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:17:00,735 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:17:00,759 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits
2025-06-17 13:17:00,759 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:17:01,180 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:17:01,180 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 13:17:01,181 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:17:01,181 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 13:17:01,225 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:17:01,226 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:17:01,227 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:17:01,236 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:17:01,712 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:17:02,785 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifulong_rate.fits>,).
2025-06-17 13:17:02,786 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:17:04,269 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_cal.fits>,).
2025-06-17 13:17:04,270 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:17:05,325 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_cal.fits>,).
2025-06-17 13:17:05,326 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:17:05,327 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:17:05,327 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:17:05,334 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:17:05,352 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2025-06-17 13:17:05,353 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['medium', 'medium']
2025-06-17 13:17:05,353 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:17:05,653 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:17:05,654 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:17:05,658 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:17:05,662 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:17:05,662 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:17:05,663 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 51 26.00 81.03037913 0.20000000 -5.10000008 5.10000008
2025-06-17 13:17:05,663 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 51 26.00 -70.07757189 0.20000000 -5.10000008 5.10000008
2025-06-17 13:17:05,663 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:17:05,664 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:17:05,664 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 2830 1.00 13.33861923 13.33861923 24.48033714
2025-06-17 13:17:05,665 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, medium
2025-06-17 13:17:05,665 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, medium
2025-06-17 13:17:05,666 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_s3d.fits
2025-06-17 13:17:07,069 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 967 with wavelength below 13.33633041381836
2025-06-17 13:17:18,296 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:17:18,297 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:17:18,310 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:17:18,599 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.026302857 -70.078960730 81.026302857 -70.076182952 81.034455412 -70.076182952 81.034455412 -70.078960730
2025-06-17 13:17:18,602 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:17:18,761 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_s3d.fits
2025-06-17 13:17:19,927 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdca96f3020>,).
2025-06-17 13:17:19,936 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:17:19,944 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:17:19,951 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:17:19,952 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:17:20,323 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:17:20,333 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:17:20,579 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:17:20,580 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:17:20,581 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:17:20,583 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 19, y_center = 28, based on TARG_RA and TARG_DEC
2025-06-17 13:17:33,186 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:17:34,338 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:17:35,947 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_x1d.fits
2025-06-17 13:17:35,948 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:17:35,949 - stpipe.Spec2Pipeline - 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
2025-06-17 13:17:35,954 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:17:35,955 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:17:36,369 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifulong_cal.fits
2025-06-17 13:17:36,370 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:17:36,371 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:17:36,663 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:17:36,741 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:17:36,750 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:17:36,770 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:17:36,779 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:17:36,787 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:17:36,811 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:17:36,812 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:17:36,813 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:17:36,814 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:17:36,815 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:17:36,817 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:17:36,817 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:17:36,819 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:17:36,823 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:17:36,824 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:17:36,825 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:17:36,826 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:17:36,827 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:17:36,828 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:17:36,829 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:17:36,831 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:17:36,832 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:17:36,833 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:17:36,834 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:17:36,835 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:17:36,836 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:17:36,837 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:17:36,839 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:17:36,840 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:17:36,840 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:17:36,841 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:17:36,842 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:17:36,844 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:17:36,845 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:17:36,847 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:17:37,941 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:17:37,978 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:17:37,988 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:17:38,025 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00001_mirifushort_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:17:38,029 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:17:38,030 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:17:38,031 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:17:38,031 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:17:38,031 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:17:38,032 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:17:38,033 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:17:38,034 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:17:38,034 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf'.
2025-06-17 13:17:38,034 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:17:38,035 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:17:38,035 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:17:38,036 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2025-06-17 13:17:38,036 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:17:38,036 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:17:38,037 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2025-06-17 13:17:38,037 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:17:38,038 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:17:38,038 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:17:38,038 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:17:38,039 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:17:38,039 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:17:38,039 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:17:38,040 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:17:38,040 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:17:38,040 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits'.
2025-06-17 13:17:38,041 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:17:38,041 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf'.
2025-06-17 13:17:38,042 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:17:38,042 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:17:38,042 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:17:38,043 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf'.
2025-06-17 13:17:38,043 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:17:38,043 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:17:38,044 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:17:38,052 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:17:38,053 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00001_mirifushort
2025-06-17 13:17:38,053 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:17:39,072 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:17:39,834 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757068164
2025-06-17 13:17:40,918 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:17:41,785 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.028357924 -70.078305088 81.032793989 -70.078305088 81.032793989 -70.076700214 81.028357924 -70.076700214
2025-06-17 13:17:41,786 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:17:41,791 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:17:42,904 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:17:42,906 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:17:43,930 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:17:43,930 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:17:44,953 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:17:44,954 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:17:45,999 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>, []).
2025-06-17 13:17:46,000 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:17:47,041 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>, []).
2025-06-17 13:17:47,042 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:17:48,093 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:17:48,100 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:17:48,101 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:17:48,101 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:17:48,103 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:17:49,137 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:17:49,714 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:17:49,809 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:18:28,213 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:19:09,480 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.04841423936220972 DN/s
2025-06-17 13:19:09,480 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:19:09,483 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:19:10,607 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:19:10,675 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2025-06-17 13:19:10,675 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:19:10,676 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:19:10,676 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:19:11,280 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:19:12,429 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:19:12,446 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2025-06-17 13:19:12,468 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:19:12,469 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:19:12,470 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:19:13,042 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:19:13,045 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:19:14,194 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:19:14,195 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:19:15,284 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:19:15,285 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:19:16,370 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:19:16,393 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits
2025-06-17 13:19:16,393 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:19:16,950 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:19:16,951 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 13:19:16,952 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:19:16,952 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 13:19:17,000 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:19:17,001 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:19:17,001 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:19:17,010 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:19:17,552 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:19:18,730 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00001_mirifushort_rate.fits>,).
2025-06-17 13:19:18,732 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:19:20,442 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_cal.fits>,).
2025-06-17 13:19:20,443 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:19:21,565 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_cal.fits>,).
2025-06-17 13:19:21,566 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:19:21,566 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:19:21,567 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:19:21,574 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:19:21,592 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2025-06-17 13:19:21,593 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['medium', 'medium']
2025-06-17 13:19:21,593 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:19:21,895 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:19:21,896 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:19:21,900 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:19:21,904 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:19:21,904 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:19:21,904 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 45 23.00 81.03057596 0.13000000 -2.92499989 2.92499989
2025-06-17 13:19:21,905 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 49 25.00 -70.07750265 0.13000000 -3.18499988 3.18499988
2025-06-17 13:19:21,905 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:19:21,906 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:19:21,906 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 4243 1.00 5.65960693 5.65960693 10.13073730
2025-06-17 13:19:21,907 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, medium
2025-06-17 13:19:21,907 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, medium
2025-06-17 13:19:21,908 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_s3d.fits
2025-06-17 13:19:23,533 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3801 with wavelength below 5.658884048461914
2025-06-17 13:19:30,458 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2469 with wavelength above 10.13226318359375
2025-06-17 13:19:36,930 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:19:36,931 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:19:36,948 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 1
2025-06-17 13:19:37,270 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.028244392 -70.078369302 81.028244392 -70.076635969 81.032907521 -70.076635969 81.032907521 -70.078369302
2025-06-17 13:19:37,273 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:19:37,450 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_s3d.fits
2025-06-17 13:19:38,643 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdca8cb9be0>,).
2025-06-17 13:19:38,653 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:19:38,660 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:19:38,668 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:19:38,669 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:19:39,043 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:19:39,055 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:19:39,406 - stpipe.Spec2Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:19:39,406 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 11.5787, y_center = 40.0786
2025-06-17 13:19:58,021 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:19:59,184 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:20:01,546 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_x1d.fits
2025-06-17 13:20:01,546 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:20:01,547 - stpipe.Spec2Pipeline - 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
2025-06-17 13:20:01,550 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:20:01,550 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:20:02,060 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00001_mirifushort_cal.fits
2025-06-17 13:20:02,060 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:20:02,061 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:20:02,347 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:20:02,427 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:20:02,435 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:20:02,455 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:20:02,464 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:20:02,472 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:20:02,495 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:20:02,496 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:20:02,497 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:20:02,498 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:20:02,499 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:20:02,500 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:20:02,501 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:20:02,502 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:20:02,506 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:20:02,507 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:20:02,509 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:20:02,510 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:20:02,511 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:20:02,512 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:20:02,513 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:20:02,515 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:20:02,516 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:20:02,517 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:20:02,518 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:20:02,519 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:20:02,520 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:20:02,521 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:20:02,522 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:20:02,523 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:20:02,524 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:20:02,526 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:20:02,526 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:20:02,527 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:20:02,529 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:20:02,530 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:20:03,721 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:20:03,755 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:20:03,765 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:20:03,802 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00002_mirifulong_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:20:03,807 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:20:03,808 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:20:03,808 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:20:03,808 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:20:03,809 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:20:03,810 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:20:03,810 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:20:03,811 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:20:03,811 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf'.
2025-06-17 13:20:03,812 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:20:03,812 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:20:03,813 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:20:03,813 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits'.
2025-06-17 13:20:03,814 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:20:03,815 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:20:03,815 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits'.
2025-06-17 13:20:03,815 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:20:03,816 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:20:03,816 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:20:03,817 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:20:03,818 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:20:03,818 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:20:03,819 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:20:03,819 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:20:03,820 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:20:03,820 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits'.
2025-06-17 13:20:03,820 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:20:03,821 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf'.
2025-06-17 13:20:03,821 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:20:03,822 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:20:03,822 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:20:03,822 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf'.
2025-06-17 13:20:03,823 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:20:03,823 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:20:03,825 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:20:03,832 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:20:03,832 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifulong
2025-06-17 13:20:03,832 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:20:04,925 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:20:05,530 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757068164
2025-06-17 13:20:06,357 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0139.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0135.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0140.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:20:07,077 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.027668797 -70.078422898 81.035434917 -70.078422898 81.035434917 -70.075776147 81.027668797 -70.075776147
2025-06-17 13:20:07,079 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:20:07,084 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:20:08,228 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:20:08,230 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:20:09,309 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:20:09,310 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:20:10,367 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:20:10,368 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:20:11,434 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>, []).
2025-06-17 13:20:11,435 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:20:12,530 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>, []).
2025-06-17 13:20:12,530 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:20:13,636 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:20:13,644 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:20:13,644 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:20:13,645 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:20:13,647 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:20:14,813 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:20:15,255 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:20:15,343 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:20:57,301 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:21:38,609 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.01782185770571232 DN/s
2025-06-17 13:21:38,610 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:21:38,613 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:21:39,750 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:21:39,817 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0823.fits
2025-06-17 13:21:39,818 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:21:39,818 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:21:39,819 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:21:40,277 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:21:41,461 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:21:41,479 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0075.fits
2025-06-17 13:21:41,502 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:21:41,502 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:21:41,503 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:21:41,951 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:21:41,953 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:21:43,095 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:21:43,095 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:21:44,207 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:21:44,207 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:21:45,306 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:21:45,331 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0213.fits
2025-06-17 13:21:45,331 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:21:45,750 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:21:45,750 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 13:21:45,751 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:21:45,751 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 13:21:45,794 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:21:45,796 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:21:45,796 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:21:45,805 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:21:46,277 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:21:47,468 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifulong_rate.fits>,).
2025-06-17 13:21:47,469 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:21:49,098 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_cal.fits>,).
2025-06-17 13:21:49,099 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:21:50,290 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_cal.fits>,).
2025-06-17 13:21:50,291 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:21:50,292 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:21:50,292 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:21:50,299 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:21:50,317 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2025-06-17 13:21:50,318 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['medium', 'medium']
2025-06-17 13:21:50,319 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:21:50,616 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:21:50,617 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:21:50,620 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:21:50,624 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:21:50,624 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:21:50,625 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 51 26.00 81.03155186 0.20000000 -5.10000008 5.10000008
2025-06-17 13:21:50,625 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 51 26.00 -70.07709952 0.20000000 -5.10000008 5.10000008
2025-06-17 13:21:50,626 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:21:50,627 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:21:50,627 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 2830 1.00 13.33861923 13.33861923 24.48033714
2025-06-17 13:21:50,628 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, medium
2025-06-17 13:21:50,628 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, medium
2025-06-17 13:21:50,629 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_s3d.fits
2025-06-17 13:21:52,022 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 967 with wavelength below 13.33633041381836
2025-06-17 13:22:03,233 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:22:03,234 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:22:03,247 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:22:03,519 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.027475672 -70.078488365 81.027475672 -70.075710587 81.035628042 -70.075710587 81.035628042 -70.078488365
2025-06-17 13:22:03,522 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:22:03,678 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_s3d.fits
2025-06-17 13:22:04,918 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdc8e360d40>,).
2025-06-17 13:22:04,928 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:22:04,936 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:22:04,944 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:22:04,944 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:22:05,318 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:22:05,330 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:22:05,571 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:22:05,571 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:22:05,572 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:22:05,575 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 26, y_center = 20, based on TARG_RA and TARG_DEC
2025-06-17 13:22:18,016 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:22:19,183 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:22:20,806 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_x1d.fits
2025-06-17 13:22:20,807 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:22:20,808 - stpipe.Spec2Pipeline - 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
2025-06-17 13:22:20,812 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:22:20,812 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:22:21,249 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifulong_cal.fits
2025-06-17 13:22:21,250 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:22:21,250 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:22:21,543 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:22:21,626 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:22:21,634 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:22:21,655 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:22:21,664 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:22:21,672 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:22:21,694 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:22:21,696 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:22:21,697 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:22:21,698 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:22:21,699 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:22:21,700 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:22:21,701 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:22:21,702 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:22:21,707 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:22:21,708 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:22:21,709 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:22:21,710 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:22:21,711 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:22:21,712 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:22:21,714 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:22:21,716 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:22:21,717 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:22:21,718 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:22:21,719 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:22:21,720 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:22:21,721 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:22:21,722 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:22:21,723 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:22:21,724 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:22:21,725 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:22:21,726 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:22:21,727 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:22:21,728 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:22:21,729 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:22:21,731 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:22:22,929 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:22:22,966 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:22:22,976 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:22:23,014 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02103_00002_mirifushort_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:22:23,018 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:22:23,019 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:22:23,019 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:22:23,020 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:22:23,020 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:22:23,020 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:22:23,021 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:22:23,021 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:22:23,022 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf'.
2025-06-17 13:22:23,023 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:22:23,023 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:22:23,024 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:22:23,024 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits'.
2025-06-17 13:22:23,024 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:22:23,025 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:22:23,025 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits'.
2025-06-17 13:22:23,026 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:22:23,026 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:22:23,026 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:22:23,027 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:22:23,028 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:22:23,029 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:22:23,029 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:22:23,030 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:22:23,030 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:22:23,031 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits'.
2025-06-17 13:22:23,031 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:22:23,032 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf'.
2025-06-17 13:22:23,033 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:22:23,033 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:22:23,033 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:22:23,034 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf'.
2025-06-17 13:22:23,034 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:22:23,035 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:22:23,035 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:22:23,042 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:22:23,043 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02103_00002_mirifushort
2025-06-17 13:22:23,043 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:22:24,168 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:22:24,925 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757068164
2025-06-17 13:22:26,011 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0121.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0129.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0135.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:22:26,854 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.029530672 -70.077832725 81.033966675 -70.077832725 81.033966675 -70.076227840 81.029530672 -70.076227840
2025-06-17 13:22:26,856 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:22:26,860 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:22:28,076 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:22:28,078 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:22:29,230 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:22:29,231 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:22:30,372 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:22:30,373 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:22:31,513 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>, []).
2025-06-17 13:22:31,514 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:22:32,635 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>, []).
2025-06-17 13:22:32,636 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:22:33,727 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:22:33,734 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:22:33,735 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:22:33,735 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:22:33,737 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:22:34,831 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:22:35,411 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:22:35,507 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:23:13,898 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:23:55,192 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.03839020676603476 DN/s
2025-06-17 13:23:55,193 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:23:55,196 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:23:56,383 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:23:56,451 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0822.fits
2025-06-17 13:23:56,452 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:23:56,452 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:23:56,453 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:23:57,055 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:23:58,269 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:23:58,285 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0073.fits
2025-06-17 13:23:58,308 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:23:58,308 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:23:58,309 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:23:58,875 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:23:58,878 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:24:00,142 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:24:00,143 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:24:01,351 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:24:01,351 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:24:02,544 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:24:02,568 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0214.fits
2025-06-17 13:24:02,569 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:24:03,127 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:24:03,128 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 13:24:03,129 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:24:03,129 - stpipe.Spec2Pipeline.photom - INFO - band: MEDIUM
2025-06-17 13:24:03,177 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:24:03,178 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:24:03,179 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:24:03,188 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:24:03,732 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:24:05,023 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02103_00002_mirifushort_rate.fits>,).
2025-06-17 13:24:05,025 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:24:06,838 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_cal.fits>,).
2025-06-17 13:24:06,839 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:24:08,078 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_cal.fits>,).
2025-06-17 13:24:08,079 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:24:08,079 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:24:08,080 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:24:08,087 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:24:08,106 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2025-06-17 13:24:08,106 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['medium', 'medium']
2025-06-17 13:24:08,107 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:24:08,406 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:24:08,407 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:24:08,411 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:24:08,415 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:24:08,415 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:24:08,416 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 45 23.00 81.03174867 0.13000000 -2.92499989 2.92499989
2025-06-17 13:24:08,416 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 49 25.00 -70.07703028 0.13000000 -3.18499988 3.18499988
2025-06-17 13:24:08,417 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:24:08,418 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:24:08,418 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 4243 1.00 5.65960693 5.65960693 10.13073730
2025-06-17 13:24:08,419 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, medium
2025-06-17 13:24:08,419 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, medium
2025-06-17 13:24:08,419 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_s3d.fits
2025-06-17 13:24:10,091 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3801 with wavelength below 5.658884048461914
2025-06-17 13:24:17,116 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2469 with wavelength above 10.13226318359375
2025-06-17 13:24:23,556 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:24:23,556 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:24:23,574 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 1
2025-06-17 13:24:23,906 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.029417162 -70.077896934 81.029417162 -70.076163601 81.034080185 -70.076163601 81.034080185 -70.077896934
2025-06-17 13:24:23,909 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:24:24,093 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_s3d.fits
2025-06-17 13:24:25,438 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdca4ea1fd0>,).
2025-06-17 13:24:25,448 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:24:25,456 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:24:25,464 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:24:25,465 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:24:25,855 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:24:25,864 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:24:26,222 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:762: NoDetectionsWarning: Sources were found, but none pass the sharpness, roundness, or peakmax criteria
warnings.warn('Sources were found, but none pass the sharpness, '
2025-06-17 13:24:26,223 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:24:26,224 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:24:26,226 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 26, y_center = 14, based on TARG_RA and TARG_DEC
2025-06-17 13:24:45,020 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:24:46,177 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:24:48,534 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_x1d.fits
2025-06-17 13:24:48,534 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:24:48,536 - stpipe.Spec2Pipeline - 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
2025-06-17 13:24:48,538 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:24:48,539 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:24:49,044 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02103_00002_mirifushort_cal.fits
2025-06-17 13:24:49,045 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:24:49,045 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:24:49,332 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:24:49,409 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:24:49,418 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:24:49,439 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:24:49,448 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:24:49,456 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:24:49,479 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:24:49,480 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:24:49,481 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:24:49,482 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:24:49,484 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:24:49,485 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:24:49,486 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:24:49,487 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:24:49,492 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:24:49,493 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:24:49,494 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:24:49,495 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:24:49,495 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:24:49,497 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:24:49,498 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:24:49,500 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:24:49,502 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:24:49,503 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:24:49,504 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:24:49,505 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:24:49,506 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:24:49,507 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:24:49,508 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:24:49,509 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:24:49,510 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:24:49,511 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:24:49,512 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:24:49,513 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:24:49,515 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:24:49,517 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:24:50,826 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:24:50,862 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:24:50,872 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:24:50,910 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00001_mirifulong_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:24:50,914 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:24:50,915 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:24:50,915 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:24:50,916 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:24:50,916 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:24:50,917 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:24:50,917 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:24:50,918 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:24:50,918 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf'.
2025-06-17 13:24:50,919 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:24:50,920 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:24:50,920 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:24:50,921 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2025-06-17 13:24:50,922 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:24:50,922 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:24:50,923 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2025-06-17 13:24:50,923 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:24:50,924 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:24:50,924 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:24:50,925 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:24:50,925 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:24:50,926 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:24:50,926 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:24:50,927 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:24:50,927 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:24:50,927 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits'.
2025-06-17 13:24:50,928 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:24:50,928 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf'.
2025-06-17 13:24:50,930 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:24:50,931 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:24:50,931 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:24:50,932 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf'.
2025-06-17 13:24:50,932 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:24:50,932 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:24:50,933 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:24:50,940 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:24:50,940 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifulong
2025-06-17 13:24:50,941 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:24:52,095 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:24:52,698 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757068164
2025-06-17 13:24:53,534 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:24:54,272 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.026421453 -70.078876819 81.034348064 -70.078876819 81.034348064 -70.076236515 81.026421453 -70.076236515
2025-06-17 13:24:54,273 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:24:54,278 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:24:55,503 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:24:55,506 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:24:56,693 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:24:56,694 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:24:57,819 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:24:57,820 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:24:58,977 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>, []).
2025-06-17 13:24:58,978 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:25:00,126 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>, []).
2025-06-17 13:25:00,127 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:25:01,344 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:25:01,352 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:25:01,352 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:25:01,353 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:25:01,354 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:25:02,516 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:25:02,962 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:25:03,052 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:25:45,113 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:26:26,496 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.009865693747997284 DN/s
2025-06-17 13:26:26,496 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:26:26,499 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:26:27,660 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:26:27,727 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2025-06-17 13:26:27,728 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:26:27,728 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:26:27,729 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:26:28,180 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:26:29,388 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:26:29,404 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2025-06-17 13:26:29,425 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:26:29,426 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:26:29,426 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:26:29,848 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:26:29,851 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:26:31,062 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:26:31,062 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:26:32,239 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:26:32,239 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:26:33,411 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:26:33,434 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits
2025-06-17 13:26:33,435 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:26:33,853 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:26:33,854 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 13:26:33,854 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:26:33,855 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 13:26:33,899 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:26:33,900 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:26:33,901 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:26:33,909 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:26:34,390 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:26:35,617 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifulong_rate.fits>,).
2025-06-17 13:26:35,618 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:26:37,250 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_cal.fits>,).
2025-06-17 13:26:37,251 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:26:38,449 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_cal.fits>,).
2025-06-17 13:26:38,450 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:26:38,450 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:26:38,451 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:26:38,458 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:26:38,476 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2025-06-17 13:26:38,477 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'short']
2025-06-17 13:26:38,477 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:26:38,779 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:26:38,780 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:26:38,783 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:26:38,787 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:26:38,787 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:26:38,788 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 53 27.00 81.03038476 0.20000000 -5.30000008 5.30000008
2025-06-17 13:26:38,788 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 51 26.00 -70.07755667 0.20000000 -5.10000008 5.10000008
2025-06-17 13:26:38,789 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:26:38,789 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:26:38,789 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 3128 1.00 11.54997730 11.54997730 20.95471191
2025-06-17 13:26:38,790 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, short
2025-06-17 13:26:38,790 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, short
2025-06-17 13:26:38,791 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_s3d.fits
2025-06-17 13:26:40,187 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2079 with wavelength below 11.548135757446289
2025-06-17 13:26:52,180 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:26:52,181 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:26:52,195 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:26:52,498 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.026145433 -70.078945506 81.026145433 -70.076167728 81.034624084 -70.076167728 81.034624084 -70.078945506
2025-06-17 13:26:52,501 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:26:52,669 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_s3d.fits
2025-06-17 13:26:53,942 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdc91774950>,).
2025-06-17 13:26:53,951 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:26:53,959 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:26:53,967 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:26:53,967 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:26:54,344 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:26:54,355 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:26:54,648 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:26:54,648 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:26:54,649 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:26:54,652 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 20, y_center = 28, based on TARG_RA and TARG_DEC
2025-06-17 13:27:08,248 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:27:09,423 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:27:11,191 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_x1d.fits
2025-06-17 13:27:11,192 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:27:11,193 - stpipe.Spec2Pipeline - 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
2025-06-17 13:27:11,195 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:27:11,196 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:27:11,618 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifulong_cal.fits
2025-06-17 13:27:11,619 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:27:11,620 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:27:11,906 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:27:11,992 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:27:12,000 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:27:12,020 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:27:12,029 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:27:12,037 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:27:12,060 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:27:12,061 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:27:12,062 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:27:12,063 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:27:12,064 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:27:12,065 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:27:12,066 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:27:12,067 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:27:12,072 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:27:12,073 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:27:12,074 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:27:12,075 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:27:12,075 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:27:12,076 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:27:12,078 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:27:12,080 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:27:12,081 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:27:12,082 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:27:12,083 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:27:12,084 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:27:12,085 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:27:12,086 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:27:12,087 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:27:12,087 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:27:12,088 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:27:12,089 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:27:12,090 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:27:12,091 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:27:12,093 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:27:12,094 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:27:13,386 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:27:13,421 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:27:13,432 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:27:13,470 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00001_mirifushort_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:27:13,475 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:27:13,476 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:27:13,476 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:27:13,477 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:27:13,477 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:27:13,477 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:27:13,478 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:27:13,478 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:27:13,479 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf'.
2025-06-17 13:27:13,479 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:27:13,480 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:27:13,480 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:27:13,480 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2025-06-17 13:27:13,481 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:27:13,481 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:27:13,481 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2025-06-17 13:27:13,482 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:27:13,482 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:27:13,483 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:27:13,483 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:27:13,483 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:27:13,484 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:27:13,484 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:27:13,485 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:27:13,485 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:27:13,485 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits'.
2025-06-17 13:27:13,486 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:27:13,486 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf'.
2025-06-17 13:27:13,486 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:27:13,487 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:27:13,487 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:27:13,488 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf'.
2025-06-17 13:27:13,490 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:27:13,490 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:27:13,491 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:27:13,498 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:27:13,498 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00001_mirifushort
2025-06-17 13:27:13,499 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:27:14,677 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:27:15,447 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757068164
2025-06-17 13:27:16,563 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:27:16,929 - stpipe.Spec2Pipeline.assign_wcs - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/selector.py:634: RuntimeWarning: invalid value encountered in add
np.empty(inputs[0].shape) + self._undefined_transform_value
2025-06-17 13:27:17,426 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.028354347 -70.078385859 81.032889179 -70.078385859 81.032889179 -70.076790777 81.028354347 -70.076790777
2025-06-17 13:27:17,427 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:27:17,432 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:27:18,768 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:27:18,771 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:27:19,960 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:27:19,961 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:27:21,140 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:27:21,140 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:27:22,295 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>, []).
2025-06-17 13:27:22,296 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:27:23,440 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>, []).
2025-06-17 13:27:23,441 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:27:24,596 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:27:24,603 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:27:24,603 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:27:24,604 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:27:24,605 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:27:25,753 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:27:26,339 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:27:26,433 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:28:06,544 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:28:47,925 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.04588758060712525 DN/s
2025-06-17 13:28:47,925 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:28:47,928 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:28:49,129 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:28:49,193 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2025-06-17 13:28:49,194 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:28:49,195 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:28:49,195 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:28:49,794 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:28:51,026 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:28:51,043 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2025-06-17 13:28:51,064 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:28:51,065 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:28:51,066 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:28:51,629 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:28:51,632 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:28:52,865 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:28:52,866 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:28:54,049 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:28:54,050 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:28:55,240 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:28:55,264 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits
2025-06-17 13:28:55,264 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:28:55,810 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:28:55,811 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 13:28:55,811 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:28:55,812 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 13:28:55,858 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:28:55,859 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:28:55,860 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:28:55,868 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:28:56,394 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:28:57,661 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00001_mirifushort_rate.fits>,).
2025-06-17 13:28:57,663 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:28:59,509 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_cal.fits>,).
2025-06-17 13:28:59,510 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:29:00,767 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_cal.fits>,).
2025-06-17 13:29:00,768 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:29:00,768 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:29:00,769 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:29:00,776 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:29:00,794 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2025-06-17 13:29:00,795 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'short']
2025-06-17 13:29:00,796 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:29:01,096 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:29:01,097 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:29:01,101 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:29:01,105 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:29:01,106 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:29:01,106 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 47 24.00 81.03062176 0.13000000 -3.05499989 3.05499989
2025-06-17 13:29:01,107 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 49 25.00 -70.07758832 0.13000000 -3.18499988 3.18499988
2025-06-17 13:29:01,108 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:29:01,108 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:29:01,108 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 4404 1.00 4.90000010 4.90000010 8.77080059
2025-06-17 13:29:01,109 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, short
2025-06-17 13:29:01,110 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, short
2025-06-17 13:29:01,110 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_s3d.fits
2025-06-17 13:29:02,733 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3697 with wavelength below 4.899390697479248
2025-06-17 13:29:09,831 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2597 with wavelength above 8.772054672241211
2025-06-17 13:29:16,472 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:29:16,473 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:29:16,491 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 1
2025-06-17 13:29:16,843 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.028184208 -70.078454968 81.028184208 -70.076721635 81.033059318 -70.076721635 81.033059318 -70.078454968
2025-06-17 13:29:16,846 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:29:17,036 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_s3d.fits
2025-06-17 13:29:18,375 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdc91776c30>,).
2025-06-17 13:29:18,384 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:29:18,392 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:29:18,400 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:29:18,400 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:29:18,784 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:29:18,800 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:29:19,178 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:746: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:29:19,178 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:29:19,179 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:29:19,182 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 16, y_center = 30, based on TARG_RA and TARG_DEC
2025-06-17 13:29:38,581 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:29:39,772 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:29:42,257 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_x1d.fits
2025-06-17 13:29:42,258 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:29:42,259 - stpipe.Spec2Pipeline - 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
2025-06-17 13:29:42,262 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:29:42,263 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:29:42,786 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00001_mirifushort_cal.fits
2025-06-17 13:29:42,787 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:29:42,787 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:29:43,077 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:29:43,185 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:29:43,194 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:29:43,214 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:29:43,223 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:29:43,232 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:29:43,255 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:29:43,257 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:29:43,258 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:29:43,259 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:29:43,260 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:29:43,261 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:29:43,262 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:29:43,263 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:29:43,268 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:29:43,269 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:29:43,270 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:29:43,271 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:29:43,272 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:29:43,272 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:29:43,274 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:29:43,276 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:29:43,278 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:29:43,279 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:29:43,280 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:29:43,281 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:29:43,282 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:29:43,283 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:29:43,284 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:29:43,285 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:29:43,285 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:29:43,286 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:29:43,287 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:29:43,288 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:29:43,290 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:29:43,291 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:29:44,725 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:29:44,761 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:29:44,772 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:29:44,810 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00002_mirifulong_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:29:44,815 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:29:44,815 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:29:44,816 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:29:44,816 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:29:44,817 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:29:44,817 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:29:44,817 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:29:44,818 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:29:44,818 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf'.
2025-06-17 13:29:44,819 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:29:44,819 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:29:44,820 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:29:44,820 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits'.
2025-06-17 13:29:44,820 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:29:44,821 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:29:44,821 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits'.
2025-06-17 13:29:44,823 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:29:44,823 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:29:44,824 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:29:44,824 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:29:44,825 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:29:44,825 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:29:44,826 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:29:44,826 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:29:44,827 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:29:44,827 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits'.
2025-06-17 13:29:44,827 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:29:44,828 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf'.
2025-06-17 13:29:44,828 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:29:44,829 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:29:44,829 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:29:44,829 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf'.
2025-06-17 13:29:44,830 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:29:44,830 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:29:44,832 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:29:44,838 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:29:44,839 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifulong
2025-06-17 13:29:44,839 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:29:46,073 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:29:46,690 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.0000087564343811
2025-06-17 13:29:47,535 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0124.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0136.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0136.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:29:48,261 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.027594392 -70.078404119 81.035520879 -70.078404119 81.035520879 -70.075763793 81.027594392 -70.075763793
2025-06-17 13:29:48,262 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:29:48,267 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:29:49,539 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:29:49,541 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:29:50,785 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:29:50,786 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:29:52,028 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:29:52,029 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:29:53,281 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>, []).
2025-06-17 13:29:53,282 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:29:54,532 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>, []).
2025-06-17 13:29:54,532 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:29:55,787 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:29:55,794 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:29:55,795 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:29:55,795 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:29:55,797 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:29:57,036 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:29:57,481 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:29:57,571 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:30:39,563 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:31:20,934 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.033130113035440445 DN/s
2025-06-17 13:31:20,935 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:31:20,938 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:31:22,264 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:31:22,336 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0821.fits
2025-06-17 13:31:22,337 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:31:22,338 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:31:22,338 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:31:22,806 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:31:24,179 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:31:24,195 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0070.fits
2025-06-17 13:31:24,218 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:31:24,218 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:31:24,219 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:31:24,659 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:31:24,662 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:31:26,022 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:31:26,023 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:31:27,331 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:31:27,332 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:31:28,656 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:31:28,681 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0215.fits
2025-06-17 13:31:28,681 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:31:29,116 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:31:29,117 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFULONG
2025-06-17 13:31:29,117 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:31:29,118 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 13:31:29,167 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:31:29,168 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:31:29,168 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:31:29,179 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:31:29,666 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:31:31,058 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifulong_rate.fits>,).
2025-06-17 13:31:31,059 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:31:32,862 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_cal.fits>,).
2025-06-17 13:31:32,863 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:31:34,232 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_cal.fits>,).
2025-06-17 13:31:34,233 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:31:34,234 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:31:34,234 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:31:34,241 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:31:34,260 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['3', '4']
2025-06-17 13:31:34,261 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'short']
2025-06-17 13:31:34,261 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:31:34,559 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:31:34,560 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:31:34,564 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:31:34,567 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:31:34,568 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:31:34,568 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 53 27.00 81.03155764 0.20000000 -5.30000008 5.30000008
2025-06-17 13:31:34,568 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 51 26.00 -70.07708396 0.20000000 -5.10000008 5.10000008
2025-06-17 13:31:34,569 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:31:34,569 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:31:34,570 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 3128 1.00 11.54997730 11.54997730 20.95471191
2025-06-17 13:31:34,570 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, short
2025-06-17 13:31:34,571 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, short
2025-06-17 13:31:34,571 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_s3d.fits
2025-06-17 13:31:36,005 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2079 with wavelength below 11.548135757446289
2025-06-17 13:31:48,061 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:31:48,062 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:31:48,077 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:31:48,379 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.027318406 -70.078472795 81.027318406 -70.075695017 81.035796865 -70.075695017 81.035796865 -70.078472795
2025-06-17 13:31:48,382 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:31:48,562 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_s3d.fits
2025-06-17 13:31:49,985 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdc8e360560>,).
2025-06-17 13:31:49,995 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:31:50,002 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:31:50,010 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:31:50,010 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:31:50,402 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:31:50,417 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:31:50,721 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:31:50,722 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:31:50,722 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:31:50,725 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 27, y_center = 20, based on TARG_RA and TARG_DEC
2025-06-17 13:32:04,448 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:32:05,629 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:32:07,395 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_x1d.fits
2025-06-17 13:32:07,396 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:32:07,398 - stpipe.Spec2Pipeline - 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
2025-06-17 13:32:07,400 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:32:07,401 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:32:07,825 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifulong_cal.fits
2025-06-17 13:32:07,826 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:32:07,827 - stpipe - INFO - Results used jwst version: 1.18.1
2025-06-17 13:32:08,122 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:32:08,192 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:32:08,200 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:32:08,221 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:32:08,230 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:32:08,238 - stpipe - INFO - PARS-SPEC2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec2pipeline_0005.asdf
2025-06-17 13:32:08,261 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-06-17 13:32:08,262 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-06-17 13:32:08,263 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-06-17 13:32:08,264 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-06-17 13:32:08,265 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-06-17 13:32:08,266 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-06-17 13:32:08,267 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-06-17 13:32:08,268 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-06-17 13:32:08,273 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-06-17 13:32:08,274 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:32:08,275 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:32:08,276 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:32:08,277 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-06-17 13:32:08,278 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:32:08,279 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:32:08,281 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:32:08,282 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-06-17 13:32:08,283 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-06-17 13:32:08,283 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-06-17 13:32:08,285 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-06-17 13:32:08,286 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-06-17 13:32:08,287 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-06-17 13:32:08,289 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-06-17 13:32:08,289 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-06-17 13:32:08,290 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-06-17 13:32:08,291 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:32:08,293 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:32:08,294 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:32:08,295 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:32:08,297 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:32:09,667 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('./mrs_demo_data/Obs004/l2asn.json',).
2025-06-17 13:32:09,701 - stpipe.Spec2Pipeline - 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
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: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
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: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: 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
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
mrs_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: fit_profile
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
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
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
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: 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
mrs_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: fit_profile
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
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
single: False
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
2025-06-17 13:32:09,712 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:32:09,752 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01523004001_02105_00002_mirifushort_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', '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']
2025-06-17 13:32:09,757 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:32:09,757 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:32:09,758 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-06-17 13:32:09,758 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-06-17 13:32:09,758 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-06-17 13:32:09,759 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:32:09,760 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-06-17 13:32:09,760 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-06-17 13:32:09,761 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf'.
2025-06-17 13:32:09,761 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:32:09,762 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-06-17 13:32:09,762 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-06-17 13:32:09,763 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits'.
2025-06-17 13:32:09,763 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-06-17 13:32:09,764 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-06-17 13:32:09,764 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits'.
2025-06-17 13:32:09,765 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-06-17 13:32:09,765 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-06-17 13:32:09,766 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-06-17 13:32:09,766 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits'.
2025-06-17 13:32:09,767 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-06-17 13:32:09,768 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is 'N/A'.
2025-06-17 13:32:09,768 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-06-17 13:32:09,769 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:32:09,769 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is 'N/A'.
2025-06-17 13:32:09,770 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits'.
2025-06-17 13:32:09,770 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:32:09,771 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf'.
2025-06-17 13:32:09,771 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-06-17 13:32:09,771 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:32:09,772 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:32:09,772 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf'.
2025-06-17 13:32:09,773 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is 'N/A'.
2025-06-17 13:32:09,773 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf'.
2025-06-17 13:32:09,776 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-06-17 13:32:09,782 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:32:09,783 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/MRS/mrs_demo_data/Obs004/stage1/jw01523004001_02105_00002_mirifushort
2025-06-17 13:32:09,783 - stpipe.Spec2Pipeline - 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 ...
2025-06-17 13:32:11,121 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:32:11,897 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 1.000008757068164
2025-06-17 13:32:13,018 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a MIRI mir_mrs pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0127.asdf', 'filteroffset': None, 'specwcs': '/home/runner/crds/references/jwst/miri/jwst_miri_specwcs_0128.asdf', 'regions': '/home/runner/crds/references/jwst/miri/jwst_miri_regions_0137.asdf', 'wavelengthrange': '/home/runner/crds/references/jwst/miri/jwst_miri_wavelengthrange_0010.asdf', 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-06-17 13:32:13,888 - stpipe.Spec2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 81.029527253 -70.077913149 81.034062024 -70.077913149 81.034062024 -70.076318056 81.029527253 -70.076318056
2025-06-17 13:32:13,890 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-06-17 13:32:13,895 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-06-17 13:32:15,327 - stpipe.Spec2Pipeline.badpix_selfcal - 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'], []).
2025-06-17 13:32:15,329 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-06-17 13:32:16,636 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:32:16,638 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-06-17 13:32:17,938 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:32:17,939 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-06-17 13:32:19,272 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>, []).
2025-06-17 13:32:19,272 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-06-17 13:32:20,682 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>, []).
2025-06-17 13:32:20,683 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2025-06-17 13:32:22,011 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:32:22,020 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is MIR_MRS
2025-06-17 13:32:22,020 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-06-17 13:32:22,021 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-06-17 13:32:22,022 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-06-17 13:32:23,370 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:32:23,979 - stpipe.Spec2Pipeline.straylight - INFO - Using mrsxartcorr reference file /home/runner/crds/references/jwst/miri/jwst_miri_mrsxartcorr_0001.fits
2025-06-17 13:32:24,081 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for left detector half, applying Cross-Artifact correction.
2025-06-17 13:33:04,179 - stpipe.Spec2Pipeline.straylight - INFO - Found parameters for right detector half, applying Cross-Artifact correction.
2025-06-17 13:33:45,518 - stpipe.Spec2Pipeline.straylight - INFO - Derived pedestal correction 0.027825779859435365 DN/s
2025-06-17 13:33:45,519 - stpipe.Spec2Pipeline.straylight - INFO - Cross-artifact model complete.
2025-06-17 13:33:45,522 - stpipe.Spec2Pipeline.straylight - INFO - Step straylight done
2025-06-17 13:33:46,880 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:33:46,946 - stpipe.Spec2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0820.fits
2025-06-17 13:33:46,947 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-06-17 13:33:46,948 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-06-17 13:33:46,948 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-06-17 13:33:47,553 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-06-17 13:33:48,963 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:33:48,980 - stpipe.Spec2Pipeline.fringe - INFO - Using FRINGE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_fringe_0072.fits
2025-06-17 13:33:49,003 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:33:49,004 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:33:49,004 - stpipe.Spec2Pipeline.fringe - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:33:49,595 - stpipe.Spec2Pipeline.fringe - INFO - DQ values in the reference file NOT used to update the output DQ.
2025-06-17 13:33:49,597 - stpipe.Spec2Pipeline.fringe - INFO - Step fringe done
2025-06-17 13:33:51,017 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:33:51,018 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2025-06-17 13:33:52,379 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:33:52,380 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-06-17 13:33:53,738 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:33:53,762 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0210.fits
2025-06-17 13:33:53,762 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: N/A
2025-06-17 13:33:54,334 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: MIRI
2025-06-17 13:33:54,335 - stpipe.Spec2Pipeline.photom - INFO - detector: MIRIFUSHORT
2025-06-17 13:33:54,336 - stpipe.Spec2Pipeline.photom - INFO - exp_type: MIR_MRS
2025-06-17 13:33:54,337 - stpipe.Spec2Pipeline.photom - INFO - band: SHORT
2025-06-17 13:33:54,384 - stpipe.Spec2Pipeline.photom - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-06-17 13:33:54,386 - stpipe.Spec2Pipeline.photom - INFO - Attempting to obtain PIXAR_SR and PIXAR_A2 values from PHOTOM reference file.
2025-06-17 13:33:54,386 - stpipe.Spec2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from PHOTOM reference file.
2025-06-17 13:33:54,395 - stpipe.Spec2Pipeline.photom - INFO - Applying MRS IFU time dependent correction.
2025-06-17 13:33:54,972 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-06-17 13:33:56,492 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step residual_fringe running with args (<IFUImageModel(1024, 1032) from jw01523004001_02105_00002_mirifushort_rate.fits>,).
2025-06-17 13:33:56,493 - stpipe.Spec2Pipeline.residual_fringe - INFO - Step skipped.
2025-06-17 13:33:58,502 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_cal.fits>,).
2025-06-17 13:33:58,503 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-06-17 13:33:59,977 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build running with args (<IFUImageModel(1024, 1032) from ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_cal.fits>,).
2025-06-17 13:33:59,978 - stpipe.Spec2Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:33:59,979 - stpipe.Spec2Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:33:59,979 - stpipe.Spec2Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:33:59,988 - stpipe.Spec2Pipeline.cube_build - INFO - Setting output type to: multi
2025-06-17 13:34:00,006 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '2']
2025-06-17 13:34:00,007 - stpipe.Spec2Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'short']
2025-06-17 13:34:00,008 - stpipe.Spec2Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:34:00,306 - stpipe.Spec2Pipeline.cube_build - INFO - Output IFUcube are constructed from all the data
2025-06-17 13:34:00,307 - stpipe.Spec2Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 1
2025-06-17 13:34:00,311 - stpipe.Spec2Pipeline.cube_build - INFO - Increasing spatial region of interest default value set for 4 dithers nan
2025-06-17 13:34:00,315 - stpipe.Spec2Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:34:00,316 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:34:00,316 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 1 47 24.00 81.03179464 0.13000000 -3.05499989 3.05499989
2025-06-17 13:34:00,317 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 2 49 25.00 -70.07711560 0.13000000 -3.18499988 3.18499988
2025-06-17 13:34:00,317 - stpipe.Spec2Pipeline.cube_build - INFO - Non-linear wavelength dimension; CDELT3 variable
2025-06-17 13:34:00,318 - stpipe.Spec2Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL Min & Max (microns)
2025-06-17 13:34:00,318 - stpipe.Spec2Pipeline.cube_build - INFO - Axis 3 4404 1.00 4.90000010 4.90000010 8.77080059
2025-06-17 13:34:00,318 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, short
2025-06-17 13:34:00,319 - stpipe.Spec2Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, short
2025-06-17 13:34:00,319 - stpipe.Spec2Pipeline.cube_build - INFO - Output Name: ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_s3d.fits
2025-06-17 13:34:01,998 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3697 with wavelength below 4.899390697479248
2025-06-17 13:34:09,209 - stpipe.Spec2Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2597 with wavelength above 8.772054672241211
2025-06-17 13:34:15,891 - stpipe.Spec2Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:34:15,892 - stpipe.Spec2Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:34:15,911 - stpipe.Spec2Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 1
2025-06-17 13:34:16,389 - stpipe.Spec2Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.029357139 -70.077982253 81.029357139 -70.076248919 81.034232138 -70.076248919 81.034232138 -70.077982253
2025-06-17 13:34:16,392 - stpipe.Spec2Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:34:16,597 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_s3d.fits
2025-06-17 13:34:18,104 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdc95f290a0>,).
2025-06-17 13:34:18,114 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:34:18,122 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf
2025-06-17 13:34:18,130 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning off residual fringe correction for MIRI MRS data because the input is not a single IFU band
2025-06-17 13:34:18,131 - stpipe.Spec2Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:34:18,523 - stpipe.Spec2Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:34:18,539 - stpipe.Spec2Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:34:18,940 - stpipe.Spec2Pipeline.extract_1d - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/photutils/detection/daofinder.py:222: NoDetectionsWarning: No sources were found.
warnings.warn('No sources were found.', NoDetectionsWarning)
2025-06-17 13:34:18,941 - stpipe.Spec2Pipeline.extract_1d - WARNING - Auto source detection failed.
2025-06-17 13:34:18,942 - stpipe.Spec2Pipeline.extract_1d - INFO - Using target coordinates.
2025-06-17 13:34:18,945 - stpipe.Spec2Pipeline.extract_1d - INFO - Using x_center = 27, y_center = 16, based on TARG_RA and TARG_DEC
2025-06-17 13:34:38,418 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:34:39,591 - stpipe.Spec2Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:34:42,032 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_x1d.fits
2025-06-17 13:34:42,032 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:34:42,034 - stpipe.Spec2Pipeline - 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
2025-06-17 13:34:42,044 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-06-17 13:34:42,045 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-06-17 13:34:42,583 - stpipe.Spec2Pipeline - INFO - Saved model in ./mrs_demo_data/Obs004/stage2/jw01523004001_02105_00002_mirifushort_cal.fits
2025-06-17 13:34:42,584 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-06-17 13:34:42,584 - stpipe - INFO - Results used jwst version: 1.18.1
# 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: 5811.5821 seconds
Runtime for Spec2: 4147.463738404 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 = {}
spec3dict['assign_mtwcs'], spec3dict['master_background'], spec3dict['outlier_detection'], spec3dict['mrs_imatch'], spec3dict['cube_build'] = {}, {}, {}, {}, {}
spec3dict['pixel_replace'], spec3dict['extract_1d'], spec3dict['spectral_leak'] = {}, {}, {}
# 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 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')
2025-06-17 13:34:42,620 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
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')
2025-06-17 13:34:43,428 - 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)
2025-06-17 13:34:43,599 - stpipe - INFO - PARS-OUTLIERDETECTIONSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-outlierdetectionstep_0052.asdf
2025-06-17 13:34:43,610 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplespecstep_0001.asdf
2025-06-17 13:34:43,620 - stpipe - INFO - PARS-EXTRACT1DSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-extract1dstep_0001.asdf
2025-06-17 13:34:43,638 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec3pipeline_0008.asdf 2.7 K bytes (1 / 1 files) (0 / 2.7 K bytes)
2025-06-17 13:34:43,820 - stpipe - INFO - PARS-SPEC3PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-spec3pipeline_0008.asdf
2025-06-17 13:34:43,837 - stpipe.Spec3Pipeline - INFO - Spec3Pipeline instance created.
2025-06-17 13:34:43,838 - stpipe.Spec3Pipeline.assign_mtwcs - INFO - AssignMTWcsStep instance created.
2025-06-17 13:34:43,839 - stpipe.Spec3Pipeline.master_background - INFO - MasterBackgroundStep instance created.
2025-06-17 13:34:43,840 - stpipe.Spec3Pipeline.mrs_imatch - INFO - MRSIMatchStep instance created.
2025-06-17 13:34:43,842 - stpipe.Spec3Pipeline.outlier_detection - INFO - OutlierDetectionStep instance created.
2025-06-17 13:34:43,843 - stpipe.Spec3Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-06-17 13:34:43,844 - stpipe.Spec3Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-06-17 13:34:43,845 - stpipe.Spec3Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-06-17 13:34:43,847 - stpipe.Spec3Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-06-17 13:34:43,848 - stpipe.Spec3Pipeline.photom - INFO - PhotomStep instance created.
2025-06-17 13:34:43,848 - stpipe.Spec3Pipeline.combine_1d - INFO - Combine1dStep instance created.
2025-06-17 13:34:43,849 - stpipe.Spec3Pipeline.spectral_leak - INFO - SpectralLeakStep instance created.
2025-06-17 13:34:45,479 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline running with args ('./mrs_demo_data/Obs003/l3asn.json',).
2025-06-17 13:34:45,495 - stpipe.Spec3Pipeline - 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
mrs_imatch:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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_degree: 1
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
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
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: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: band
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
single: False
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
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
mrs_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: ''
2025-06-17 13:34:45,505 - stpipe.Spec3Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:34:47,238 - stpipe.Spec3Pipeline - INFO - Prefetching reference files for dataset: 'jw01523003001_03102_00001_mirifulong_cal.fits' reftypes = ['apcorr', 'area', 'cubepar', 'extract1d', 'mrsptcorr', 'pastasoss', 'photom', 'psf', 'speckernel', 'specprofile']
2025-06-17 13:34:47,243 - 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)
2025-06-17 13:34:47,421 - stpipe.Spec3Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0008.asdf'.
2025-06-17 13:34:47,422 - stpipe.Spec3Pipeline - INFO - Prefetch for AREA reference file is 'N/A'.
2025-06-17 13:34:47,422 - stpipe.Spec3Pipeline - INFO - Prefetch for CUBEPAR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits'.
2025-06-17 13:34:47,423 - stpipe.Spec3Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf'.
2025-06-17 13:34:47,423 - stpipe.Spec3Pipeline - INFO - Prefetch for MRSPTCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mrsptcorr_0002.fits'.
2025-06-17 13:34:47,423 - stpipe.Spec3Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-06-17 13:34:47,424 - stpipe.Spec3Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0211.fits'.
2025-06-17 13:34:47,425 - stpipe.Spec3Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-06-17 13:34:47,425 - stpipe.Spec3Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-06-17 13:34:47,426 - stpipe.Spec3Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-06-17 13:34:47,427 - stpipe.Spec3Pipeline - INFO - Starting calwebb_spec3 ...
2025-06-17 13:34:47,436 - stpipe.Spec3Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-06-17 13:35:44,453 - stpipe.Spec3Pipeline.master_background - INFO - Step master_background running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdcae00f530>,).
2025-06-17 13:35:44,803 - stpipe.Spec3Pipeline.master_background - INFO - Using exposure time as the weight.
2025-06-17 13:35:45,523 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 1, slit MIR_MRS
2025-06-17 13:35:45,529 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 2, slit MIR_MRS
2025-06-17 13:35:45,537 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 3, slit MIR_MRS
2025-06-17 13:35:45,543 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 4, slit MIR_MRS
2025-06-17 13:35:45,551 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 5, slit MIR_MRS
2025-06-17 13:35:45,557 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 6, slit MIR_MRS
2025-06-17 13:35:45,566 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 7, slit MIR_MRS
2025-06-17 13:35:45,572 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 8, slit MIR_MRS
2025-06-17 13:35:45,581 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 9, slit MIR_MRS
2025-06-17 13:35:45,588 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 10, slit MIR_MRS
2025-06-17 13:35:45,597 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 11, slit MIR_MRS
2025-06-17 13:35:45,604 - stpipe.Spec3Pipeline.master_background - INFO - Accumulating data from input spectrum 12, slit MIR_MRS
2025-06-17 13:35:45,616 - stpipe.Spec3Pipeline.master_background - WARNING - 6 elements of output had no corresponding input data;
2025-06-17 13:35:45,616 - stpipe.Spec3Pipeline.master_background - WARNING - these elements will be omitted.
2025-06-17 13:36:26,119 - stpipe.Spec3Pipeline.master_background - INFO - Step master_background done
2025-06-17 13:36:29,084 - stpipe.Spec3Pipeline.mrs_imatch - INFO - Step mrs_imatch running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdc8e3628d0>,).
2025-06-17 13:36:29,087 - stpipe.Spec3Pipeline.mrs_imatch - INFO - Step skipped.
2025-06-17 13:36:31,413 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdc8e3628d0>,).
2025-06-17 13:36:31,414 - stpipe.Spec3Pipeline.outlier_detection - INFO - Outlier Detection mode: ifu
2025-06-17 13:36:31,415 - stpipe.Spec3Pipeline.outlier_detection - INFO - Outlier Detection asn_id: a3001
2025-06-17 13:36:31,415 - stpipe.Spec3Pipeline.outlier_detection - INFO - Performing IFU outlier_detection for exptype MIR_MRS
2025-06-17 13:36:31,427 - stpipe.Spec3Pipeline.outlier_detection - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/outlier_detection/ifu.py:225: RuntimeWarning: All-NaN slice encountered
combdiff = np.nanmin(comb, axis=0)
2025-06-17 13:36:31,555 - stpipe.Spec3Pipeline.outlier_detection - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/outlier_detection/ifu.py:230: RuntimeWarning: All-NaN slice encountered
minarr = np.nanmin(diffarr, axis=0)
2025-06-17 13:36:32,167 - stpipe.Spec3Pipeline.outlier_detection - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/stcal/outlier_detection/utils.py:51: RuntimeWarning: All-NaN slice encountered
return np.nanmedian(windows, axis=np.arange(-len(kern_size), 0))
2025-06-17 13:36:32,361 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,379 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,396 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,413 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,431 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,448 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,466 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,483 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,500 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,518 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,536 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:32,553 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 3688 (0.35%)
2025-06-17 13:36:33,350 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,368 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,386 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,404 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,422 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,440 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,458 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,476 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,494 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,513 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,531 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,549 - stpipe.Spec3Pipeline.outlier_detection - INFO - Total # pixels flagged as outliers: 4084 (0.39%)
2025-06-17 13:36:33,996 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00001_mirifulong_a3001_crf.fits
2025-06-17 13:36:34,496 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00001_mirifushort_a3001_crf.fits
2025-06-17 13:36:34,916 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00002_mirifulong_a3001_crf.fits
2025-06-17 13:36:35,414 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00002_mirifushort_a3001_crf.fits
2025-06-17 13:36:35,824 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00003_mirifulong_a3001_crf.fits
2025-06-17 13:36:36,379 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00003_mirifushort_a3001_crf.fits
2025-06-17 13:36:36,793 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00004_mirifulong_a3001_crf.fits
2025-06-17 13:36:37,310 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03102_00004_mirifushort_a3001_crf.fits
2025-06-17 13:36:37,724 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00001_mirifulong_a3001_crf.fits
2025-06-17 13:36:38,233 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00001_mirifushort_a3001_crf.fits
2025-06-17 13:36:38,646 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00002_mirifulong_a3001_crf.fits
2025-06-17 13:36:39,194 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00002_mirifushort_a3001_crf.fits
2025-06-17 13:36:39,608 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00003_mirifulong_a3001_crf.fits
2025-06-17 13:36:40,134 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00003_mirifushort_a3001_crf.fits
2025-06-17 13:36:40,550 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00004_mirifulong_a3001_crf.fits
2025-06-17 13:36:41,057 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03104_00004_mirifushort_a3001_crf.fits
2025-06-17 13:36:41,515 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00001_mirifulong_a3001_crf.fits
2025-06-17 13:36:42,028 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00001_mirifushort_a3001_crf.fits
2025-06-17 13:36:42,445 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00002_mirifulong_a3001_crf.fits
2025-06-17 13:36:42,953 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00002_mirifushort_a3001_crf.fits
2025-06-17 13:36:43,374 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00003_mirifulong_a3001_crf.fits
2025-06-17 13:36:43,885 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00003_mirifushort_a3001_crf.fits
2025-06-17 13:36:44,326 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00004_mirifulong_a3001_crf.fits
2025-06-17 13:36:44,839 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/jw01523003001_03106_00004_mirifushort_a3001_crf.fits
2025-06-17 13:36:44,840 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection done
2025-06-17 13:36:47,316 - stpipe.Spec3Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdc8e3628d0>,).
2025-06-17 13:36:47,869 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:36:56,880 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 3946 total pixels replaced.
2025-06-17 13:36:57,428 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:37:05,386 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4545 total pixels replaced.
2025-06-17 13:37:05,791 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:37:14,882 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 3947 total pixels replaced.
2025-06-17 13:37:15,422 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:37:23,422 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4545 total pixels replaced.
2025-06-17 13:37:23,845 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:37:32,876 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 3946 total pixels replaced.
2025-06-17 13:37:33,419 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:37:41,356 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4545 total pixels replaced.
2025-06-17 13:37:41,772 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:37:50,905 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 3946 total pixels replaced.
2025-06-17 13:37:51,442 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:37:59,314 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4545 total pixels replaced.
2025-06-17 13:37:59,717 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:38:08,370 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4069 total pixels replaced.
2025-06-17 13:38:08,914 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:38:16,715 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4549 total pixels replaced.
2025-06-17 13:38:20,210 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:38:28,932 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4069 total pixels replaced.
2025-06-17 13:38:29,480 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:38:37,335 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4549 total pixels replaced.
2025-06-17 13:38:37,746 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:38:46,466 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4069 total pixels replaced.
2025-06-17 13:38:47,019 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:38:54,884 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4549 total pixels replaced.
2025-06-17 13:38:55,305 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:39:04,020 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4069 total pixels replaced.
2025-06-17 13:39:04,576 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:39:12,438 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4549 total pixels replaced.
2025-06-17 13:39:12,869 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:39:21,468 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4104 total pixels replaced.
2025-06-17 13:39:22,032 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:39:29,845 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4620 total pixels replaced.
2025-06-17 13:39:30,258 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:39:38,928 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4103 total pixels replaced.
2025-06-17 13:39:39,484 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:39:47,361 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4621 total pixels replaced.
2025-06-17 13:39:47,778 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:39:56,465 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4103 total pixels replaced.
2025-06-17 13:40:00,497 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:40:08,311 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4620 total pixels replaced.
2025-06-17 13:40:08,725 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:40:17,419 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4103 total pixels replaced.
2025-06-17 13:40:17,982 - stpipe.Spec3Pipeline.pixel_replace - INFO - Using minimum gradient method.
2025-06-17 13:40:25,829 - stpipe.Spec3Pipeline.pixel_replace - INFO - Input MRS frame had 4620 total pixels replaced.
2025-06-17 13:40:25,864 - stpipe.Spec3Pipeline.pixel_replace - INFO - Step pixel_replace done
2025-06-17 13:40:29,166 - stpipe.Spec3Pipeline.cube_build - INFO - Step cube_build running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdca9225370>,).
2025-06-17 13:40:29,168 - stpipe.Spec3Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2025-06-17 13:40:29,169 - stpipe.Spec3Pipeline.cube_build - INFO - Input interpolation: drizzle
2025-06-17 13:40:29,170 - stpipe.Spec3Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2025-06-17 13:40:29,303 - stpipe.Spec3Pipeline.cube_build - INFO - Setting output type to: band
2025-06-17 13:40:29,619 - stpipe.Spec3Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '1', '1', '2', '2', '2', '3', '3', '3', '4', '4', '4']
2025-06-17 13:40:29,620 - stpipe.Spec3Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'medium', 'long', 'short', 'medium', 'long', 'short', 'medium', 'long', 'short', 'medium', 'long']
2025-06-17 13:40:29,621 - stpipe.Spec3Pipeline.cube_build - INFO - Reading cube parameter file /home/runner/crds/references/jwst/miri/jwst_miri_cubepar_0014.fits
2025-06-17 13:40:29,962 - stpipe.Spec3Pipeline.cube_build - INFO - Output Cubes are single channel, single sub-channel IFU Cubes
2025-06-17 13:40:29,962 - stpipe.Spec3Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 12
2025-06-17 13:40:29,964 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:40:30,219 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:40:30,460 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:40:30,700 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:40:30,944 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:40:30,945 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:40:30,945 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 47 24.00 81.08652390 0.13000000 -3.05499989 3.05499989
2025-06-17 13:40:30,946 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 67 34.00 -70.08386499 0.13000000 -4.35499984 4.35499984
2025-06-17 13:40:30,946 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:40:30,947 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 1050 1.00 4.90040010 0.00080000 4.90000010 5.74000007
2025-06-17 13:40:30,947 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, short
2025-06-17 13:40:30,948 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['short']
2025-06-17 13:40:30,948 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch1-short
2025-06-17 13:40:32,675 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3379 with wavelength below 4.898601539532876
2025-06-17 13:40:32,677 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3474 with wavelength above 5.741398629981802
2025-06-17 13:40:38,693 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3379 with wavelength below 4.89860153953351
2025-06-17 13:40:38,694 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3474 with wavelength above 5.741398629981169
2025-06-17 13:40:44,597 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3379 with wavelength below 4.898601539532876
2025-06-17 13:40:44,598 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3474 with wavelength above 5.741398629981802
2025-06-17 13:40:50,544 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3379 with wavelength below 4.89860153953351
2025-06-17 13:40:50,545 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3474 with wavelength above 5.741398629981169
2025-06-17 13:40:54,829 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:40:54,830 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:40:54,838 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:40:55,142 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:40:55,410 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:40:55,654 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:40:55,896 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:40:56,140 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:40:56,141 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:40:56,141 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 47 24.00 81.08644129 0.13000000 -3.05499989 3.05499989
2025-06-17 13:40:56,142 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 67 34.00 -70.08384600 0.13000000 -4.35499984 4.35499984
2025-06-17 13:40:56,142 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:40:56,143 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 1213 1.00 5.66039985 0.00080000 5.65999985 6.63039982
2025-06-17 13:40:56,143 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, medium
2025-06-17 13:40:56,144 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['medium']
2025-06-17 13:40:56,144 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch1-medium
2025-06-17 13:40:57,879 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3662 with wavelength below 5.658443765540777
2025-06-17 13:40:57,880 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3170 with wavelength above 6.631955904769076
2025-06-17 13:41:04,184 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3662 with wavelength below 5.658443765540777
2025-06-17 13:41:04,185 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3170 with wavelength above 6.631955904769076
2025-06-17 13:41:10,511 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3662 with wavelength below 5.658443765540777
2025-06-17 13:41:10,512 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3170 with wavelength above 6.631955904769076
2025-06-17 13:41:16,754 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3662 with wavelength below 5.658443765540777
2025-06-17 13:41:16,755 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3170 with wavelength above 6.631955904769076
2025-06-17 13:41:21,328 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:41:21,329 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:41:21,336 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:41:21,639 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:41:21,868 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:41:22,110 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:41:22,355 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:41:22,599 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:41:22,599 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:41:22,603 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 47 24.00 81.08653175 0.13000000 -3.05499989 3.05499989
2025-06-17 13:41:22,605 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 67 34.00 -70.08391798 0.13000000 -4.35499984 4.35499984
2025-06-17 13:41:22,605 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:41:22,606 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 1400 1.00 6.53040021 0.00080000 6.53000021 7.65000018
2025-06-17 13:41:22,606 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, long
2025-06-17 13:41:22,607 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['long']
2025-06-17 13:41:22,608 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch1-long
2025-06-17 13:41:24,347 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3033 with wavelength below 6.528268498504163
2025-06-17 13:41:24,347 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 4193 with wavelength above 7.651731892818956
2025-06-17 13:41:30,872 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3033 with wavelength below 6.528268498504163
2025-06-17 13:41:30,873 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 4193 with wavelength above 7.651731892818956
2025-06-17 13:41:37,499 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3033 with wavelength below 6.528268498504163
2025-06-17 13:41:37,502 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 4193 with wavelength above 7.651731892818956
2025-06-17 13:41:43,171 - stpipe.Spec3Pipeline.cube_build - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/selector.py:634: RuntimeWarning: invalid value encountered in add
np.empty(inputs[0].shape) + self._undefined_transform_value
2025-06-17 13:41:44,219 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 3033 with wavelength below 6.528268498505007
2025-06-17 13:41:44,219 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 4193 with wavelength above 7.651731892818113
2025-06-17 13:41:49,265 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:41:49,266 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:41:49,275 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:41:49,589 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:41:49,590 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:41:49,591 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 43 22.00 81.08646617 0.17000000 -3.65500004 3.65500004
2025-06-17 13:41:49,591 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 59 30.00 -70.08378967 0.17000000 -5.01500005 5.01500005
2025-06-17 13:41:49,592 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:41:49,592 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 970 1.00 7.51065023 0.00130000 7.51000023 8.77100023
2025-06-17 13:41:49,592 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, short
2025-06-17 13:41:49,593 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['short']
2025-06-17 13:41:49,593 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch2-short
2025-06-17 13:41:51,188 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2433 with wavelength below 7.507832450399061
2025-06-17 13:41:51,189 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2271 with wavelength above 8.773168010797466
2025-06-17 13:41:56,517 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2433 with wavelength below 7.507832450400023
2025-06-17 13:41:56,518 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2271 with wavelength above 8.773168010796503
2025-06-17 13:42:01,959 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2433 with wavelength below 7.507832450399061
2025-06-17 13:42:01,960 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2271 with wavelength above 8.773168010797466
2025-06-17 13:42:07,335 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2433 with wavelength below 7.507832450400023
2025-06-17 13:42:07,336 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2271 with wavelength above 8.773168010796503
2025-06-17 13:42:11,161 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:42:11,161 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:42:11,167 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:42:11,444 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:42:11,445 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:42:11,445 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 41 21.00 81.08642000 0.17000000 -3.48500004 3.48500004
2025-06-17 13:42:11,446 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 59 30.00 -70.08370448 0.17000000 -5.01500005 5.01500005
2025-06-17 13:42:11,446 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:42:11,447 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 1124 1.00 8.67065008 0.00130000 8.67000008 10.13120008
2025-06-17 13:42:11,447 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, medium
2025-06-17 13:42:11,447 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['medium']
2025-06-17 13:42:11,448 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch2-medium
2025-06-17 13:42:13,063 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 1537 with wavelength below 8.667601400109556
2025-06-17 13:42:13,064 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2126 with wavelength above 10.1335987564562
2025-06-17 13:42:18,745 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 1537 with wavelength below 8.667601400109556
2025-06-17 13:42:18,746 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2126 with wavelength above 10.1335987564562
2025-06-17 13:42:24,546 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 1537 with wavelength below 8.667601400109556
2025-06-17 13:42:24,547 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2126 with wavelength above 10.1335987564562
2025-06-17 13:42:30,278 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 1537 with wavelength below 8.667601400109556
2025-06-17 13:42:30,279 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2126 with wavelength above 10.1335987564562
2025-06-17 13:42:34,474 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:42:34,475 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:42:34,481 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:42:34,769 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:42:34,769 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:42:34,770 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 43 22.00 81.08630843 0.17000000 -3.65500004 3.65500004
2025-06-17 13:42:34,770 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 59 30.00 -70.08375261 0.17000000 -5.01500005 5.01500005
2025-06-17 13:42:34,771 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:42:34,771 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 1300 1.00 10.01065023 0.00130000 10.01000023 11.70000023
2025-06-17 13:42:34,772 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, long
2025-06-17 13:42:34,772 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['long']
2025-06-17 13:42:34,773 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch2-long
2025-06-17 13:42:36,449 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 984 with wavelength below 10.007327663197035
2025-06-17 13:42:36,450 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2080 with wavelength above 11.70267279916737
2025-06-17 13:42:42,619 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 984 with wavelength below 10.007327663197035
2025-06-17 13:42:42,621 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2080 with wavelength above 11.70267279916737
2025-06-17 13:42:52,936 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 984 with wavelength below 10.007327663197035
2025-06-17 13:42:52,938 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2080 with wavelength above 11.70267279916737
2025-06-17 13:42:59,026 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 984 with wavelength below 10.007327663198316
2025-06-17 13:42:59,028 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 2080 with wavelength above 11.70267279916609
2025-06-17 13:43:03,599 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:43:03,600 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:43:03,608 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:43:03,898 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:04,161 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:04,378 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:04,605 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:04,834 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:43:04,836 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:43:04,836 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 49 25.00 81.08700069 0.20000000 -4.90000007 4.90000007
2025-06-17 13:43:04,838 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 59 30.00 -70.08377866 0.20000000 -5.90000009 5.90000009
2025-06-17 13:43:04,838 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:43:04,839 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 769 1.00 11.55125019 0.00250000 11.55000019 13.47250015
2025-06-17 13:43:04,840 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, short
2025-06-17 13:43:04,842 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['short']
2025-06-17 13:43:04,843 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch3-short
2025-06-17 13:43:06,358 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 1806 with wavelength below 11.546439300025126
2025-06-17 13:43:06,359 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 157 with wavelength above 13.476061038473377
2025-06-17 13:43:11,771 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 1806 with wavelength below 11.54643930002659
2025-06-17 13:43:11,772 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 157 with wavelength above 13.476061038471913
2025-06-17 13:43:17,173 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 1806 with wavelength below 11.54643930002659
2025-06-17 13:43:17,174 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 157 with wavelength above 13.476061038471913
2025-06-17 13:43:22,575 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 1806 with wavelength below 11.546439300025126
2025-06-17 13:43:22,575 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 157 with wavelength above 13.476061038473377
2025-06-17 13:43:26,515 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:43:26,516 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:43:26,522 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:43:26,800 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:27,015 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:27,246 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:27,475 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:27,757 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:43:27,758 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:43:27,758 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 47 24.00 81.08695423 0.20000000 -4.70000007 4.70000007
2025-06-17 13:43:27,759 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 59 30.00 -70.08372103 0.20000000 -5.90000009 5.90000009
2025-06-17 13:43:27,759 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:43:27,760 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 892 1.00 13.34125015 0.00250000 13.34000015 15.57000010
2025-06-17 13:43:27,761 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, medium
2025-06-17 13:43:27,761 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['medium']
2025-06-17 13:43:27,761 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch3-medium
2025-06-17 13:43:29,177 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 936 with wavelength below 13.336085437749636
2025-06-17 13:43:29,178 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 456 with wavelength above 15.57391481758176
2025-06-17 13:43:34,794 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 936 with wavelength below 13.336085437749636
2025-06-17 13:43:34,795 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 456 with wavelength above 15.57391481758176
2025-06-17 13:43:40,418 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 936 with wavelength below 13.336085437749636
2025-06-17 13:43:40,419 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 456 with wavelength above 15.57391481758176
2025-06-17 13:43:46,111 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 936 with wavelength below 13.336085437751324
2025-06-17 13:43:46,112 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 456 with wavelength above 15.573914817580073
2025-06-17 13:43:50,353 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:43:50,354 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:43:50,360 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:43:50,627 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:50,842 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:51,068 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:51,296 - stpipe.Spec3Pipeline.cube_build - INFO - Mapping all pixels to output to determine IFU foot print
2025-06-17 13:43:51,522 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:43:51,523 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:43:51,523 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 47 24.00 81.08687152 0.20000000 -4.70000007 4.70000007
2025-06-17 13:43:51,524 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 59 30.00 -70.08374464 0.20000000 -5.90000009 5.90000009
2025-06-17 13:43:51,524 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:43:51,525 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 1028 1.00 15.41124985 0.00250000 15.40999985 17.97999979
2025-06-17 13:43:51,525 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, long
2025-06-17 13:43:51,526 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['long']
2025-06-17 13:43:51,526 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch3-long
2025-06-17 13:43:52,911 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 754 with wavelength below 15.405681102293547
2025-06-17 13:43:52,912 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 968 with wavelength above 17.984318535086693
2025-06-17 13:43:58,887 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 754 with wavelength below 15.405681102295494
2025-06-17 13:43:58,888 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 968 with wavelength above 17.984318535084746
2025-06-17 13:44:04,811 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 754 with wavelength below 15.405681102293547
2025-06-17 13:44:04,812 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 968 with wavelength above 17.984318535086693
2025-06-17 13:44:10,700 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 754 with wavelength below 15.405681102295494
2025-06-17 13:44:10,701 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 968 with wavelength above 17.984318535084746
2025-06-17 13:44:15,241 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:44:15,242 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:44:15,248 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:44:15,523 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:44:15,524 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:44:15,524 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 35 18.00 81.08622845 0.34999999 -6.12499990 6.12499990
2025-06-17 13:44:15,525 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 41 21.00 -70.08375844 0.34999999 -7.17499988 7.17499988
2025-06-17 13:44:15,525 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:44:15,525 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 542 1.00 17.70300076 0.00600000 17.70000076 20.95200079
2025-06-17 13:44:15,526 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, short
2025-06-17 13:44:15,527 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['short']
2025-06-17 13:44:15,528 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch4-short
2025-06-17 13:44:30,060 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:44:30,061 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:44:30,064 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:44:30,301 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:44:30,301 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:44:30,302 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 35 18.00 81.08622287 0.34999999 -6.12499990 6.12499990
2025-06-17 13:44:30,303 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 41 21.00 -70.08377411 0.34999999 -7.17499988 7.17499988
2025-06-17 13:44:30,303 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:44:30,304 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 632 1.00 20.69300053 0.00600000 20.69000053 24.48200057
2025-06-17 13:44:30,304 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, medium
2025-06-17 13:44:30,305 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['medium']
2025-06-17 13:44:30,306 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch4-medium
2025-06-17 13:44:31,624 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 249 with wavelength below 20.682598635781634
2025-06-17 13:44:35,331 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 249 with wavelength below 20.682598635781634
2025-06-17 13:44:39,094 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 249 with wavelength below 20.682598635781634
2025-06-17 13:44:42,852 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 249 with wavelength below 20.682598635784423
2025-06-17 13:44:45,342 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:44:45,342 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:44:45,346 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:44:45,588 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2025-06-17 13:44:45,589 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2025-06-17 13:44:45,589 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 35 18.00 81.08608968 0.34999999 -6.12499990 6.12499990
2025-06-17 13:44:45,590 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 41 21.00 -70.08376496 0.34999999 -7.17499988 7.17499988
2025-06-17 13:44:45,590 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2025-06-17 13:44:45,590 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 717 1.00 24.40299962 0.00600000 24.39999962 28.70199966
2025-06-17 13:44:45,591 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, long
2025-06-17 13:44:45,591 - stpipe.Spec3Pipeline.cube_build - INFO - Subchannel listing: ['long']
2025-06-17 13:44:45,592 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: Level3_ch4-long
2025-06-17 13:44:46,961 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 13075 with wavelength below 24.391886480783615
2025-06-17 13:44:50,822 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 13075 with wavelength below 24.391886480786855
2025-06-17 13:44:54,643 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 13075 with wavelength below 24.391886480783615
2025-06-17 13:44:58,514 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 13075 with wavelength below 24.391886480786855
2025-06-17 13:45:01,086 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2025-06-17 13:45:01,087 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2025-06-17 13:45:01,090 - stpipe.Spec3Pipeline.cube_build - INFO - Number of spectral tear planes adjusted: 0
2025-06-17 13:45:01,331 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.084085568 -70.085056644 81.084085568 -70.082673311 81.088962228 -70.082673311 81.088962228 -70.085056644
2025-06-17 13:45:01,333 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.084002959 -70.085037648 81.084002959 -70.082654315 81.088879614 -70.082654315 81.088879614 -70.085037648
2025-06-17 13:45:01,335 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.084093412 -70.085109631 81.084093412 -70.082726298 81.088970084 -70.082726298 81.088970084 -70.085109631
2025-06-17 13:45:01,337 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.083554839 -70.085159093 81.083554839 -70.082420204 81.089377502 -70.082420204 81.089377502 -70.085159093
2025-06-17 13:45:01,339 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.083647313 -70.085073907 81.083647313 -70.082335019 81.089192683 -70.082335019 81.089192683 -70.085073907
2025-06-17 13:45:01,341 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.083397104 -70.085122027 81.083397104 -70.082383138 81.089219757 -70.082383138 81.089219757 -70.085122027
2025-06-17 13:45:01,342 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.083086250 -70.085389729 81.083086250 -70.082167507 81.090915127 -70.082167507 81.090915127 -70.085389729
2025-06-17 13:45:01,344 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.083202904 -70.085332105 81.083202904 -70.082109883 81.090705557 -70.082109883 81.090705557 -70.085332105
2025-06-17 13:45:01,346 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.083120189 -70.085355711 81.083120189 -70.082133489 81.090622851 -70.082133489 81.090622851 -70.085355711
2025-06-17 13:45:01,347 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.081376102 -70.085702820 81.081376102 -70.081813931 81.091080794 -70.081813931 81.091080794 -70.085702820
2025-06-17 13:45:01,349 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.081370524 -70.085718484 81.081370524 -70.081829595 81.091075222 -70.081829595 81.091075222 -70.085718484
2025-06-17 13:45:01,351 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 81.081237335 -70.085709341 81.081237335 -70.081820452 81.090942030 -70.081820452 81.090942030 -70.085709341
2025-06-17 13:45:01,690 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-short_s3d.fits
2025-06-17 13:45:01,952 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-medium_s3d.fits
2025-06-17 13:45:02,215 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-long_s3d.fits
2025-06-17 13:45:02,449 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-short_s3d.fits
2025-06-17 13:45:02,689 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-medium_s3d.fits
2025-06-17 13:45:02,958 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-long_s3d.fits
2025-06-17 13:45:03,188 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-short_s3d.fits
2025-06-17 13:45:03,423 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-medium_s3d.fits
2025-06-17 13:45:03,663 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-long_s3d.fits
2025-06-17 13:45:03,885 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-short_s3d.fits
2025-06-17 13:45:04,112 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-medium_s3d.fits
2025-06-17 13:45:04,327 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-long_s3d.fits
2025-06-17 13:45:04,328 - stpipe.Spec3Pipeline.cube_build - INFO - Step cube_build done
2025-06-17 13:45:08,609 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdca9225be0>,).
2025-06-17 13:45:08,824 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:45:08,835 - 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)
2025-06-17 13:45:09,153 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0007.asdf
2025-06-17 13:45:09,164 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:45:09,571 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:45:09,574 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:45:09,702 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:45:09,703 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 24.0247, y_center = 36.407
2025-06-17 13:45:14,345 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:45:15,013 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:45:16,188 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:45:16,834 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:45:16,845 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0007.asdf
2025-06-17 13:45:16,856 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:45:17,260 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:45:17,263 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:45:17,429 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:45:17,430 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 23.1472, y_center = 35.9305
2025-06-17 13:45:22,864 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:45:24,121 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:45:25,335 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:45:26,074 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:45:26,085 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0007.asdf
2025-06-17 13:45:26,096 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:45:26,484 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:45:26,488 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:45:26,709 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:45:26,710 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 24.3218, y_center = 37.7779
2025-06-17 13:45:32,951 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:45:34,417 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:45:35,608 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:45:36,439 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:45:36,450 - 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)
2025-06-17 13:45:36,726 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0005.asdf
2025-06-17 13:45:36,738 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:45:37,129 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:45:37,131 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:45:37,227 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:45:37,228 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 21.5424, y_center = 29.838
2025-06-17 13:45:41,474 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:45:43,521 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:45:44,715 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:45:45,323 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:45:45,335 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0005.asdf
2025-06-17 13:45:45,346 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:45:45,753 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:45:45,756 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:45:45,869 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:45:45,870 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 20.4788, y_center = 27.9365
2025-06-17 13:45:50,759 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:45:54,718 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:45:55,919 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:45:56,611 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:45:56,623 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0005.asdf
2025-06-17 13:45:56,635 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:45:57,041 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:45:57,044 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:45:57,194 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:45:57,194 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 20.2757, y_center = 29.1416
2025-06-17 13:46:03,006 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:46:06,528 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:46:07,722 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:46:08,500 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:46:08,511 - 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)
2025-06-17 13:46:08,790 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0006.asdf
2025-06-17 13:46:08,802 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:46:09,203 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:46:09,206 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:46:09,294 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:46:09,294 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 27.7429, y_center = 29.582
2025-06-17 13:46:12,694 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:46:14,016 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:46:15,202 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:46:15,702 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:46:15,715 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0006.asdf
2025-06-17 13:46:15,726 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:46:16,124 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:46:16,127 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:46:16,236 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:46:16,236 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 26.3113, y_center = 28.4657
2025-06-17 13:46:20,187 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:46:21,843 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:46:23,036 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:46:23,604 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:46:23,615 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0006.asdf
2025-06-17 13:46:23,626 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:46:24,030 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:46:24,033 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:46:24,163 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:46:24,164 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 26.0272, y_center = 28.7832
2025-06-17 13:46:28,752 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:46:30,017 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:46:31,228 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:46:31,867 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:46:31,880 - 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)
2025-06-17 13:46:32,155 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0004.asdf
2025-06-17 13:46:32,167 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:46:32,573 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:46:32,574 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:46:32,609 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:46:32,609 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 16.4092, y_center = 20.168
2025-06-17 13:46:34,975 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:46:35,747 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:46:36,950 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:46:37,333 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:46:37,344 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0004.asdf
2025-06-17 13:46:37,356 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:46:37,770 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:46:37,771 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:46:37,819 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:46:37,820 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 16.4176, y_center = 20.2906
2025-06-17 13:46:40,568 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:46:41,376 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:46:42,586 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:46:43,018 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds/references/jwst/miri/jwst_miri_extract1d_0004.asdf
2025-06-17 13:46:43,029 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0004.asdf
2025-06-17 13:46:43,040 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = POINT
2025-06-17 13:46:43,446 - stpipe.Spec3Pipeline.extract_1d - INFO - Input model does not break out variance information. Passing only generalized errors.
2025-06-17 13:46:43,448 - stpipe.Spec3Pipeline.extract_1d - INFO - Using auto source detection.
2025-06-17 13:46:43,466 - stpipe.Spec3Pipeline.extract_1d - INFO - Auto source detection success.
2025-06-17 13:46:43,467 - stpipe.Spec3Pipeline.extract_1d - INFO - Using x_center = 15.9161, y_center = 20.1751
2025-06-17 13:46:46,614 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying 1d residual fringe correction.
2025-06-17 13:46:47,332 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying ERR covariance prefactor of 1.8
2025-06-17 13:46:48,538 - stpipe.Spec3Pipeline.extract_1d - INFO - Applying Aperture correction.
2025-06-17 13:46:49,066 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d done
2025-06-17 13:46:52,378 - stpipe.Spec3Pipeline.spectral_leak - INFO - Step spectral_leak running with args (<jwst.datamodels.container.ModelContainer object at 0x7fdcc858f800>,).
2025-06-17 13:46:52,621 - stpipe.Spec3Pipeline.spectral_leak - INFO - Found CH 1B in input data
2025-06-17 13:46:52,622 - stpipe.Spec3Pipeline.spectral_leak - INFO - Found CH 3A in the input data
2025-06-17 13:46:52,765 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-short_x1d.fits
2025-06-17 13:46:52,839 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-medium_x1d.fits
2025-06-17 13:46:52,916 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch1-long_x1d.fits
2025-06-17 13:46:52,990 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-short_x1d.fits
2025-06-17 13:46:53,064 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-medium_x1d.fits
2025-06-17 13:46:53,137 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch2-long_x1d.fits
2025-06-17 13:46:53,212 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-short_x1d.fits
2025-06-17 13:46:53,286 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-medium_x1d.fits
2025-06-17 13:46:53,361 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch3-long_x1d.fits
2025-06-17 13:46:53,435 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-short_x1d.fits
2025-06-17 13:46:53,509 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-medium_x1d.fits
2025-06-17 13:46:53,583 - stpipe.Spec3Pipeline.spectral_leak - INFO - Saved model in ./mrs_demo_data/Obs003/stage3/Level3_ch4-long_x1d.fits
2025-06-17 13:46:53,584 - stpipe.Spec3Pipeline.spectral_leak - INFO - Step spectral_leak done
2025-06-17 13:46:53,599 - stpipe.Spec3Pipeline - INFO - Ending calwebb_spec3
2025-06-17 13:46:53,616 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline done
2025-06-17 13:46:53,617 - stpipe - INFO - Results used jwst version: 1.18.1
# 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: 6542.6146 seconds
Runtime for Spec3: 731.0282061060007 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')
