MIRI Imaging Pipeline Notebook#
Authors: M. Cracraft
Last Updated: May 5, 2025
Pipeline Version: 1.18.0 (Build 11.3)
Purpose:
This notebook provides a framework for processing generic Mid-Infrared Instrument
(MIRI) Imaging data through all
three James Webb Space Telescope (JWST) pipeline stages. Data is assumed
to be located in one observation folder 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 an example dataset is from
Program ID
1040 (PI: O. Detre, Co-I: A. Noriega-Crespo) which is an external flat commissioning program.
The MIRI imaging dataset uses a 5-step dither pattern. 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 and uses the context associated with this version of the JWST Calibration Pipeline. Information about this an other contexts can be found in the JWST Calibration Reference Data System (CRDS) server. If you use different pipeline
versions, please refer to the table here to determine what context to use. To learn more about the differences for the pipeline, read the relevant documentation
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:
September 25, 2024: original notebook released
November 22, 2024: Updates to workflow when skipping pipeline modules
January 16, 2025: Add handling for dedicated backgrounds, update to jwst 1.17.1
May 5, 2025: Updated to jwst 1.18.0 (no significant changes)
Table of Contents#
Configuration
Package Imports
Demo Mode Setup (ignore if not using demo data)
Directory Setup
Detector 1 Pipeline
Image2 Pipeline
Image3 Pipeline
Visualize the data
1. Configuration#
Set basic configuration for running notebook.
Install dependencies and parameters#
To make sure that the pipeline version is compatabile with the steps
discussed below and the required dependencies and packages are installed,
you can create a fresh conda environment and install the provided
requirements.txt file before starting this notebook:
conda create -n miri_imaging_pipeline python=3.11
conda activate miri_imaging_pipeline
pip install -r requirements.txt
Set the basic parameters to use with this notebook. These will affect what data is used, where data is located (if already in disk), and pipeline modules run in this data. The list of parameters are:
demo_mode
directories with data
pipeline modules
# 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 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/APT1040/data/Obs001/')
# Point to where background observation data are
# Assumes uncalibrated data in bg_dir/uncal/ and results in stage1 directory
#bg_dir = os.path.join(user_home_dir, 'FlightData/APT1714/data/Obs02/')
bg_dir = '' # If no background observation, use an empty string
# --------------------------Set Processing Steps--------------------------
# 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
doimage2 = True # calwebb_image2
doimage3 = True # calwebb_image3
doviz = True # Visualize calwebb_image3 results
# Background processing (if present)
dodet1bg = True # calwebb_detector1
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----------------------
# Each version of the calibration pipeline is associated with a specific CRDS
# context file. The pipeline will select the appropriate context file behind
# the scenes while running. However, if you wish to override the default context
# file and run the pipeline with a different context, you can set that using
# the CRDS_CONTEXT environment variable. Here we show how this is done,
# although we leave the line commented out in order to use the default context.
# If you wish to specify a different context, uncomment the line below.
#%env CRDS_CONTEXT jwst_1293.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 in use
print(f"CRDS local filepath: {os.environ['CRDS_PATH']}")
print(f"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 time
from pathlib import Path
#import urllib.request
# Numpy for doing calculations
import numpy as np
# To display full ouptut of cell, not just the last result
from IPython.core.interactiveshell import InteractiveShell
InteractiveShell.ast_node_interactivity = "all"
# --------------------Astroquery Imports------------------------------
# ASCII files, and downloading demo files
from astroquery.mast import Observations
# ----------------Matplotlib for visualizing images-------------------
import matplotlib.pyplot as plt
# -------------------Astropy routines for visualizing detected sources----------
from astropy.table import Table
from astropy.io import fits
# ----------------------JWST calibration pipeline------------------------
import jwst
import crds
from jwst.pipeline import Detector1Pipeline
from jwst.pipeline import Image2Pipeline
from jwst.pipeline import Image3Pipeline
# JWST pipeline utilities
from jwst import datamodels
from jwst.datamodels import ImageModel
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
# Echo pipeline version and CRDS context in use
print(f"JWST Calibration Pipeline Version: {jwst.__version__}")
print(f"Using CRDS Context: {crds.get_context_name('jwst')}")
JWST Calibration Pipeline Version: 1.18.0
CRDS - INFO - Calibration SW Found: jwst 1.18.0 (/usr/share/miniconda/lib/python3.13/site-packages/jwst-1.18.0.dist-info)
Using CRDS Context: jwst_1364.pmap
# 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.
For illustrative purposes, we focus on data taken through the MIRI
F770W filter
and start with uncalibrated data products. The files are named
jw01040001005_03103_0000n_miri_uncal.fits, where n refers to the
dither step number which ranges from 1 - 5.
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 = '01040'
sci_observtn = "001"
visit = "005"
data_dir = os.path.join('.', 'mir_im_demo_data')
download_dir = data_dir
sci_dir = os.path.join(data_dir, 'Obs' + sci_observtn)
uncal_dir = os.path.join(sci_dir, 'uncal')
bg_dir = ''
# Ensure filepaths for input data exist
if not os.path.exists(uncal_dir):
os.makedirs(uncal_dir)
# Create directory if it does not exist
if not os.path.isdir(data_dir):
os.mkdir(data_dir)
Running in demonstration mode and will download example data from MAST!
Identify list of science (SCI) uncalibrated files associated with visits.
Selects only filter f770w data
# 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/IMAGE"],
provenance_name=["CALJWST"], # Executed observations
filters=['F770W'], # Data for Specific Filter
obs_id=['jw' + program + '-o' + sci_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'])
# Download only the files in a single visit
sci_files_to_download = [match for match in sci_files_to_download if ('jw' + program + sci_observtn + visit) in match]
sci_files_to_download = sorted(sci_files_to_download)
print(f"Science files selected for downloading: {len(sci_files_to_download)}")
Science files selected for downloading: 5
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))
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01040001005_03103_00001_mirimage_uncal.fits to ./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00001_mirimage_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01040001005_03103_00002_mirimage_uncal.fits to ./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00002_mirimage_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01040001005_03103_00003_mirimage_uncal.fits to ./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00003_mirimage_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01040001005_03103_00004_mirimage_uncal.fits to ./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00004_mirimage_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01040001005_03103_00005_mirimage_uncal.fits to ./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00005_mirimage_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
image2_dir = os.path.join(sci_dir, 'stage2') # calwebb_spec2 pipeline outputs will go here
image3_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
# 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(image2_dir):
os.makedirs(image2_dir)
if not os.path.exists(image3_dir):
os.makedirs(image3_dir)
if ((bg_dir != '') & (not os.path.exists(det1_bgdir))):
os.makedirs(det1_bgdir)
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime so far: {time1 - time0:0.0f} seconds")
Runtime so far: 27 seconds
5. Detector1 Pipeline#
Run the datasets through the
Detector1
stage of the pipeline to apply detector level calibrations and create a
countrate data product where slopes are fitted to the integration ramps.
These *_rate.fits products are 2D (nrows x ncols), averaged over all
integrations. 3D countrate data products (*_rateints.fits) are also
created (nintegrations x nrows x ncols) which have the fitted ramp slopes
for each integration.
By default, all steps in the Detector1 stage of the pipeline are run for
MIRI except: the group_scale, ipc and the gain_scale steps.
MIRI performs a few pipeline steps in calwebb_detector1 that are not performed for other instruments.
The emicorr step corrects
for known noise patterns in MIRI data. For certain subarrays, these noise patterns are clearly imprinted on
the data in the rate.fits files.
The firstframe step flags the first frame in each integration as bad, if the number of groups per integration is greater than 3.
The lastframe step
flags the last frame in each integration as bad, if the number of groups per integration is greater than 2.
The reset correction step
corrects for the reset anomaly effect. This effect is caused by the non-ideal behavior of the field effect
transistor (FET) upon resetting in the dark causing the initial frames in an integration to be offset
from their expected values.
The rscd step reads a reference
file for each data file and determines how many frames at the start of a ramp should be flagged as bad. There are a
number of nonlinearities at the start of MIRI ramps, and the flagging allows the more linear portion of the ramp to
be used for jump detection and ramp fitting, without using the initial, non-linear portion of the ramp. The number
of groups flagged depend on filter and subarray.
As of CRDS context jwst_1201.pmap and later, the
jump step
of the DETECTOR1 stage of the pipeline will remove residuals associated
with showers
for the MIRI imaging mode, but only for data with filter F1500W and shorter. The default parameters for this correction,
where find_showers set to True turns on the shower
removal algorithm, are specified in the pars-jumpstep parameter
reference files. Users may wish to alter parameters to optimize removal of
shower residuals. Available parameters are discussed in the
Detection and Flagging of Showers and Snowballs in JWST Technical Report (Regan 2023).
# 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['firstframe'], det1dict['lastframe'] = {}, {}, {}
det1dict['reset'], det1dict['linearity'], det1dict['rscd'] = {}, {}, {}
det1dict['dark_current'], det1dict['refpix'], det1dict['jump'] = {}, {}, {}
det1dict['ramp_fit'], det1dict['gain_scale'] = {}, {}
# Overrides for whether or not certain steps should be skipped
# skipping the refpix step
#det1dict['refpix']['skip'] = True
#det1dict['jump']['find_showers'] = False # Turn off detection of cosmic ray showers
# 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 (off by default). Choose what fraction of cores to use (quarter, half, or all)
det1dict['jump']['maximum_cores'] = 'half'
# Alter parameters to optimize removal of shower residuals (example)
#det1dict['jump']['after_jump_flag_dn1'] = X # A floating point value in units of DN
#det1dict['jump']['after_jump_flag_time1'] = x.x # A floating point value in units of seconds
Calibrating Science Files#
Look for input science files and run calwebb_detector1 pipeline using the call method.
uncal_files = sorted(glob.glob(os.path.join(uncal_dir, '*_uncal.fits')))
uncal_bgfiles = sorted(glob.glob(os.path.join(uncal_bgdir, '*_uncal.fits')))
print('Found ' + str(len(uncal_files)) + ' science input files')
print('Found ' + str(len(uncal_bgfiles)) + ' background input files')
Found 5 science input files
Found 0 background input files
Look at the first file to determine exposure parameters and practice using JWST datamodels¶
if dodet1:
# print file name
print(uncal_files[0])
# Open file as JWST datamodel
examine = datamodels.open(uncal_files[0])
# Print out exposure info
print(f"Instrument: {examine.meta.instrument.name}")
print(f"Filter: {examine.meta.instrument.filter}")
print(f"Number of integrations: {examine.meta.exposure.nints}")
print(f"Number of groups: {examine.meta.exposure.ngroups}")
print(f"Readout pattern: {examine.meta.exposure.readpatt}")
print(f"Dither position number: {examine.meta.dither.position_number}")
print("\n")
./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00001_mirimage_uncal.fits
Instrument: MIRI
Filter: F770W
Number of integrations: 1
Number of groups: 6
Readout pattern: FASTR1
Dither position number: 1
From the above, we confirm that the demo data file is for the MIRI instrument
using the F770W filter in the Filter Wheel. This observation uses
the MIRI readout pattern FASTR1,
6 groups per integration, and 1 integration per exposure. This data file
is the 1st dither position in this exposure sequence. For more information
about how JWST exposures are defined by up-the-ramp sampling, see the
Understanding Exposure Times JDox article.
This metadata will be the same for all exposures in this observation other than the dither position number.
# Run Detector1 stage of pipeline, specifying:
# output directory to save *_rate.fits files
# save_results flag set to True so the rate files are saved
if dodet1:
for uncal in uncal_files:
rate_result = Detector1Pipeline.call(uncal, output_dir=det1_dir, steps=det1dict, save_results=True,)
else:
print('Skipping Detector1 processing')
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2025-05-13 13:49:02,464 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_msaoper_0016.rmap 1.5 K bytes (25 / 204 files) (86.4 K / 741.0 K bytes)
2025-05-13 13:49:02,523 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_msa_0027.rmap 1.3 K bytes (26 / 204 files) (87.9 K / 741.0 K bytes)
2025-05-13 13:49:02,576 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_mask_0043.rmap 3.5 K bytes (27 / 204 files) (89.2 K / 741.0 K bytes)
2025-05-13 13:49:02,617 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_linearity_0017.rmap 1.6 K bytes (28 / 204 files) (92.7 K / 741.0 K bytes)
2025-05-13 13:49:02,670 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_ipc_0006.rmap 876 bytes (29 / 204 files) (94.3 K / 741.0 K bytes)
2025-05-13 13:49:02,718 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_ifuslicer_0017.rmap 1.5 K bytes (30 / 204 files) (95.2 K / 741.0 K bytes)
2025-05-13 13:49:02,763 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_ifupost_0019.rmap 1.5 K bytes (31 / 204 files) (96.7 K / 741.0 K bytes)
2025-05-13 13:49:02,837 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_ifufore_0017.rmap 1.5 K bytes (32 / 204 files) (98.2 K / 741.0 K bytes)
2025-05-13 13:49:02,883 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_gain_0023.rmap 1.8 K bytes (33 / 204 files) (99.7 K / 741.0 K bytes)
2025-05-13 13:49:02,959 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_fpa_0028.rmap 1.3 K bytes (34 / 204 files) (101.5 K / 741.0 K bytes)
2025-05-13 13:49:02,997 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_fore_0026.rmap 5.0 K bytes (35 / 204 files) (102.7 K / 741.0 K bytes)
2025-05-13 13:49:03,106 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_flat_0015.rmap 3.8 K bytes (36 / 204 files) (107.7 K / 741.0 K bytes)
2025-05-13 13:49:03,156 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_fflat_0026.rmap 7.2 K bytes (37 / 204 files) (111.5 K / 741.0 K bytes)
2025-05-13 13:49:03,291 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_extract1d_0018.rmap 2.3 K bytes (38 / 204 files) (118.7 K / 741.0 K bytes)
2025-05-13 13:49:03,335 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_disperser_0028.rmap 5.7 K bytes (39 / 204 files) (121.0 K / 741.0 K bytes)
2025-05-13 13:49:03,377 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_dflat_0007.rmap 1.1 K bytes (40 / 204 files) (126.7 K / 741.0 K bytes)
2025-05-13 13:49:03,435 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_dark_0074.rmap 34.2 K bytes (41 / 204 files) (127.9 K / 741.0 K bytes)
2025-05-13 13:49:03,497 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_cubepar_0015.rmap 966 bytes (42 / 204 files) (162.1 K / 741.0 K bytes)
2025-05-13 13:49:03,539 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_collimator_0026.rmap 1.3 K bytes (43 / 204 files) (163.1 K / 741.0 K bytes)
2025-05-13 13:49:03,586 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_camera_0026.rmap 1.3 K bytes (44 / 204 files) (164.4 K / 741.0 K bytes)
2025-05-13 13:49:03,657 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_barshadow_0007.rmap 1.8 K bytes (45 / 204 files) (165.7 K / 741.0 K bytes)
2025-05-13 13:49:03,697 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_area_0018.rmap 6.3 K bytes (46 / 204 files) (167.5 K / 741.0 K bytes)
2025-05-13 13:49:03,742 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_apcorr_0009.rmap 5.6 K bytes (47 / 204 files) (173.8 K / 741.0 K bytes)
2025-05-13 13:49:03,785 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_nirspec_0398.imap 5.8 K bytes (48 / 204 files) (179.3 K / 741.0 K bytes)
2025-05-13 13:49:03,826 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_wfssbkg_0010.rmap 3.1 K bytes (49 / 204 files) (185.1 K / 741.0 K bytes)
2025-05-13 13:49:03,874 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_wavelengthrange_0006.rmap 862 bytes (50 / 204 files) (188.2 K / 741.0 K bytes)
2025-05-13 13:49:03,915 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_trappars_0004.rmap 753 bytes (51 / 204 files) (189.1 K / 741.0 K bytes)
2025-05-13 13:49:03,961 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_trapdensity_0005.rmap 705 bytes (52 / 204 files) (189.9 K / 741.0 K bytes)
2025-05-13 13:49:04,004 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_throughput_0005.rmap 1.3 K bytes (53 / 204 files) (190.6 K / 741.0 K bytes)
2025-05-13 13:49:04,044 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_superbias_0030.rmap 7.4 K bytes (54 / 204 files) (191.8 K / 741.0 K bytes)
2025-05-13 13:49:04,086 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_specwcs_0014.rmap 3.1 K bytes (55 / 204 files) (199.2 K / 741.0 K bytes)
2025-05-13 13:49:04,135 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_specprofile_0008.rmap 2.4 K bytes (56 / 204 files) (202.4 K / 741.0 K bytes)
2025-05-13 13:49:04,183 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_speckernel_0006.rmap 1.0 K bytes (57 / 204 files) (204.7 K / 741.0 K bytes)
2025-05-13 13:49:04,223 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_sirskernel_0001.rmap 627 bytes (58 / 204 files) (205.8 K / 741.0 K bytes)
2025-05-13 13:49:04,263 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_saturation_0015.rmap 829 bytes (59 / 204 files) (206.4 K / 741.0 K bytes)
2025-05-13 13:49:04,304 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_readnoise_0011.rmap 987 bytes (60 / 204 files) (207.2 K / 741.0 K bytes)
2025-05-13 13:49:04,354 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_photom_0036.rmap 1.3 K bytes (61 / 204 files) (208.2 K / 741.0 K bytes)
2025-05-13 13:49:04,425 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_persat_0007.rmap 674 bytes (62 / 204 files) (209.5 K / 741.0 K bytes)
2025-05-13 13:49:04,469 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pathloss_0003.rmap 758 bytes (63 / 204 files) (210.1 K / 741.0 K bytes)
2025-05-13 13:49:04,518 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pastasoss_0004.rmap 818 bytes (64 / 204 files) (210.9 K / 741.0 K bytes)
2025-05-13 13:49:04,570 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-undersamplecorrectionstep_0001.rmap 904 bytes (65 / 204 files) (211.7 K / 741.0 K bytes)
2025-05-13 13:49:04,609 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-tweakregstep_0012.rmap 3.1 K bytes (66 / 204 files) (212.6 K / 741.0 K bytes)
2025-05-13 13:49:04,650 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-spec2pipeline_0008.rmap 984 bytes (67 / 204 files) (215.8 K / 741.0 K bytes)
2025-05-13 13:49:04,702 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-sourcecatalogstep_0002.rmap 2.3 K bytes (68 / 204 files) (216.7 K / 741.0 K bytes)
2025-05-13 13:49:04,742 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-resamplestep_0002.rmap 687 bytes (69 / 204 files) (219.1 K / 741.0 K bytes)
2025-05-13 13:49:04,780 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-outlierdetectionstep_0004.rmap 2.7 K bytes (70 / 204 files) (219.7 K / 741.0 K bytes)
2025-05-13 13:49:04,827 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-jumpstep_0007.rmap 6.4 K bytes (71 / 204 files) (222.4 K / 741.0 K bytes)
2025-05-13 13:49:04,867 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-image2pipeline_0005.rmap 1.0 K bytes (72 / 204 files) (228.8 K / 741.0 K bytes)
2025-05-13 13:49:04,908 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_niriss_pars-detector1pipeline_0002.rmap 1.0 K bytes (73 / 204 files) (229.8 K / 741.0 K bytes)
2025-05-13 13:49:04,954 - 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)
2025-05-13 13:49:05,000 - 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)
2025-05-13 13:49:05,050 - 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)
2025-05-13 13:49:05,096 - 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)
2025-05-13 13:49:05,144 - 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)
2025-05-13 13:49:05,189 - 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)
2025-05-13 13:49:05,235 - 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)
2025-05-13 13:49:05,281 - 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)
2025-05-13 13:49:05,329 - 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)
2025-05-13 13:49:05,375 - 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)
2025-05-13 13:49:05,416 - 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)
2025-05-13 13:49:05,455 - 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)
2025-05-13 13:49:05,501 - 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)
2025-05-13 13:49:05,545 - 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)
2025-05-13 13:49:05,587 - 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)
2025-05-13 13:49:05,627 - 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)
2025-05-13 13:49:05,674 - 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)
2025-05-13 13:49:05,799 - 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)
2025-05-13 13:49:05,839 - 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)
2025-05-13 13:49:05,878 - 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)
2025-05-13 13:49:05,925 - 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)
2025-05-13 13:49:05,976 - 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)
2025-05-13 13:49:06,014 - 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)
2025-05-13 13:49:06,060 - 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)
2025-05-13 13:49:06,100 - 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)
2025-05-13 13:49:06,149 - 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)
2025-05-13 13:49:06,191 - 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)
2025-05-13 13:49:06,231 - 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)
2025-05-13 13:49:06,292 - 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)
2025-05-13 13:49:06,340 - 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)
2025-05-13 13:49:06,397 - 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)
2025-05-13 13:49:06,436 - 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)
2025-05-13 13:49:06,495 - 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)
2025-05-13 13:49:06,558 - 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)
2025-05-13 13:49:06,598 - 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)
2025-05-13 13:49:06,664 - 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)
2025-05-13 13:49:06,713 - 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)
2025-05-13 13:49:06,752 - 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)
2025-05-13 13:49:06,800 - 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)
2025-05-13 13:49:06,845 - 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)
2025-05-13 13:49:06,890 - 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)
2025-05-13 13:49:06,931 - 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)
2025-05-13 13:49:06,989 - 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)
2025-05-13 13:49:07,034 - 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)
2025-05-13 13:49:07,089 - 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)
2025-05-13 13:49:07,141 - 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)
2025-05-13 13:49:07,183 - 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)
2025-05-13 13:49:07,224 - 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)
2025-05-13 13:49:07,279 - 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)
2025-05-13 13:49:07,319 - 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)
2025-05-13 13:49:07,357 - 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)
2025-05-13 13:49:07,395 - 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)
2025-05-13 13:49:07,461 - 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)
2025-05-13 13:49:07,510 - 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)
2025-05-13 13:49:07,565 - 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)
2025-05-13 13:49:07,602 - 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)
2025-05-13 13:49:07,646 - 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)
2025-05-13 13:49:07,684 - 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)
2025-05-13 13:49:07,725 - 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)
2025-05-13 13:49:07,763 - 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)
2025-05-13 13:49:07,810 - 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)
2025-05-13 13:49:07,848 - 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)
2025-05-13 13:49:07,887 - 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)
2025-05-13 13:49:07,929 - 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)
2025-05-13 13:49:07,967 - 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)
2025-05-13 13:49:08,006 - 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)
2025-05-13 13:49:08,057 - 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)
2025-05-13 13:49:08,095 - 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)
2025-05-13 13:49:08,141 - 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)
2025-05-13 13:49:08,179 - 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)
2025-05-13 13:49:08,221 - 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)
2025-05-13 13:49:08,265 - 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)
2025-05-13 13:49:08,305 - 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)
2025-05-13 13:49:08,343 - 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)
2025-05-13 13:49:08,390 - 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)
2025-05-13 13:49:08,430 - 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)
2025-05-13 13:49:08,477 - 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)
2025-05-13 13:49:08,521 - 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)
2025-05-13 13:49:08,561 - 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)
2025-05-13 13:49:08,605 - 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)
2025-05-13 13:49:08,654 - 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)
2025-05-13 13:49:08,696 - 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)
2025-05-13 13:49:08,743 - 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)
2025-05-13 13:49:08,790 - 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)
2025-05-13 13:49:08,848 - 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)
2025-05-13 13:49:08,896 - 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)
2025-05-13 13:49:08,942 - 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)
2025-05-13 13:49:08,982 - 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)
2025-05-13 13:49:09,026 - 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)
2025-05-13 13:49:09,072 - 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)
2025-05-13 13:49:09,110 - 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)
2025-05-13 13:49:09,156 - 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)
2025-05-13 13:49:09,206 - 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)
2025-05-13 13:49:09,253 - 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)
2025-05-13 13:49:09,294 - 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)
2025-05-13 13:49:09,338 - 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)
2025-05-13 13:49:09,379 - 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)
2025-05-13 13:49:09,430 - 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)
2025-05-13 13:49:09,478 - 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)
2025-05-13 13:49:09,526 - 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)
2025-05-13 13:49:09,564 - 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)
2025-05-13 13:49:09,614 - 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)
2025-05-13 13:49:09,673 - 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)
2025-05-13 13:49:09,719 - 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)
2025-05-13 13:49:09,763 - 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)
2025-05-13 13:49:09,808 - 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)
2025-05-13 13:49:09,848 - 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)
2025-05-13 13:49:09,896 - 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)
2025-05-13 13:49:09,936 - 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)
2025-05-13 13:49:09,980 - 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)
2025-05-13 13:49:10,022 - 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)
2025-05-13 13:49:10,066 - 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)
2025-05-13 13:49:10,113 - 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)
2025-05-13 13:49:10,154 - 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)
2025-05-13 13:49:10,197 - 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)
2025-05-13 13:49:10,238 - 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)
2025-05-13 13:49:10,277 - 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)
2025-05-13 13:49:10,317 - 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)
2025-05-13 13:49:10,365 - 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)
2025-05-13 13:49:10,411 - 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)
2025-05-13 13:49:10,465 - 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)
2025-05-13 13:49:10,503 - 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)
2025-05-13 13:49:10,550 - 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)
2025-05-13 13:49:10,590 - 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)
2025-05-13 13:49:10,631 - 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)
2025-05-13 13:49:10,670 - 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)
2025-05-13 13:49:10,718 - 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)
2025-05-13 13:49:10,767 - 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)
2025-05-13 13:49:10,807 - 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)
2025-05-13 13:49:10,847 - 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)
2025-05-13 13:49:10,887 - CRDS - INFO - Fetching /home/runner/crds/mappings/jwst/jwst_1364.pmap 580 bytes (204 / 204 files) (740.4 K / 741.0 K bytes)
2025-05-13 13:49:11,094 - 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)
2025-05-13 13:49:11,144 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-05-13 13:49:11,159 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf 936 bytes (1 / 1 files) (0 / 936 bytes)
2025-05-13 13:49:11,208 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-05-13 13:49:11,218 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0005.asdf 1.9 K bytes (1 / 1 files) (0 / 1.9 K bytes)
2025-05-13 13:49:11,269 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0005.asdf
2025-05-13 13:49:11,280 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0008.asdf 1.7 K bytes (1 / 1 files) (0 / 1.7 K bytes)
2025-05-13 13:49:11,320 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0008.asdf
2025-05-13 13:49:11,338 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:49:11,339 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:49:11,340 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:49:11,340 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:49:11,341 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:49:11,342 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:49:11,343 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:49:11,346 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:49:11,347 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:49:11,348 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:49:11,349 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:49:11,350 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:49:11,351 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:49:11,352 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:49:11,353 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:49:11,354 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:49:11,356 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:49:11,357 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:49:11,358 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:49:11,359 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:49:11,451 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00001_mirimage_uncal.fits',).
2025-05-13 13:49:11,472 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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: False
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: 6.0
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000
min_jump_to_flag_neighbors: 30
after_jump_flag_dn1: 500
after_jump_flag_time1: 15
after_jump_flag_dn2: 1000
after_jump_flag_time2: 3000
expand_large_events: False
min_sat_area: 1
min_jump_area: 0
expand_factor: 0
use_ellipses: False
sat_required_snowball: False
min_sat_radius_extend: 0.0
sat_expand: 0
edge_size: 0
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 3.0
extend_min_area: 50
extend_inner_radius: 1
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 30
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: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:49:11,525 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00001_mirimage_uncal.fits' reftypes = ['dark', 'emicorr', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:49:11,528 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits 6.1 G bytes (1 / 9 files) (0 / 6.3 G bytes)
2025-05-13 13:52:34,147 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf 16.9 K bytes (2 / 9 files) (6.1 G / 6.3 G bytes)
2025-05-13 13:52:34,193 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits 12.7 M bytes (3 / 9 files) (6.1 G / 6.3 G bytes)
2025-05-13 13:52:34,404 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits 25.4 M bytes (4 / 9 files) (6.1 G / 6.3 G bytes)
2025-05-13 13:52:34,732 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits 4.3 M bytes (5 / 9 files) (6.1 G / 6.3 G bytes)
2025-05-13 13:52:34,855 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits 4.2 M bytes (6 / 9 files) (6.1 G / 6.3 G bytes)
2025-05-13 13:52:34,975 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits 173.3 M bytes (7 / 9 files) (6.1 G / 6.3 G bytes)
2025-05-13 13:52:36,417 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits 37.4 K bytes (8 / 9 files) (6.3 G / 6.3 G bytes)
2025-05-13 13:52:36,467 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits 8.5 M bytes (9 / 9 files) (6.3 G / 6.3 G bytes)
2025-05-13 13:52:36,673 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits'.
2025-05-13 13:52:36,674 - stpipe.Detector1Pipeline - INFO - Prefetch for EMICORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf'.
2025-05-13 13:52:36,674 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits'.
2025-05-13 13:52:36,675 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits'.
2025-05-13 13:52:36,676 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits'.
2025-05-13 13:52:36,676 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:52:36,676 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits'.
2025-05-13 13:52:36,677 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits'.
2025-05-13 13:52:36,678 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits'.
2025-05-13 13:52:36,678 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits'.
2025-05-13 13:52:36,679 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-05-13 13:52:36,679 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:52:36,679 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:52:36,681 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:52:36,917 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:36,925 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:52:36,925 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:52:36,927 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:52:37,049 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:37,065 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits
2025-05-13 13:52:37,111 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:37,124 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:37,140 - CRDS - INFO - Calibration SW Found: jwst 1.18.0 (/usr/share/miniconda/lib/python3.13/site-packages/jwst-1.18.0.dist-info)
2025-05-13 13:52:37,197 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:52:37,325 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:37,356 - stpipe.Detector1Pipeline.emicorr - INFO - Using CRDS reference file: /home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf
2025-05-13 13:52:37,373 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'sequential' algorithm is selected and ngroups=6.
2025-05-13 13:52:37,373 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'joint' algorithm is recommended for ngroups < 10.
2025-05-13 13:52:37,374 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to get subarray case.
2025-05-13 13:52:37,375 - stpipe.Detector1Pipeline.emicorr - INFO - With configuration: Subarray=FULL, Read_pattern=FASTR1, Detector=MIRIMAGE
2025-05-13 13:52:37,376 - stpipe.Detector1Pipeline.emicorr - INFO - Will correct data for the following 1 frequencies:
2025-05-13 13:52:37,376 - stpipe.Detector1Pipeline.emicorr - INFO - ['Hz10']
2025-05-13 13:52:37,377 - stpipe.Detector1Pipeline.emicorr - INFO - Running EMI fit with algorithm = 'sequential'.
2025-05-13 13:52:37,377 - stpipe.Detector1Pipeline.emicorr - INFO - Correcting for frequency: 10.039216 Hz (1 out of 1)
2025-05-13 13:52:37,378 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting self-superbias from each group of each integration
2025-05-13 13:52:37,379 - stpipe.Detector1Pipeline.emicorr - INFO - Doing phase calculation per integration
2025-05-13 13:52:37,658 - stpipe.Detector1Pipeline.emicorr - INFO - Calculating the phase amplitude for 500 bins
2025-05-13 13:52:38,627 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to measure phase shift
2025-05-13 13:52:38,666 - stpipe.Detector1Pipeline.emicorr - INFO - Creating phased-matched noise model to subtract from data
2025-05-13 13:52:38,671 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting EMI noise from data
2025-05-13 13:52:38,688 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr done
2025-05-13 13:52:38,809 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:38,832 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits
2025-05-13 13:52:38,854 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:38,862 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:38,887 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:52:38,934 - stpipe.Detector1Pipeline.saturation - INFO - Detected 820 saturated pixels
2025-05-13 13:52:38,937 - stpipe.Detector1Pipeline.saturation - INFO - Detected 76 A/D floor pixels
2025-05-13 13:52:38,941 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:52:39,056 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:39,056 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:52:39,182 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:39,204 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-05-13 13:52:39,319 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:39,353 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-05-13 13:52:39,476 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:39,500 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits
2025-05-13 13:52:39,556 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:39,566 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:39,611 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-05-13 13:52:39,724 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:39,743 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits
2025-05-13 13:52:39,768 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:39,777 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:39,869 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:52:39,989 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:40,007 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits
2025-05-13 13:52:40,060 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-05-13 13:52:40,063 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-05-13 13:52:40,184 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:40,203 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits
2025-05-13 13:52:43,222 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-05-13 13:52:43,223 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2025-05-13 13:52:43,224 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-05-13 13:52:44,219 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:52:44,348 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:44,349 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-05-13 13:52:44,472 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:44,473 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:52:44,602 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:44,610 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:52:44,610 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:52:44,635 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:52:44,644 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:52:44,692 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:52:44,692 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:52:45,735 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-05-13 13:52:45,746 - stpipe.Detector1Pipeline.jump - WARNING - Not enough differences for shower detections
2025-05-13 13:52:45,747 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-05-13 13:52:45,747 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 1.05525 sec
2025-05-13 13:52:45,757 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 1.147168
2025-05-13 13:52:45,759 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:52:45,879 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:45,880 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:52:45,999 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:46,050 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:52:46,050 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:52:46,074 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:52:46,075 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:52:46,150 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:52:46,155 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-05-13 13:52:46,156 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-05-13 13:52:46,554 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.3964574337005615
2025-05-13 13:52:46,602 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:52:46,718 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:46,750 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:52:46,751 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:52:46,753 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:52:46,873 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01040001005_03103_00001_mirimage_uncal.fits>,).
2025-05-13 13:52:46,901 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:52:46,902 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:52:46,904 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:52:46,975 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00001_mirimage_rateints.fits
2025-05-13 13:52:46,976 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:52:46,977 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:52:47,045 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00001_mirimage_rate.fits
2025-05-13 13:52:47,046 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:52:47,046 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:52:47,116 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-05-13 13:52:47,129 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-05-13 13:52:47,139 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0005.asdf
2025-05-13 13:52:47,149 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0008.asdf
2025-05-13 13:52:47,166 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:52:47,167 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:52:47,168 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:52:47,169 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:52:47,170 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:52:47,171 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:52:47,172 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:52:47,173 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:52:47,174 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:52:47,175 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:52:47,176 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:52:47,177 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:52:47,178 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:52:47,178 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:52:47,179 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:52:47,180 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:52:47,183 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:52:47,184 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:52:47,185 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:52:47,186 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:52:47,311 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00002_mirimage_uncal.fits',).
2025-05-13 13:52:47,333 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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: False
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: 6.0
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000
min_jump_to_flag_neighbors: 30
after_jump_flag_dn1: 500
after_jump_flag_time1: 15
after_jump_flag_dn2: 1000
after_jump_flag_time2: 3000
expand_large_events: False
min_sat_area: 1
min_jump_area: 0
expand_factor: 0
use_ellipses: False
sat_required_snowball: False
min_sat_radius_extend: 0.0
sat_expand: 0
edge_size: 0
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 3.0
extend_min_area: 50
extend_inner_radius: 1
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 30
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: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:52:47,389 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00002_mirimage_uncal.fits' reftypes = ['dark', 'emicorr', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:52:47,392 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits'.
2025-05-13 13:52:47,392 - stpipe.Detector1Pipeline - INFO - Prefetch for EMICORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf'.
2025-05-13 13:52:47,393 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits'.
2025-05-13 13:52:47,393 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits'.
2025-05-13 13:52:47,394 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits'.
2025-05-13 13:52:47,394 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:52:47,395 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits'.
2025-05-13 13:52:47,395 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits'.
2025-05-13 13:52:47,395 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits'.
2025-05-13 13:52:47,397 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits'.
2025-05-13 13:52:47,397 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-05-13 13:52:47,397 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:52:47,398 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:52:47,399 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:52:47,622 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:47,630 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:52:47,631 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:52:47,632 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:52:47,757 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:47,773 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits
2025-05-13 13:52:47,810 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:47,821 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:47,831 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:52:47,964 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:47,997 - stpipe.Detector1Pipeline.emicorr - INFO - Using CRDS reference file: /home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf
2025-05-13 13:52:48,016 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'sequential' algorithm is selected and ngroups=6.
2025-05-13 13:52:48,016 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'joint' algorithm is recommended for ngroups < 10.
2025-05-13 13:52:48,017 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to get subarray case.
2025-05-13 13:52:48,017 - stpipe.Detector1Pipeline.emicorr - INFO - With configuration: Subarray=FULL, Read_pattern=FASTR1, Detector=MIRIMAGE
2025-05-13 13:52:48,018 - stpipe.Detector1Pipeline.emicorr - INFO - Will correct data for the following 1 frequencies:
2025-05-13 13:52:48,018 - stpipe.Detector1Pipeline.emicorr - INFO - ['Hz10']
2025-05-13 13:52:48,018 - stpipe.Detector1Pipeline.emicorr - INFO - Running EMI fit with algorithm = 'sequential'.
2025-05-13 13:52:48,019 - stpipe.Detector1Pipeline.emicorr - INFO - Correcting for frequency: 10.039216 Hz (1 out of 1)
2025-05-13 13:52:48,020 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting self-superbias from each group of each integration
2025-05-13 13:52:48,022 - stpipe.Detector1Pipeline.emicorr - INFO - Doing phase calculation per integration
2025-05-13 13:52:48,268 - stpipe.Detector1Pipeline.emicorr - INFO - Calculating the phase amplitude for 500 bins
2025-05-13 13:52:49,307 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to measure phase shift
2025-05-13 13:52:49,344 - stpipe.Detector1Pipeline.emicorr - INFO - Creating phased-matched noise model to subtract from data
2025-05-13 13:52:49,349 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting EMI noise from data
2025-05-13 13:52:49,366 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr done
2025-05-13 13:52:49,500 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:49,515 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits
2025-05-13 13:52:49,537 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:49,546 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:49,562 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:52:49,609 - stpipe.Detector1Pipeline.saturation - INFO - Detected 845 saturated pixels
2025-05-13 13:52:49,612 - stpipe.Detector1Pipeline.saturation - INFO - Detected 80 A/D floor pixels
2025-05-13 13:52:49,616 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:52:49,759 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:49,760 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:52:49,896 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:49,921 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-05-13 13:52:50,055 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:50,077 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-05-13 13:52:50,214 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:50,230 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits
2025-05-13 13:52:50,284 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:50,293 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:50,340 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-05-13 13:52:50,470 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:50,486 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits
2025-05-13 13:52:50,510 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:50,519 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:52:50,607 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:52:50,739 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:50,755 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits
2025-05-13 13:52:50,813 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-05-13 13:52:50,816 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-05-13 13:52:50,954 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:50,970 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits
2025-05-13 13:52:57,571 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-05-13 13:52:57,572 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2025-05-13 13:52:57,572 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-05-13 13:52:58,391 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:52:58,583 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:58,583 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-05-13 13:52:58,723 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:58,723 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:52:58,865 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:52:58,874 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:52:58,874 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:52:58,902 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:52:58,912 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:52:58,958 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:52:58,959 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:52:59,904 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-05-13 13:52:59,914 - stpipe.Detector1Pipeline.jump - WARNING - Not enough differences for shower detections
2025-05-13 13:52:59,915 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-05-13 13:52:59,915 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.956785 sec
2025-05-13 13:52:59,925 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 1.051004
2025-05-13 13:52:59,927 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:53:00,058 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:53:00,059 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:53:00,197 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:53:00,236 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:53:00,237 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:53:00,262 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:53:00,262 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:53:00,327 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:53:00,333 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-05-13 13:53:00,334 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-05-13 13:53:00,729 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.39385056495666504
2025-05-13 13:53:00,772 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:53:00,902 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:53:00,929 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:53:00,929 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:53:00,932 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:01,063 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01040001005_03103_00002_mirimage_uncal.fits>,).
2025-05-13 13:53:01,091 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:53:01,092 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:53:01,095 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:01,164 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00002_mirimage_rateints.fits
2025-05-13 13:53:01,165 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:53:01,166 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:01,235 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00002_mirimage_rate.fits
2025-05-13 13:53:01,235 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:53:01,236 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:53:01,306 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-05-13 13:53:01,319 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-05-13 13:53:01,329 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0005.asdf
2025-05-13 13:53:01,340 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0008.asdf
2025-05-13 13:53:01,357 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:53:01,358 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:53:01,359 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:53:01,360 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:53:01,361 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:53:01,362 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:53:01,363 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:53:01,364 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:53:01,365 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:53:01,366 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:53:01,366 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:53:01,367 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:53:01,368 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:53:01,369 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:53:01,370 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:53:01,371 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:53:01,373 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:53:01,374 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:53:01,376 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:53:01,377 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:53:01,507 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00003_mirimage_uncal.fits',).
2025-05-13 13:53:01,529 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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: False
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: 6.0
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000
min_jump_to_flag_neighbors: 30
after_jump_flag_dn1: 500
after_jump_flag_time1: 15
after_jump_flag_dn2: 1000
after_jump_flag_time2: 3000
expand_large_events: False
min_sat_area: 1
min_jump_area: 0
expand_factor: 0
use_ellipses: False
sat_required_snowball: False
min_sat_radius_extend: 0.0
sat_expand: 0
edge_size: 0
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 3.0
extend_min_area: 50
extend_inner_radius: 1
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 30
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: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:53:01,586 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00003_mirimage_uncal.fits' reftypes = ['dark', 'emicorr', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:53:01,589 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits'.
2025-05-13 13:53:01,590 - stpipe.Detector1Pipeline - INFO - Prefetch for EMICORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf'.
2025-05-13 13:53:01,590 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits'.
2025-05-13 13:53:01,591 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits'.
2025-05-13 13:53:01,591 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits'.
2025-05-13 13:53:01,592 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:53:01,592 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits'.
2025-05-13 13:53:01,593 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits'.
2025-05-13 13:53:01,593 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits'.
2025-05-13 13:53:01,594 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits'.
2025-05-13 13:53:01,594 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-05-13 13:53:01,594 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:53:01,595 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:53:01,596 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:53:01,831 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:01,839 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:53:01,840 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:53:01,841 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:53:01,972 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:01,988 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits
2025-05-13 13:53:02,026 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:02,038 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:02,049 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:53:02,183 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:02,217 - stpipe.Detector1Pipeline.emicorr - INFO - Using CRDS reference file: /home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf
2025-05-13 13:53:02,235 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'sequential' algorithm is selected and ngroups=6.
2025-05-13 13:53:02,236 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'joint' algorithm is recommended for ngroups < 10.
2025-05-13 13:53:02,237 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to get subarray case.
2025-05-13 13:53:02,237 - stpipe.Detector1Pipeline.emicorr - INFO - With configuration: Subarray=FULL, Read_pattern=FASTR1, Detector=MIRIMAGE
2025-05-13 13:53:02,237 - stpipe.Detector1Pipeline.emicorr - INFO - Will correct data for the following 1 frequencies:
2025-05-13 13:53:02,238 - stpipe.Detector1Pipeline.emicorr - INFO - ['Hz10']
2025-05-13 13:53:02,238 - stpipe.Detector1Pipeline.emicorr - INFO - Running EMI fit with algorithm = 'sequential'.
2025-05-13 13:53:02,239 - stpipe.Detector1Pipeline.emicorr - INFO - Correcting for frequency: 10.039216 Hz (1 out of 1)
2025-05-13 13:53:02,240 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting self-superbias from each group of each integration
2025-05-13 13:53:02,242 - stpipe.Detector1Pipeline.emicorr - INFO - Doing phase calculation per integration
2025-05-13 13:53:02,482 - stpipe.Detector1Pipeline.emicorr - INFO - Calculating the phase amplitude for 500 bins
2025-05-13 13:53:03,490 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to measure phase shift
2025-05-13 13:53:03,527 - stpipe.Detector1Pipeline.emicorr - INFO - Creating phased-matched noise model to subtract from data
2025-05-13 13:53:03,532 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting EMI noise from data
2025-05-13 13:53:03,547 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr done
2025-05-13 13:53:03,672 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:03,688 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits
2025-05-13 13:53:03,709 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:03,719 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:03,740 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:53:03,786 - stpipe.Detector1Pipeline.saturation - INFO - Detected 801 saturated pixels
2025-05-13 13:53:03,789 - stpipe.Detector1Pipeline.saturation - INFO - Detected 59 A/D floor pixels
2025-05-13 13:53:03,793 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:53:03,920 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:03,921 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:53:04,049 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:04,070 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-05-13 13:53:04,192 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:04,215 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-05-13 13:53:04,337 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:04,353 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits
2025-05-13 13:53:04,398 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:04,408 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:04,450 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-05-13 13:53:04,578 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:04,595 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits
2025-05-13 13:53:04,619 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:04,629 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:04,716 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:53:04,844 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:04,860 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits
2025-05-13 13:53:04,911 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-05-13 13:53:04,915 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-05-13 13:53:05,046 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:05,063 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits
2025-05-13 13:53:06,097 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-05-13 13:53:06,098 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2025-05-13 13:53:06,098 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-05-13 13:53:06,952 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:53:07,109 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:07,110 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-05-13 13:53:07,242 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:07,243 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:53:07,370 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:07,378 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:53:07,379 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:53:07,406 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:53:07,415 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:53:07,460 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:53:07,460 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:53:08,381 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-05-13 13:53:08,387 - stpipe.Detector1Pipeline.jump - WARNING - Not enough differences for shower detections
2025-05-13 13:53:08,388 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-05-13 13:53:08,389 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.928353 sec
2025-05-13 13:53:08,398 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 1.019818
2025-05-13 13:53:08,401 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:53:08,529 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:08,530 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:53:08,661 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:08,698 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:53:08,698 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:53:08,723 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:53:08,723 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:53:08,793 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:53:08,798 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-05-13 13:53:08,799 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-05-13 13:53:09,196 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.3956754207611084
2025-05-13 13:53:09,238 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:53:09,359 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:09,385 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:53:09,385 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:53:09,388 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:09,512 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01040001005_03103_00003_mirimage_uncal.fits>,).
2025-05-13 13:53:09,540 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:53:09,541 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:53:09,543 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:09,610 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00003_mirimage_rateints.fits
2025-05-13 13:53:09,611 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:53:09,612 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:09,680 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00003_mirimage_rate.fits
2025-05-13 13:53:09,680 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:53:09,681 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:53:09,752 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-05-13 13:53:09,765 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-05-13 13:53:09,775 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0005.asdf
2025-05-13 13:53:09,785 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0008.asdf
2025-05-13 13:53:09,802 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:53:09,803 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:53:09,804 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:53:09,805 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:53:09,806 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:53:09,807 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:53:09,808 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:53:09,809 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:53:09,810 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:53:09,811 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:53:09,813 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:53:09,814 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:53:09,815 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:53:09,816 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:53:09,817 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:53:09,818 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:53:09,821 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:53:09,822 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:53:09,823 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:53:09,824 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:53:09,958 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00004_mirimage_uncal.fits',).
2025-05-13 13:53:09,979 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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: False
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: 6.0
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000
min_jump_to_flag_neighbors: 30
after_jump_flag_dn1: 500
after_jump_flag_time1: 15
after_jump_flag_dn2: 1000
after_jump_flag_time2: 3000
expand_large_events: False
min_sat_area: 1
min_jump_area: 0
expand_factor: 0
use_ellipses: False
sat_required_snowball: False
min_sat_radius_extend: 0.0
sat_expand: 0
edge_size: 0
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 3.0
extend_min_area: 50
extend_inner_radius: 1
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 30
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: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:53:10,034 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00004_mirimage_uncal.fits' reftypes = ['dark', 'emicorr', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:53:10,038 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits'.
2025-05-13 13:53:10,038 - stpipe.Detector1Pipeline - INFO - Prefetch for EMICORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf'.
2025-05-13 13:53:10,039 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits'.
2025-05-13 13:53:10,039 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits'.
2025-05-13 13:53:10,040 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits'.
2025-05-13 13:53:10,040 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:53:10,041 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits'.
2025-05-13 13:53:10,041 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits'.
2025-05-13 13:53:10,042 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits'.
2025-05-13 13:53:10,042 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits'.
2025-05-13 13:53:10,043 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-05-13 13:53:10,043 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:53:10,044 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:53:10,045 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:53:10,269 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:10,277 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:53:10,277 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:53:10,279 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:53:10,404 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:10,420 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits
2025-05-13 13:53:10,458 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:10,471 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:10,485 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:53:10,613 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:10,641 - stpipe.Detector1Pipeline.emicorr - INFO - Using CRDS reference file: /home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf
2025-05-13 13:53:10,658 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'sequential' algorithm is selected and ngroups=6.
2025-05-13 13:53:10,658 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'joint' algorithm is recommended for ngroups < 10.
2025-05-13 13:53:10,659 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to get subarray case.
2025-05-13 13:53:10,659 - stpipe.Detector1Pipeline.emicorr - INFO - With configuration: Subarray=FULL, Read_pattern=FASTR1, Detector=MIRIMAGE
2025-05-13 13:53:10,660 - stpipe.Detector1Pipeline.emicorr - INFO - Will correct data for the following 1 frequencies:
2025-05-13 13:53:10,660 - stpipe.Detector1Pipeline.emicorr - INFO - ['Hz10']
2025-05-13 13:53:10,660 - stpipe.Detector1Pipeline.emicorr - INFO - Running EMI fit with algorithm = 'sequential'.
2025-05-13 13:53:10,661 - stpipe.Detector1Pipeline.emicorr - INFO - Correcting for frequency: 10.039216 Hz (1 out of 1)
2025-05-13 13:53:10,662 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting self-superbias from each group of each integration
2025-05-13 13:53:10,664 - stpipe.Detector1Pipeline.emicorr - INFO - Doing phase calculation per integration
2025-05-13 13:53:10,931 - stpipe.Detector1Pipeline.emicorr - INFO - Calculating the phase amplitude for 500 bins
2025-05-13 13:53:11,830 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to measure phase shift
2025-05-13 13:53:11,868 - stpipe.Detector1Pipeline.emicorr - INFO - Creating phased-matched noise model to subtract from data
2025-05-13 13:53:11,873 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting EMI noise from data
2025-05-13 13:53:11,893 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr done
2025-05-13 13:53:12,022 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:12,038 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits
2025-05-13 13:53:12,060 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:12,070 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:12,089 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:53:12,138 - stpipe.Detector1Pipeline.saturation - INFO - Detected 845 saturated pixels
2025-05-13 13:53:12,141 - stpipe.Detector1Pipeline.saturation - INFO - Detected 61 A/D floor pixels
2025-05-13 13:53:12,145 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:53:12,276 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:12,277 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:53:12,407 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:12,428 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-05-13 13:53:12,559 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:12,585 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-05-13 13:53:12,711 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:12,726 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits
2025-05-13 13:53:12,783 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:12,792 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:12,834 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-05-13 13:53:12,964 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:12,979 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits
2025-05-13 13:53:13,004 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:13,014 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:13,106 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:53:13,231 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:13,248 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits
2025-05-13 13:53:13,298 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-05-13 13:53:13,301 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-05-13 13:53:13,433 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:13,449 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits
2025-05-13 13:53:14,483 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-05-13 13:53:14,484 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2025-05-13 13:53:14,484 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-05-13 13:53:15,231 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:53:15,393 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:15,394 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-05-13 13:53:15,531 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:15,532 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:53:15,669 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:15,677 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:53:15,678 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:53:15,700 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:53:15,708 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:53:15,754 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:53:15,755 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:53:16,683 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-05-13 13:53:16,696 - stpipe.Detector1Pipeline.jump - WARNING - Not enough differences for shower detections
2025-05-13 13:53:16,696 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-05-13 13:53:16,697 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.941723 sec
2025-05-13 13:53:16,706 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 1.028653
2025-05-13 13:53:16,708 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:53:16,835 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:16,836 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:53:16,956 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:16,997 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:53:16,998 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:53:17,023 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:53:17,023 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:53:17,094 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:53:17,100 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-05-13 13:53:17,101 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-05-13 13:53:17,496 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.3941161632537842
2025-05-13 13:53:17,538 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:53:17,668 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:17,694 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:53:17,695 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:53:17,698 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:17,824 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01040001005_03103_00004_mirimage_uncal.fits>,).
2025-05-13 13:53:17,853 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:53:17,853 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:53:17,856 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:17,923 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00004_mirimage_rateints.fits
2025-05-13 13:53:17,924 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:53:17,924 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:17,992 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00004_mirimage_rate.fits
2025-05-13 13:53:17,993 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:53:17,993 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:53:18,065 - stpipe - INFO - PARS-EMICORRSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-emicorrstep_0003.asdf
2025-05-13 13:53:18,079 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-darkcurrentstep_0001.asdf
2025-05-13 13:53:18,088 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-jumpstep_0005.asdf
2025-05-13 13:53:18,099 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-detector1pipeline_0008.asdf
2025-05-13 13:53:18,117 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:53:18,118 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:53:18,119 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:53:18,120 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:53:18,120 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:53:18,121 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:53:18,122 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:53:18,123 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:53:18,124 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:53:18,125 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:53:18,126 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:53:18,126 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:53:18,127 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:53:18,128 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:53:18,129 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:53:18,130 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:53:18,132 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:53:18,133 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:53:18,135 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:53:18,136 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:53:18,259 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('./mir_im_demo_data/Obs001/uncal/jw01040001005_03103_00005_mirimage_uncal.fits',).
2025-05-13 13:53:18,280 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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: False
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: 6.0
four_group_rejection_threshold: 5.0
maximum_cores: half
flag_4_neighbors: True
max_jump_to_flag_neighbors: 1000
min_jump_to_flag_neighbors: 30
after_jump_flag_dn1: 500
after_jump_flag_time1: 15
after_jump_flag_dn2: 1000
after_jump_flag_time2: 3000
expand_large_events: False
min_sat_area: 1
min_jump_area: 0
expand_factor: 0
use_ellipses: False
sat_required_snowball: False
min_sat_radius_extend: 0.0
sat_expand: 0
edge_size: 0
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: True
max_shower_amplitude: 4.0
extend_snr_threshold: 3.0
extend_min_area: 50
extend_inner_radius: 1
extend_outer_radius: 2.6
extend_ellipse_expand_ratio: 1.1
time_masked_after_shower: 30
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: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:53:18,337 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00005_mirimage_uncal.fits' reftypes = ['dark', 'emicorr', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:53:18,340 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits'.
2025-05-13 13:53:18,341 - stpipe.Detector1Pipeline - INFO - Prefetch for EMICORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf'.
2025-05-13 13:53:18,341 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits'.
2025-05-13 13:53:18,342 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits'.
2025-05-13 13:53:18,342 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits'.
2025-05-13 13:53:18,343 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:53:18,344 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits'.
2025-05-13 13:53:18,344 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits'.
2025-05-13 13:53:18,345 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits'.
2025-05-13 13:53:18,345 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits'.
2025-05-13 13:53:18,346 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is 'N/A'.
2025-05-13 13:53:18,346 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:53:18,346 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:53:18,347 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:53:18,574 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:18,582 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:53:18,582 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:53:18,584 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:53:18,711 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:18,727 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds/references/jwst/miri/jwst_miri_mask_0036.fits
2025-05-13 13:53:18,764 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:18,776 - stpipe.Detector1Pipeline.dq_init - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:18,787 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:53:18,918 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:18,951 - stpipe.Detector1Pipeline.emicorr - INFO - Using CRDS reference file: /home/runner/crds/references/jwst/miri/jwst_miri_emicorr_0002.asdf
2025-05-13 13:53:18,970 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'sequential' algorithm is selected and ngroups=6.
2025-05-13 13:53:18,970 - stpipe.Detector1Pipeline.emicorr - WARNING - The 'joint' algorithm is recommended for ngroups < 10.
2025-05-13 13:53:18,971 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to get subarray case.
2025-05-13 13:53:18,971 - stpipe.Detector1Pipeline.emicorr - INFO - With configuration: Subarray=FULL, Read_pattern=FASTR1, Detector=MIRIMAGE
2025-05-13 13:53:18,972 - stpipe.Detector1Pipeline.emicorr - INFO - Will correct data for the following 1 frequencies:
2025-05-13 13:53:18,973 - stpipe.Detector1Pipeline.emicorr - INFO - ['Hz10']
2025-05-13 13:53:18,973 - stpipe.Detector1Pipeline.emicorr - INFO - Running EMI fit with algorithm = 'sequential'.
2025-05-13 13:53:18,974 - stpipe.Detector1Pipeline.emicorr - INFO - Correcting for frequency: 10.039216 Hz (1 out of 1)
2025-05-13 13:53:18,975 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting self-superbias from each group of each integration
2025-05-13 13:53:18,977 - stpipe.Detector1Pipeline.emicorr - INFO - Doing phase calculation per integration
2025-05-13 13:53:19,207 - stpipe.Detector1Pipeline.emicorr - INFO - Calculating the phase amplitude for 500 bins
2025-05-13 13:53:20,151 - stpipe.Detector1Pipeline.emicorr - INFO - Using reference file to measure phase shift
2025-05-13 13:53:20,188 - stpipe.Detector1Pipeline.emicorr - INFO - Creating phased-matched noise model to subtract from data
2025-05-13 13:53:20,193 - stpipe.Detector1Pipeline.emicorr - INFO - Subtracting EMI noise from data
2025-05-13 13:53:20,209 - stpipe.Detector1Pipeline.emicorr - INFO - Step emicorr done
2025-05-13 13:53:20,340 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:20,357 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds/references/jwst/miri/jwst_miri_saturation_0034.fits
2025-05-13 13:53:20,379 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:20,389 - stpipe.Detector1Pipeline.saturation - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:20,409 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:53:20,453 - stpipe.Detector1Pipeline.saturation - INFO - Detected 826 saturated pixels
2025-05-13 13:53:20,456 - stpipe.Detector1Pipeline.saturation - INFO - Detected 59 A/D floor pixels
2025-05-13 13:53:20,460 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:53:20,592 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:20,592 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:53:20,719 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:20,740 - stpipe.Detector1Pipeline.firstframe - INFO - Step firstframe done
2025-05-13 13:53:20,869 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:20,893 - stpipe.Detector1Pipeline.lastframe - INFO - Step lastframe done
2025-05-13 13:53:21,019 - stpipe.Detector1Pipeline.reset - INFO - Step reset running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:21,035 - stpipe.Detector1Pipeline.reset - INFO - Using RESET reference file /home/runner/crds/references/jwst/miri/jwst_miri_reset_0077.fits
2025-05-13 13:53:21,082 - stpipe.Detector1Pipeline.reset - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:21,092 - stpipe.Detector1Pipeline.reset - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:21,135 - stpipe.Detector1Pipeline.reset - INFO - Step reset done
2025-05-13 13:53:21,259 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:21,275 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds/references/jwst/miri/jwst_miri_linearity_0032.fits
2025-05-13 13:53:21,299 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword RESERVED_4 does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:21,309 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword UNRELIABLE_RESET does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:21,394 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:53:21,516 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:21,532 - stpipe.Detector1Pipeline.rscd - INFO - Using RSCD reference file /home/runner/crds/references/jwst/miri/jwst_miri_rscd_0017.fits
2025-05-13 13:53:21,584 - stpipe.Detector1Pipeline.rscd - INFO - Number of groups to skip for integrations 2 and higher: 2
2025-05-13 13:53:21,587 - stpipe.Detector1Pipeline.rscd - INFO - Step rscd done
2025-05-13 13:53:21,722 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:21,739 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds/references/jwst/miri/jwst_miri_dark_0103.fits
2025-05-13 13:53:22,774 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 1.0 e-/sec
2025-05-13 13:53:22,775 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2025-05-13 13:53:22,775 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=2, ngroups=360, nframes=1, groupgap=0
2025-05-13 13:53:23,552 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:53:23,702 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:23,703 - stpipe.Detector1Pipeline.refpix - INFO - Step skipped.
2025-05-13 13:53:23,809 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:23,810 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:53:23,909 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:23,917 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:53:23,917 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:53:23,944 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:53:23,952 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:53:23,996 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:53:23,997 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:53:24,897 - stpipe.Detector1Pipeline.jump - INFO - Flagging Showers
2025-05-13 13:53:24,904 - stpipe.Detector1Pipeline.jump - WARNING - Not enough differences for shower detections
2025-05-13 13:53:24,904 - stpipe.Detector1Pipeline.jump - INFO - Total showers= 0
2025-05-13 13:53:24,905 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.907936 sec
2025-05-13 13:53:24,914 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 0.996835
2025-05-13 13:53:24,916 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:53:25,026 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:25,027 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:53:25,122 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:25,157 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds/references/jwst/miri/jwst_miri_readnoise_0085.fits
2025-05-13 13:53:25,158 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds/references/jwst/miri/jwst_miri_gain_0034.fits
2025-05-13 13:53:25,182 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:53:25,183 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:53:25,252 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:53:25,257 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of leading groups that are flagged as DO_NOT_USE: 1
2025-05-13 13:53:25,258 - stpipe.Detector1Pipeline.ramp_fit - INFO - MIRI dataset has all pixels in the final group flagged as DO_NOT_USE.
2025-05-13 13:53:25,653 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.3934752941131592
2025-05-13 13:53:25,694 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:53:25,797 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:25,823 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:53:25,823 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:53:25,825 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:25,928 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 1024, 1032) from jw01040001005_03103_00005_mirimage_uncal.fits>,).
2025-05-13 13:53:25,956 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2025-05-13 13:53:25,957 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2025-05-13 13:53:25,959 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:26,025 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00005_mirimage_rateints.fits
2025-05-13 13:53:26,026 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:53:26,027 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:26,093 - stpipe.Detector1Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00005_mirimage_rate.fits
2025-05-13 13:53:26,094 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:53:26,094 - stpipe - INFO - Results used jwst version: 1.18.0
Calibrating Background Files#
Look for input background files and run calwebb_detector1 pipeline using the call method.
# Run Detector1 stage of pipeline on any background files
if dodet1bg:
for uncal in uncal_bgfiles:
rate_result = Detector1Pipeline.call(uncal, output_dir=det1_bgdir, steps=det1dict, save_results=True,)
else:
print('Skipping Detector1 BG processing')
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime for Detector1: {time1 - time0:0.0f} seconds")
Runtime for Detector1: 293 seconds
Exploring the data#
Identify *_rate.fits files and verify which pipeline steps were run and
which calibration reference files were applied.
The header contains information about which calibration steps were
completed and skipped and which reference files were used to process the
data.
if dodet1:
# find rate files
rate_files = sorted(glob.glob(os.path.join(det1_dir, '*_rate.fits')))
# Read in file as datamodel
rate_f = datamodels.open(rate_files[0])
# Check which steps were run
rate_f.meta.cal_step.instance
# Check which reference files were used to calibrate the dataset:
rate_f.meta.ref_file.instance
{'charge_migration': 'SKIPPED',
'clean_flicker_noise': 'SKIPPED',
'dark_sub': 'COMPLETE',
'dq_init': 'COMPLETE',
'emicorr': 'COMPLETE',
'firstframe': 'COMPLETE',
'gain_scale': 'SKIPPED',
'group_scale': 'SKIPPED',
'ipc': 'SKIPPED',
'jump': 'COMPLETE',
'lastframe': 'COMPLETE',
'linearity': 'COMPLETE',
'ramp_fit': 'COMPLETE',
'refpix': 'SKIPPED',
'reset': 'COMPLETE',
'rscd': 'COMPLETE',
'saturation': 'COMPLETE'}
{'crds': {'context_used': 'jwst_1364.pmap', 'sw_version': '12.1.5'},
'dark': {'name': 'crds://jwst_miri_dark_0103.fits'},
'emicorr': {'name': 'crds://jwst_miri_emicorr_0002.asdf'},
'gain': {'name': 'crds://jwst_miri_gain_0034.fits'},
'linearity': {'name': 'crds://jwst_miri_linearity_0032.fits'},
'mask': {'name': 'crds://jwst_miri_mask_0036.fits'},
'readnoise': {'name': 'crds://jwst_miri_readnoise_0085.fits'},
'reset': {'name': 'crds://jwst_miri_reset_0077.fits'},
'rscd': {'name': 'crds://jwst_miri_rscd_0017.fits'},
'saturation': {'name': 'crds://jwst_miri_saturation_0034.fits'}}
6. Image2 Pipeline#
In the Image2 stage of the pipeline,
calibrated unrectified data products are created (*_cal.fits or
*_calints.fits files, depending on whether the input files are
*_rate.fits or *_rateints.fits).
In this pipeline processing stage, the background subtraction step is performed if the data have a dedicated background defined, the world coordinate system (WCS) is assigned, the data are flat fielded, and a photometric calibration is applied to convert from units of countrate (ADU/s) to surface brightness (MJy/sr).
The resampling
step is performed, to create resampled images of each dither position, but this is
only a quick-look product. The resampling step occurs during the Image3 stage by
default. While the resampling step is done in the Image2 stage, the data quality
from the Image3 stage will be better since the bad pixels, which adversely affect
both the centroids and photometry in individual images, will be mostly
removed.
time_image2 = time.perf_counter()
# Set up a dictionary to define how the Image2 pipeline should be configured.
# Boilerplate dictionary setup
image2dict = {}
image2dict['bkg_subtract'] = {}
image2dict['assign_wcs'], image2dict['flat_field'] = {}, {}
image2dict['photom'], image2dict['resample'] = {}, {}
# Overrides for whether or not certain steps should be skipped (example)
#image2dict['resample']['skip'] = False
# Change the nsigma used for clipping the input background data
image2dict['bkg_subtract']['sigma'] = 2
# Overrides for various reference files
# Files should be in the base local directory or provide full path
#image2dict['assign_wcs']['override_distortion'] = 'myfile.asdf' # Spatial distortion (ASDF file)
#image2dict['assign_wcs']['override_filteroffset'] = 'myfile.asdf' # Imager filter offsets (ASDF file)
#image2dict['assign_wcs']['override_specwcs'] = 'myfile.asdf' # Spectral distortion (ASDF file)
#image2dict['assign_wcs']['override_wavelengthrange'] = 'myfile.asdf' # Wavelength channel mapping (ASDF file)
#image2dict['flat_field']['override_flat'] = 'myfile.fits' # Pixel flatfield
#image2dict['photom']['override_photom'] = 'myfile.fits' # Photometric calibration array
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, 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
# Filter configuration for this sci file
with fits.open(onescifile) as hdu:
hdu.verify()
hdr = hdu[0].header
this_filter = hdr['FILTER']
# If backgrounds were provided, find which are appropriate to this
# filter and add to association
for file in bgfiles:
with fits.open(file) as hdu:
hdu.verify()
if (hdu[0].header['FILTER'] == this_filter):
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
# Find all Science rate.fits files
sstring = os.path.join(det1_dir, 'jw*rate.fits') # Use files from the detector1 output folder
rate_files = sorted(glob.glob(sstring))
for ii in range(0, len(rate_files)):
rate_files[ii] = os.path.abspath(rate_files[ii])
rate_files = np.array(rate_files)
# Background Files
sstring = os.path.join(det1_bgdir, 'jw*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)
print(f"Found {str(len(rate_files))} science files")
print(f"Found {str(len(bgfiles))} background files")
Found 5 science files
Found 0 background files
# Run Image2 stage of pipeline, specifying the output directory to save *_cal.fits files
# and save_results flag set to True so the rate files are saved
if doimage2:
for rate in rate_files:
asnfile = os.path.join(sci_dir, 'l2asn.json')
writel2asn(rate, bgfiles, asnfile, 'Level2')
cal_result = Image2Pipeline.call(asnfile, output_dir=image2_dir, steps=image2dict, save_results=True)
else:
print("Skipping Image2 processing.")
2025-05-13 13:53:26,199 - 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)
2025-05-13 13:53:26,310 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplestep_0001.asdf 1.0 K bytes (1 / 1 files) (0 / 1.0 K bytes)
2025-05-13 13:53:26,353 - stpipe - INFO - PARS-RESAMPLESTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplestep_0001.asdf
2025-05-13 13:53:26,362 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-image2pipeline_0004.asdf 1.2 K bytes (1 / 1 files) (0 / 1.2 K bytes)
2025-05-13 13:53:26,405 - stpipe - INFO - PARS-IMAGE2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-image2pipeline_0004.asdf
2025-05-13 13:53:26,417 - stpipe.Image2Pipeline - INFO - Image2Pipeline instance created.
2025-05-13 13:53:26,418 - stpipe.Image2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:53:26,419 - stpipe.Image2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:53:26,420 - stpipe.Image2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:53:26,422 - stpipe.Image2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:53:26,424 - stpipe.Image2Pipeline.resample - INFO - ResampleStep instance created.
2025-05-13 13:53:26,539 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline running with args ('./mir_im_demo_data/Obs001/l2asn.json',).
2025-05-13 13:53:26,547 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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
steps:
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: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 2
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
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
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
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
resample:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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
crpix: None
crval: None
rotation: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
2025-05-13 13:53:26,556 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:26,594 - stpipe.Image2Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00001_mirimage_rate.fits' reftypes = ['area', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'ifufore', 'ifupost', 'ifuslicer', 'msa', 'ote', 'photom', 'regions', 'sflat', 'specwcs', 'wavelengthrange', 'wfssbkg']
2025-05-13 13:53:26,598 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits 4.2 M bytes (1 / 5 files) (0 / 25.4 M bytes)
2025-05-13 13:53:26,745 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf 12.4 K bytes (2 / 5 files) (4.2 M / 25.4 M bytes)
2025-05-13 13:53:26,790 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf 2.5 K bytes (3 / 5 files) (4.2 M / 25.4 M bytes)
2025-05-13 13:53:26,849 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits 21.2 M bytes (4 / 5 files) (4.3 M / 25.4 M bytes)
2025-05-13 13:53:28,569 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits 14.4 K bytes (5 / 5 files) (25.4 M / 25.4 M bytes)
2025-05-13 13:53:28,613 - stpipe.Image2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits'.
2025-05-13 13:53:28,614 - stpipe.Image2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-05-13 13:53:28,614 - stpipe.Image2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-05-13 13:53:28,615 - stpipe.Image2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-05-13 13:53:28,615 - stpipe.Image2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-05-13 13:53:28,616 - stpipe.Image2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf'.
2025-05-13 13:53:28,616 - stpipe.Image2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-05-13 13:53:28,616 - stpipe.Image2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf'.
2025-05-13 13:53:28,617 - stpipe.Image2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits'.
2025-05-13 13:53:28,618 - stpipe.Image2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-05-13 13:53:28,619 - stpipe.Image2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-05-13 13:53:28,619 - stpipe.Image2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:53:28,620 - stpipe.Image2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:53:28,620 - stpipe.Image2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:53:28,621 - stpipe.Image2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-05-13 13:53:28,621 - stpipe.Image2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-05-13 13:53:28,622 - stpipe.Image2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits'.
2025-05-13 13:53:28,622 - stpipe.Image2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:53:28,622 - stpipe.Image2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-05-13 13:53:28,623 - stpipe.Image2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:53:28,624 - stpipe.Image2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is 'N/A'.
2025-05-13 13:53:28,624 - stpipe.Image2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:53:28,625 - stpipe.Image2Pipeline - INFO - Starting calwebb_image2 ...
2025-05-13 13:53:28,631 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:28,632 - stpipe.Image2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00001_mirimage
2025-05-13 13:53:28,632 - stpipe.Image2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00001_mirimage_rate.fits ...
2025-05-13 13:53:28,776 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00001_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:28,956 - stpipe.Image2Pipeline.assign_wcs - INFO - Created a MIRI mir_image pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf', 'filteroffset': '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf', 'specwcs': None, 'regions': None, 'wavelengthrange': None, 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-05-13 13:53:29,005 - stpipe.Image2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 80.522590500 -69.442259683 80.541421228 -69.472834075 80.628988786 -69.466212483 80.610814720 -69.435536112
2025-05-13 13:53:29,006 - stpipe.Image2Pipeline.assign_wcs - INFO - assign_wcs updated S_REGION to POLYGON ICRS 80.522590500 -69.442259683 80.541421228 -69.472834075 80.628988786 -69.466212483 80.610814720 -69.435536112
2025-05-13 13:53:29,006 - stpipe.Image2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 13:53:29,043 - stpipe.Image2Pipeline.assign_wcs - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:29,055 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 13:53:29,168 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00001_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:29,235 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:29,236 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:29,236 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:29,238 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword DIFF_PATTERN does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:29,240 - stpipe.Image2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits
2025-05-13 13:53:29,240 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-05-13 13:53:29,241 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-05-13 13:53:29,241 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-05-13 13:53:29,305 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 13:53:29,415 - stpipe.Image2Pipeline.photom - INFO - Step photom running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00001_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:29,443 - stpipe.Image2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits
2025-05-13 13:53:29,443 - stpipe.Image2Pipeline.photom - INFO - Using area reference file: /home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits
2025-05-13 13:53:29,466 - stpipe.Image2Pipeline.photom - INFO - Using instrument: MIRI
2025-05-13 13:53:29,467 - stpipe.Image2Pipeline.photom - INFO - detector: MIRIMAGE
2025-05-13 13:53:29,467 - stpipe.Image2Pipeline.photom - INFO - exp_type: MIR_IMAGE
2025-05-13 13:53:29,468 - stpipe.Image2Pipeline.photom - INFO - filter: F770W
2025-05-13 13:53:29,497 - stpipe.Image2Pipeline.photom - INFO - Pixel area map copied to output.
2025-05-13 13:53:29,498 - stpipe.Image2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from AREA reference file.
2025-05-13 13:53:29,499 - stpipe.Image2Pipeline.photom - INFO - subarray: FULL
2025-05-13 13:53:29,500 - stpipe.Image2Pipeline.photom - INFO - Applying the time-dependent correction to the PHOTOM value.
2025-05-13 13:53:29,504 - stpipe.Image2Pipeline.photom - INFO - PHOTMJSR value: 0.257756
2025-05-13 13:53:29,522 - stpipe.Image2Pipeline.photom - INFO - Step photom done
2025-05-13 13:53:29,636 - stpipe.Image2Pipeline.resample - INFO - Step resample running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00001_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:29,668 - stpipe.Image2Pipeline.resample - INFO - Pixel scale ratio (pscale_out/pscale_in): 1.0
2025-05-13 13:53:29,668 - stpipe.Image2Pipeline.resample - INFO - Computed output pixel scale: 0.1109170593250524 arcsec.
2025-05-13 13:53:29,676 - stpipe.Image2Pipeline.resample - INFO - Output pixel scale: 0.1109170593250524 arcsec.
2025-05-13 13:53:29,677 - stpipe.Image2Pipeline.resample - INFO - Driz parameter kernel: square
2025-05-13 13:53:29,677 - stpipe.Image2Pipeline.resample - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:53:29,678 - stpipe.Image2Pipeline.resample - INFO - Driz parameter fillval: NAN
2025-05-13 13:53:29,678 - stpipe.Image2Pipeline.resample - INFO - Driz parameter weight_type: exptime
2025-05-13 13:53:29,681 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:30,197 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:30,442 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:30,656 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:30,870 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:31,149 - stpipe.Image2Pipeline.resample - INFO - Update S_REGION to POLYGON ICRS 80.522470429 -69.442135349 80.541076560 -69.472844668 80.629483847 -69.466224545 80.610757145 -69.435524685
2025-05-13 13:53:31,239 - stpipe.Image2Pipeline.resample - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00001_mirimage_i2d.fits
2025-05-13 13:53:31,240 - stpipe.Image2Pipeline.resample - INFO - Step resample done
2025-05-13 13:53:31,241 - stpipe.Image2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00001_mirimage
2025-05-13 13:53:31,242 - stpipe.Image2Pipeline - INFO - ... ending calwebb_image2
2025-05-13 13:53:31,242 - stpipe.Image2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:31,364 - stpipe.Image2Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00001_mirimage_cal.fits
2025-05-13 13:53:31,365 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline done
2025-05-13 13:53:31,365 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:53:31,375 - 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)
2025-05-13 13:53:31,426 - stpipe - INFO - PARS-RESAMPLESTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplestep_0001.asdf
2025-05-13 13:53:31,435 - stpipe - INFO - PARS-IMAGE2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-image2pipeline_0004.asdf
2025-05-13 13:53:31,445 - stpipe.Image2Pipeline - INFO - Image2Pipeline instance created.
2025-05-13 13:53:31,446 - stpipe.Image2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:53:31,447 - stpipe.Image2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:53:31,448 - stpipe.Image2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:53:31,449 - stpipe.Image2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:53:31,450 - stpipe.Image2Pipeline.resample - INFO - ResampleStep instance created.
2025-05-13 13:53:31,579 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline running with args ('./mir_im_demo_data/Obs001/l2asn.json',).
2025-05-13 13:53:31,587 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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
steps:
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: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 2
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
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
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
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
resample:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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
crpix: None
crval: None
rotation: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
2025-05-13 13:53:31,596 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:31,633 - stpipe.Image2Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00002_mirimage_rate.fits' reftypes = ['area', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'ifufore', 'ifupost', 'ifuslicer', 'msa', 'ote', 'photom', 'regions', 'sflat', 'specwcs', 'wavelengthrange', 'wfssbkg']
2025-05-13 13:53:31,637 - stpipe.Image2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits'.
2025-05-13 13:53:31,638 - stpipe.Image2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-05-13 13:53:31,638 - stpipe.Image2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-05-13 13:53:31,639 - stpipe.Image2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-05-13 13:53:31,639 - stpipe.Image2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-05-13 13:53:31,640 - stpipe.Image2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf'.
2025-05-13 13:53:31,640 - stpipe.Image2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-05-13 13:53:31,641 - stpipe.Image2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf'.
2025-05-13 13:53:31,641 - stpipe.Image2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits'.
2025-05-13 13:53:31,642 - stpipe.Image2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-05-13 13:53:31,642 - stpipe.Image2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-05-13 13:53:31,643 - stpipe.Image2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:53:31,643 - stpipe.Image2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:53:31,644 - stpipe.Image2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:53:31,644 - stpipe.Image2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-05-13 13:53:31,645 - stpipe.Image2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-05-13 13:53:31,645 - stpipe.Image2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits'.
2025-05-13 13:53:31,646 - stpipe.Image2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:53:31,646 - stpipe.Image2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-05-13 13:53:31,647 - stpipe.Image2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:53:31,647 - stpipe.Image2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is 'N/A'.
2025-05-13 13:53:31,647 - stpipe.Image2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:53:31,648 - stpipe.Image2Pipeline - INFO - Starting calwebb_image2 ...
2025-05-13 13:53:31,655 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:31,655 - stpipe.Image2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00002_mirimage
2025-05-13 13:53:31,656 - stpipe.Image2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00002_mirimage_rate.fits ...
2025-05-13 13:53:31,814 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00002_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:31,982 - stpipe.Image2Pipeline.assign_wcs - INFO - Created a MIRI mir_image pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf', 'filteroffset': '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf', 'specwcs': None, 'regions': None, 'wavelengthrange': None, 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-05-13 13:53:32,027 - stpipe.Image2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 80.519758777 -69.441179342 80.538584462 -69.471754044 80.626148504 -69.465133898 80.607979465 -69.434457227
2025-05-13 13:53:32,028 - stpipe.Image2Pipeline.assign_wcs - INFO - assign_wcs updated S_REGION to POLYGON ICRS 80.519758777 -69.441179342 80.538584462 -69.471754044 80.626148504 -69.465133898 80.607979465 -69.434457227
2025-05-13 13:53:32,029 - stpipe.Image2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 13:53:32,060 - stpipe.Image2Pipeline.assign_wcs - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:32,071 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 13:53:32,190 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00002_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:32,252 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:32,253 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:32,253 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:32,255 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword DIFF_PATTERN does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:32,257 - stpipe.Image2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits
2025-05-13 13:53:32,257 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-05-13 13:53:32,258 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-05-13 13:53:32,258 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-05-13 13:53:32,328 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 13:53:32,462 - stpipe.Image2Pipeline.photom - INFO - Step photom running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00002_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:32,485 - stpipe.Image2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits
2025-05-13 13:53:32,485 - stpipe.Image2Pipeline.photom - INFO - Using area reference file: /home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits
2025-05-13 13:53:32,510 - stpipe.Image2Pipeline.photom - INFO - Using instrument: MIRI
2025-05-13 13:53:32,511 - stpipe.Image2Pipeline.photom - INFO - detector: MIRIMAGE
2025-05-13 13:53:32,511 - stpipe.Image2Pipeline.photom - INFO - exp_type: MIR_IMAGE
2025-05-13 13:53:32,511 - stpipe.Image2Pipeline.photom - INFO - filter: F770W
2025-05-13 13:53:32,537 - stpipe.Image2Pipeline.photom - INFO - Pixel area map copied to output.
2025-05-13 13:53:32,538 - stpipe.Image2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from AREA reference file.
2025-05-13 13:53:32,539 - stpipe.Image2Pipeline.photom - INFO - subarray: FULL
2025-05-13 13:53:32,540 - stpipe.Image2Pipeline.photom - INFO - Applying the time-dependent correction to the PHOTOM value.
2025-05-13 13:53:32,544 - stpipe.Image2Pipeline.photom - INFO - PHOTMJSR value: 0.257756
2025-05-13 13:53:32,562 - stpipe.Image2Pipeline.photom - INFO - Step photom done
2025-05-13 13:53:32,707 - stpipe.Image2Pipeline.resample - INFO - Step resample running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00002_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:32,740 - stpipe.Image2Pipeline.resample - INFO - Pixel scale ratio (pscale_out/pscale_in): 1.0
2025-05-13 13:53:32,741 - stpipe.Image2Pipeline.resample - INFO - Computed output pixel scale: 0.11091705945609492 arcsec.
2025-05-13 13:53:32,749 - stpipe.Image2Pipeline.resample - INFO - Output pixel scale: 0.11091705945609492 arcsec.
2025-05-13 13:53:32,749 - stpipe.Image2Pipeline.resample - INFO - Driz parameter kernel: square
2025-05-13 13:53:32,749 - stpipe.Image2Pipeline.resample - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:53:32,750 - stpipe.Image2Pipeline.resample - INFO - Driz parameter fillval: NAN
2025-05-13 13:53:32,750 - stpipe.Image2Pipeline.resample - INFO - Driz parameter weight_type: exptime
2025-05-13 13:53:32,754 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:33,265 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:33,510 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:33,720 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:33,930 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:34,209 - stpipe.Image2Pipeline.resample - INFO - Update S_REGION to POLYGON ICRS 80.519638728 -69.441055005 80.538239808 -69.471764631 80.626643538 -69.465145969 80.607921894 -69.434445799
2025-05-13 13:53:34,300 - stpipe.Image2Pipeline.resample - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00002_mirimage_i2d.fits
2025-05-13 13:53:34,301 - stpipe.Image2Pipeline.resample - INFO - Step resample done
2025-05-13 13:53:34,302 - stpipe.Image2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00002_mirimage
2025-05-13 13:53:34,302 - stpipe.Image2Pipeline - INFO - ... ending calwebb_image2
2025-05-13 13:53:34,303 - stpipe.Image2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:34,428 - stpipe.Image2Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00002_mirimage_cal.fits
2025-05-13 13:53:34,429 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline done
2025-05-13 13:53:34,430 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:53:34,440 - 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)
2025-05-13 13:53:34,495 - stpipe - INFO - PARS-RESAMPLESTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplestep_0001.asdf
2025-05-13 13:53:34,505 - stpipe - INFO - PARS-IMAGE2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-image2pipeline_0004.asdf
2025-05-13 13:53:34,516 - stpipe.Image2Pipeline - INFO - Image2Pipeline instance created.
2025-05-13 13:53:34,517 - stpipe.Image2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:53:34,518 - stpipe.Image2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:53:34,520 - stpipe.Image2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:53:34,520 - stpipe.Image2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:53:34,522 - stpipe.Image2Pipeline.resample - INFO - ResampleStep instance created.
2025-05-13 13:53:34,678 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline running with args ('./mir_im_demo_data/Obs001/l2asn.json',).
2025-05-13 13:53:34,685 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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
steps:
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: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 2
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
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
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
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
resample:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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
crpix: None
crval: None
rotation: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
2025-05-13 13:53:34,695 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:34,733 - stpipe.Image2Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00003_mirimage_rate.fits' reftypes = ['area', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'ifufore', 'ifupost', 'ifuslicer', 'msa', 'ote', 'photom', 'regions', 'sflat', 'specwcs', 'wavelengthrange', 'wfssbkg']
2025-05-13 13:53:34,738 - stpipe.Image2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits'.
2025-05-13 13:53:34,738 - stpipe.Image2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-05-13 13:53:34,739 - stpipe.Image2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-05-13 13:53:34,740 - stpipe.Image2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-05-13 13:53:34,740 - stpipe.Image2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-05-13 13:53:34,741 - stpipe.Image2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf'.
2025-05-13 13:53:34,741 - stpipe.Image2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-05-13 13:53:34,742 - stpipe.Image2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf'.
2025-05-13 13:53:34,742 - stpipe.Image2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits'.
2025-05-13 13:53:34,743 - stpipe.Image2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-05-13 13:53:34,743 - stpipe.Image2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-05-13 13:53:34,743 - stpipe.Image2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:53:34,744 - stpipe.Image2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:53:34,744 - stpipe.Image2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:53:34,745 - stpipe.Image2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-05-13 13:53:34,746 - stpipe.Image2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-05-13 13:53:34,746 - stpipe.Image2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits'.
2025-05-13 13:53:34,747 - stpipe.Image2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:53:34,747 - stpipe.Image2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-05-13 13:53:34,748 - stpipe.Image2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:53:34,748 - stpipe.Image2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is 'N/A'.
2025-05-13 13:53:34,749 - stpipe.Image2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:53:34,749 - stpipe.Image2Pipeline - INFO - Starting calwebb_image2 ...
2025-05-13 13:53:34,756 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:34,757 - stpipe.Image2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00003_mirimage
2025-05-13 13:53:34,757 - stpipe.Image2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00003_mirimage_rate.fits ...
2025-05-13 13:53:34,943 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00003_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:35,115 - stpipe.Image2Pipeline.assign_wcs - INFO - Created a MIRI mir_image pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf', 'filteroffset': '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf', 'specwcs': None, 'regions': None, 'wavelengthrange': None, 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-05-13 13:53:35,166 - stpipe.Image2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 80.517110392 -69.438899816 80.535930509 -69.469474789 80.623486030 -69.462855905 80.605322513 -69.432178972
2025-05-13 13:53:35,167 - stpipe.Image2Pipeline.assign_wcs - INFO - assign_wcs updated S_REGION to POLYGON ICRS 80.517110392 -69.438899816 80.535930509 -69.469474789 80.623486030 -69.462855905 80.605322513 -69.432178972
2025-05-13 13:53:35,168 - stpipe.Image2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 13:53:35,198 - stpipe.Image2Pipeline.assign_wcs - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:35,210 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 13:53:35,348 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00003_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:35,418 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:35,418 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:35,419 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:35,421 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword DIFF_PATTERN does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:35,423 - stpipe.Image2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits
2025-05-13 13:53:35,423 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-05-13 13:53:35,424 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-05-13 13:53:35,425 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-05-13 13:53:35,494 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 13:53:35,629 - stpipe.Image2Pipeline.photom - INFO - Step photom running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00003_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:35,651 - stpipe.Image2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits
2025-05-13 13:53:35,651 - stpipe.Image2Pipeline.photom - INFO - Using area reference file: /home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits
2025-05-13 13:53:35,675 - stpipe.Image2Pipeline.photom - INFO - Using instrument: MIRI
2025-05-13 13:53:35,676 - stpipe.Image2Pipeline.photom - INFO - detector: MIRIMAGE
2025-05-13 13:53:35,677 - stpipe.Image2Pipeline.photom - INFO - exp_type: MIR_IMAGE
2025-05-13 13:53:35,677 - stpipe.Image2Pipeline.photom - INFO - filter: F770W
2025-05-13 13:53:35,703 - stpipe.Image2Pipeline.photom - INFO - Pixel area map copied to output.
2025-05-13 13:53:35,703 - stpipe.Image2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from AREA reference file.
2025-05-13 13:53:35,704 - stpipe.Image2Pipeline.photom - INFO - subarray: FULL
2025-05-13 13:53:35,705 - stpipe.Image2Pipeline.photom - INFO - Applying the time-dependent correction to the PHOTOM value.
2025-05-13 13:53:35,710 - stpipe.Image2Pipeline.photom - INFO - PHOTMJSR value: 0.257756
2025-05-13 13:53:35,728 - stpipe.Image2Pipeline.photom - INFO - Step photom done
2025-05-13 13:53:35,871 - stpipe.Image2Pipeline.resample - INFO - Step resample running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00003_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:35,903 - stpipe.Image2Pipeline.resample - INFO - Pixel scale ratio (pscale_out/pscale_in): 1.0
2025-05-13 13:53:35,904 - stpipe.Image2Pipeline.resample - INFO - Computed output pixel scale: 0.11091705946185215 arcsec.
2025-05-13 13:53:35,911 - stpipe.Image2Pipeline.resample - INFO - Output pixel scale: 0.11091705946185215 arcsec.
2025-05-13 13:53:35,911 - stpipe.Image2Pipeline.resample - INFO - Driz parameter kernel: square
2025-05-13 13:53:35,912 - stpipe.Image2Pipeline.resample - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:53:35,912 - stpipe.Image2Pipeline.resample - INFO - Driz parameter fillval: NAN
2025-05-13 13:53:35,912 - stpipe.Image2Pipeline.resample - INFO - Driz parameter weight_type: exptime
2025-05-13 13:53:35,916 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:36,425 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:36,669 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:36,878 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:37,088 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:37,366 - stpipe.Image2Pipeline.resample - INFO - Update S_REGION to POLYGON ICRS 80.516990370 -69.438775477 80.535585888 -69.469485370 80.623981006 -69.462867984 80.605264948 -69.432167544
2025-05-13 13:53:37,456 - stpipe.Image2Pipeline.resample - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00003_mirimage_i2d.fits
2025-05-13 13:53:37,457 - stpipe.Image2Pipeline.resample - INFO - Step resample done
2025-05-13 13:53:37,458 - stpipe.Image2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00003_mirimage
2025-05-13 13:53:37,459 - stpipe.Image2Pipeline - INFO - ... ending calwebb_image2
2025-05-13 13:53:37,459 - stpipe.Image2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:37,582 - stpipe.Image2Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00003_mirimage_cal.fits
2025-05-13 13:53:37,583 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline done
2025-05-13 13:53:37,583 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:53:37,593 - 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)
2025-05-13 13:53:37,644 - stpipe - INFO - PARS-RESAMPLESTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplestep_0001.asdf
2025-05-13 13:53:37,652 - stpipe - INFO - PARS-IMAGE2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-image2pipeline_0004.asdf
2025-05-13 13:53:37,663 - stpipe.Image2Pipeline - INFO - Image2Pipeline instance created.
2025-05-13 13:53:37,664 - stpipe.Image2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:53:37,665 - stpipe.Image2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:53:37,666 - stpipe.Image2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:53:37,667 - stpipe.Image2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:53:37,669 - stpipe.Image2Pipeline.resample - INFO - ResampleStep instance created.
2025-05-13 13:53:37,812 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline running with args ('./mir_im_demo_data/Obs001/l2asn.json',).
2025-05-13 13:53:37,819 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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
steps:
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: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 2
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
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
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
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
resample:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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
crpix: None
crval: None
rotation: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
2025-05-13 13:53:37,829 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:37,866 - stpipe.Image2Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00004_mirimage_rate.fits' reftypes = ['area', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'ifufore', 'ifupost', 'ifuslicer', 'msa', 'ote', 'photom', 'regions', 'sflat', 'specwcs', 'wavelengthrange', 'wfssbkg']
2025-05-13 13:53:37,870 - stpipe.Image2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits'.
2025-05-13 13:53:37,870 - stpipe.Image2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-05-13 13:53:37,871 - stpipe.Image2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-05-13 13:53:37,871 - stpipe.Image2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-05-13 13:53:37,872 - stpipe.Image2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-05-13 13:53:37,873 - stpipe.Image2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf'.
2025-05-13 13:53:37,873 - stpipe.Image2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-05-13 13:53:37,874 - stpipe.Image2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf'.
2025-05-13 13:53:37,874 - stpipe.Image2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits'.
2025-05-13 13:53:37,875 - stpipe.Image2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-05-13 13:53:37,875 - stpipe.Image2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-05-13 13:53:37,876 - stpipe.Image2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:53:37,876 - stpipe.Image2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:53:37,877 - stpipe.Image2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:53:37,877 - stpipe.Image2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-05-13 13:53:37,877 - stpipe.Image2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-05-13 13:53:37,878 - stpipe.Image2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits'.
2025-05-13 13:53:37,878 - stpipe.Image2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:53:37,879 - stpipe.Image2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-05-13 13:53:37,879 - stpipe.Image2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:53:37,880 - stpipe.Image2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is 'N/A'.
2025-05-13 13:53:37,880 - stpipe.Image2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:53:37,881 - stpipe.Image2Pipeline - INFO - Starting calwebb_image2 ...
2025-05-13 13:53:37,888 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:37,888 - stpipe.Image2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00004_mirimage
2025-05-13 13:53:37,889 - stpipe.Image2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00004_mirimage_rate.fits ...
2025-05-13 13:53:38,069 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00004_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:38,237 - stpipe.Image2Pipeline.assign_wcs - INFO - Created a MIRI mir_image pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf', 'filteroffset': '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf', 'specwcs': None, 'regions': None, 'wavelengthrange': None, 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-05-13 13:53:38,282 - stpipe.Image2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 80.513336007 -69.439821549 80.532151500 -69.470396934 80.619711963 -69.463779964 80.601553105 -69.433102634
2025-05-13 13:53:38,283 - stpipe.Image2Pipeline.assign_wcs - INFO - assign_wcs updated S_REGION to POLYGON ICRS 80.513336007 -69.439821549 80.532151500 -69.470396934 80.619711963 -69.463779964 80.601553105 -69.433102634
2025-05-13 13:53:38,284 - stpipe.Image2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 13:53:38,315 - stpipe.Image2Pipeline.assign_wcs - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:38,327 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 13:53:38,457 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00004_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:38,521 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:38,521 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:38,522 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:38,524 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword DIFF_PATTERN does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:38,525 - stpipe.Image2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits
2025-05-13 13:53:38,526 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-05-13 13:53:38,526 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-05-13 13:53:38,526 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-05-13 13:53:38,588 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 13:53:38,714 - stpipe.Image2Pipeline.photom - INFO - Step photom running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00004_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:38,736 - stpipe.Image2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits
2025-05-13 13:53:38,736 - stpipe.Image2Pipeline.photom - INFO - Using area reference file: /home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits
2025-05-13 13:53:38,761 - stpipe.Image2Pipeline.photom - INFO - Using instrument: MIRI
2025-05-13 13:53:38,761 - stpipe.Image2Pipeline.photom - INFO - detector: MIRIMAGE
2025-05-13 13:53:38,762 - stpipe.Image2Pipeline.photom - INFO - exp_type: MIR_IMAGE
2025-05-13 13:53:38,762 - stpipe.Image2Pipeline.photom - INFO - filter: F770W
2025-05-13 13:53:38,787 - stpipe.Image2Pipeline.photom - INFO - Pixel area map copied to output.
2025-05-13 13:53:38,788 - stpipe.Image2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from AREA reference file.
2025-05-13 13:53:38,789 - stpipe.Image2Pipeline.photom - INFO - subarray: FULL
2025-05-13 13:53:38,790 - stpipe.Image2Pipeline.photom - INFO - Applying the time-dependent correction to the PHOTOM value.
2025-05-13 13:53:38,794 - stpipe.Image2Pipeline.photom - INFO - PHOTMJSR value: 0.257756
2025-05-13 13:53:38,812 - stpipe.Image2Pipeline.photom - INFO - Step photom done
2025-05-13 13:53:38,936 - stpipe.Image2Pipeline.resample - INFO - Step resample running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00004_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:38,969 - stpipe.Image2Pipeline.resample - INFO - Pixel scale ratio (pscale_out/pscale_in): 1.0
2025-05-13 13:53:38,969 - stpipe.Image2Pipeline.resample - INFO - Computed output pixel scale: 0.11091705976530741 arcsec.
2025-05-13 13:53:38,976 - stpipe.Image2Pipeline.resample - INFO - Output pixel scale: 0.11091705976530741 arcsec.
2025-05-13 13:53:38,977 - stpipe.Image2Pipeline.resample - INFO - Driz parameter kernel: square
2025-05-13 13:53:38,977 - stpipe.Image2Pipeline.resample - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:53:38,977 - stpipe.Image2Pipeline.resample - INFO - Driz parameter fillval: NAN
2025-05-13 13:53:38,978 - stpipe.Image2Pipeline.resample - INFO - Driz parameter weight_type: exptime
2025-05-13 13:53:38,981 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:39,477 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:39,721 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:39,931 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:40,139 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:40,417 - stpipe.Image2Pipeline.resample - INFO - Update S_REGION to POLYGON ICRS 80.513216002 -69.439697207 80.531806864 -69.470407508 80.620206961 -69.463792053 80.601495541 -69.433091204
2025-05-13 13:53:40,507 - stpipe.Image2Pipeline.resample - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00004_mirimage_i2d.fits
2025-05-13 13:53:40,508 - stpipe.Image2Pipeline.resample - INFO - Step resample done
2025-05-13 13:53:40,509 - stpipe.Image2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00004_mirimage
2025-05-13 13:53:40,510 - stpipe.Image2Pipeline - INFO - ... ending calwebb_image2
2025-05-13 13:53:40,510 - stpipe.Image2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:40,633 - stpipe.Image2Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00004_mirimage_cal.fits
2025-05-13 13:53:40,633 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline done
2025-05-13 13:53:40,634 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:53:40,644 - 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)
2025-05-13 13:53:40,694 - stpipe - INFO - PARS-RESAMPLESTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplestep_0001.asdf
2025-05-13 13:53:40,702 - stpipe - INFO - PARS-IMAGE2PIPELINE parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-image2pipeline_0004.asdf
2025-05-13 13:53:40,712 - stpipe.Image2Pipeline - INFO - Image2Pipeline instance created.
2025-05-13 13:53:40,713 - stpipe.Image2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:53:40,714 - stpipe.Image2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:53:40,715 - stpipe.Image2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:53:40,716 - stpipe.Image2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:53:40,717 - stpipe.Image2Pipeline.resample - INFO - ResampleStep instance created.
2025-05-13 13:53:40,836 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline running with args ('./mir_im_demo_data/Obs001/l2asn.json',).
2025-05-13 13:53:40,844 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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
steps:
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: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 2
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
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
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
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
resample:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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
crpix: None
crval: None
rotation: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
2025-05-13 13:53:40,853 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:40,889 - stpipe.Image2Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00005_mirimage_rate.fits' reftypes = ['area', 'camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'ifufore', 'ifupost', 'ifuslicer', 'msa', 'ote', 'photom', 'regions', 'sflat', 'specwcs', 'wavelengthrange', 'wfssbkg']
2025-05-13 13:53:40,893 - stpipe.Image2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits'.
2025-05-13 13:53:40,894 - stpipe.Image2Pipeline - INFO - Prefetch for CAMERA reference file is 'N/A'.
2025-05-13 13:53:40,894 - stpipe.Image2Pipeline - INFO - Prefetch for COLLIMATOR reference file is 'N/A'.
2025-05-13 13:53:40,895 - stpipe.Image2Pipeline - INFO - Prefetch for DFLAT reference file is 'N/A'.
2025-05-13 13:53:40,895 - stpipe.Image2Pipeline - INFO - Prefetch for DISPERSER reference file is 'N/A'.
2025-05-13 13:53:40,895 - stpipe.Image2Pipeline - INFO - Prefetch for DISTORTION reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf'.
2025-05-13 13:53:40,896 - stpipe.Image2Pipeline - INFO - Prefetch for FFLAT reference file is 'N/A'.
2025-05-13 13:53:40,897 - stpipe.Image2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf'.
2025-05-13 13:53:40,897 - stpipe.Image2Pipeline - INFO - Prefetch for FLAT reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits'.
2025-05-13 13:53:40,898 - stpipe.Image2Pipeline - INFO - Prefetch for FORE reference file is 'N/A'.
2025-05-13 13:53:40,898 - stpipe.Image2Pipeline - INFO - Prefetch for FPA reference file is 'N/A'.
2025-05-13 13:53:40,898 - stpipe.Image2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:53:40,899 - stpipe.Image2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:53:40,899 - stpipe.Image2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:53:40,900 - stpipe.Image2Pipeline - INFO - Prefetch for MSA reference file is 'N/A'.
2025-05-13 13:53:40,900 - stpipe.Image2Pipeline - INFO - Prefetch for OTE reference file is 'N/A'.
2025-05-13 13:53:40,900 - stpipe.Image2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits'.
2025-05-13 13:53:40,901 - stpipe.Image2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:53:40,901 - stpipe.Image2Pipeline - INFO - Prefetch for SFLAT reference file is 'N/A'.
2025-05-13 13:53:40,902 - stpipe.Image2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:53:40,902 - stpipe.Image2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is 'N/A'.
2025-05-13 13:53:40,903 - stpipe.Image2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:53:40,903 - stpipe.Image2Pipeline - INFO - Starting calwebb_image2 ...
2025-05-13 13:53:40,911 - stpipe.Image2Pipeline - 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)
2025-05-13 13:53:40,911 - stpipe.Image2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00005_mirimage
2025-05-13 13:53:40,911 - stpipe.Image2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00005_mirimage_rate.fits ...
2025-05-13 13:53:41,082 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00005_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:41,251 - stpipe.Image2Pipeline.assign_wcs - INFO - Created a MIRI mir_image pipeline with references {'distortion': '/home/runner/crds/references/jwst/miri/jwst_miri_distortion_0047.asdf', 'filteroffset': '/home/runner/crds/references/jwst/miri/jwst_miri_filteroffset_0008.asdf', 'specwcs': None, 'regions': None, 'wavelengthrange': None, 'camera': None, 'collimator': None, 'disperser': None, 'fore': None, 'fpa': None, 'msa': None, 'ote': None, 'ifupost': None, 'ifufore': None, 'ifuslicer': None}
2025-05-13 13:53:41,295 - stpipe.Image2Pipeline.assign_wcs - INFO - Update S_REGION to POLYGON ICRS 80.515622414 -69.443455639 80.534444344 -69.474030778 80.622018926 -69.467412656 80.603853712 -69.436735566
2025-05-13 13:53:41,296 - stpipe.Image2Pipeline.assign_wcs - INFO - assign_wcs updated S_REGION to POLYGON ICRS 80.515622414 -69.443455639 80.534444344 -69.474030778 80.622018926 -69.467412656 80.603853712 -69.436735566
2025-05-13 13:53:41,296 - stpipe.Image2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 13:53:41,327 - stpipe.Image2Pipeline.assign_wcs - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:41,338 - stpipe.Image2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 13:53:41,456 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00005_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:41,518 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_PARTIAL_DATA does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:41,518 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_LOW_QUAL does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:41,519 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword CDP_UNRELIABLE_ERROR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:41,521 - stpipe.Image2Pipeline.flat_field - WARNING - Keyword DIFF_PATTERN does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:41,522 - stpipe.Image2Pipeline.flat_field - INFO - Using FLAT reference file: /home/runner/crds/references/jwst/miri/jwst_miri_flat_0785.fits
2025-05-13 13:53:41,522 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type FFLAT
2025-05-13 13:53:41,523 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type SFLAT
2025-05-13 13:53:41,523 - stpipe.Image2Pipeline.flat_field - INFO - No reference found for type DFLAT
2025-05-13 13:53:41,587 - stpipe.Image2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 13:53:41,712 - stpipe.Image2Pipeline.photom - INFO - Step photom running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00005_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:41,734 - stpipe.Image2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds/references/jwst/miri/jwst_miri_photom_0218.fits
2025-05-13 13:53:41,735 - stpipe.Image2Pipeline.photom - INFO - Using area reference file: /home/runner/crds/references/jwst/miri/jwst_miri_area_0006.fits
2025-05-13 13:53:41,759 - stpipe.Image2Pipeline.photom - INFO - Using instrument: MIRI
2025-05-13 13:53:41,760 - stpipe.Image2Pipeline.photom - INFO - detector: MIRIMAGE
2025-05-13 13:53:41,760 - stpipe.Image2Pipeline.photom - INFO - exp_type: MIR_IMAGE
2025-05-13 13:53:41,761 - stpipe.Image2Pipeline.photom - INFO - filter: F770W
2025-05-13 13:53:41,786 - stpipe.Image2Pipeline.photom - INFO - Pixel area map copied to output.
2025-05-13 13:53:41,787 - stpipe.Image2Pipeline.photom - INFO - Values for PIXAR_SR and PIXAR_A2 obtained from AREA reference file.
2025-05-13 13:53:41,788 - stpipe.Image2Pipeline.photom - INFO - subarray: FULL
2025-05-13 13:53:41,789 - stpipe.Image2Pipeline.photom - INFO - Applying the time-dependent correction to the PHOTOM value.
2025-05-13 13:53:41,793 - stpipe.Image2Pipeline.photom - INFO - PHOTMJSR value: 0.257756
2025-05-13 13:53:41,811 - stpipe.Image2Pipeline.photom - INFO - Step photom done
2025-05-13 13:53:41,940 - stpipe.Image2Pipeline.resample - INFO - Step resample running with args (<ImageModel(1024, 1032) from ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00005_mirimage_image2pipeline.fits>,).
2025-05-13 13:53:41,972 - stpipe.Image2Pipeline.resample - INFO - Pixel scale ratio (pscale_out/pscale_in): 1.0
2025-05-13 13:53:41,972 - stpipe.Image2Pipeline.resample - INFO - Computed output pixel scale: 0.11091705981137293 arcsec.
2025-05-13 13:53:41,979 - stpipe.Image2Pipeline.resample - INFO - Output pixel scale: 0.11091705981137293 arcsec.
2025-05-13 13:53:41,980 - stpipe.Image2Pipeline.resample - INFO - Driz parameter kernel: square
2025-05-13 13:53:41,980 - stpipe.Image2Pipeline.resample - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:53:41,981 - stpipe.Image2Pipeline.resample - INFO - Driz parameter fillval: NAN
2025-05-13 13:53:41,981 - stpipe.Image2Pipeline.resample - INFO - Driz parameter weight_type: exptime
2025-05-13 13:53:41,985 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:42,487 - stpipe.Image2Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:53:42,732 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:42,941 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:43,149 - stpipe.Image2Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1019, 1029)
2025-05-13 13:53:43,421 - stpipe.Image2Pipeline.resample - INFO - Update S_REGION to POLYGON ICRS 80.515502376 -69.443331301 80.534099655 -69.474041358 80.622514014 -69.467424739 80.603796137 -69.436724137
2025-05-13 13:53:43,509 - stpipe.Image2Pipeline.resample - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00005_mirimage_i2d.fits
2025-05-13 13:53:43,510 - stpipe.Image2Pipeline.resample - INFO - Step resample done
2025-05-13 13:53:43,511 - stpipe.Image2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/MIRI/Imaging/mir_im_demo_data/Obs001/stage1/jw01040001005_03103_00005_mirimage
2025-05-13 13:53:43,511 - stpipe.Image2Pipeline - INFO - ... ending calwebb_image2
2025-05-13 13:53:43,512 - stpipe.Image2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:43,632 - stpipe.Image2Pipeline - INFO - Saved model in ./mir_im_demo_data/Obs001/stage2/jw01040001005_03103_00005_mirimage_cal.fits
2025-05-13 13:53:43,633 - stpipe.Image2Pipeline - INFO - Step Image2Pipeline done
2025-05-13 13:53:43,633 - stpipe - INFO - Results used jwst version: 1.18.0
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime so far: {time1 - time0:0.0f} seconds")
print(f"Runtime for Image2: {time1 - time_image2:0.0f} seconds")
Runtime so far: 311 seconds
Runtime for Image2: 17 seconds
Verify which pipeline steps were run and reference files used#
if doimage2:
# Identify *_cal.fits files
cal_files = sorted(glob.glob(os.path.join(image2_dir, '*_cal.fits')))
cal_f = datamodels.open(cal_files[0])
# Check which steps were run:
cal_f.meta.cal_step.instance
# Check which reference files were used to calibrate the dataset:
cal_f.meta.ref_file.instance
{'assign_wcs': 'COMPLETE',
'charge_migration': 'SKIPPED',
'clean_flicker_noise': 'SKIPPED',
'dark_sub': 'COMPLETE',
'dq_init': 'COMPLETE',
'emicorr': 'COMPLETE',
'firstframe': 'COMPLETE',
'flat_field': 'COMPLETE',
'gain_scale': 'SKIPPED',
'group_scale': 'SKIPPED',
'ipc': 'SKIPPED',
'jump': 'COMPLETE',
'lastframe': 'COMPLETE',
'linearity': 'COMPLETE',
'photom': 'COMPLETE',
'ramp_fit': 'COMPLETE',
'refpix': 'SKIPPED',
'reset': 'COMPLETE',
'rscd': 'COMPLETE',
'saturation': 'COMPLETE'}
{'area': {'name': 'crds://jwst_miri_area_0006.fits'},
'camera': {'name': 'N/A'},
'collimator': {'name': 'N/A'},
'crds': {'context_used': 'jwst_1364.pmap', 'sw_version': '12.1.5'},
'dark': {'name': 'crds://jwst_miri_dark_0103.fits'},
'dflat': {'name': 'N/A'},
'disperser': {'name': 'N/A'},
'distortion': {'name': 'crds://jwst_miri_distortion_0047.asdf'},
'emicorr': {'name': 'crds://jwst_miri_emicorr_0002.asdf'},
'fflat': {'name': 'N/A'},
'filteroffset': {'name': 'crds://jwst_miri_filteroffset_0008.asdf'},
'flat': {'name': 'crds://jwst_miri_flat_0785.fits'},
'fore': {'name': 'N/A'},
'fpa': {'name': 'N/A'},
'gain': {'name': 'crds://jwst_miri_gain_0034.fits'},
'ifufore': {'name': 'N/A'},
'ifupost': {'name': 'N/A'},
'ifuslicer': {'name': 'N/A'},
'linearity': {'name': 'crds://jwst_miri_linearity_0032.fits'},
'mask': {'name': 'crds://jwst_miri_mask_0036.fits'},
'msa': {'name': 'N/A'},
'ote': {'name': 'N/A'},
'photom': {'name': 'crds://jwst_miri_photom_0218.fits'},
'readnoise': {'name': 'crds://jwst_miri_readnoise_0085.fits'},
'regions': {'name': 'N/A'},
'reset': {'name': 'crds://jwst_miri_reset_0077.fits'},
'rscd': {'name': 'crds://jwst_miri_rscd_0017.fits'},
'saturation': {'name': 'crds://jwst_miri_saturation_0034.fits'},
'sflat': {'name': 'N/A'},
'specwcs': {'name': 'N/A'},
'wavelengthrange': {'name': 'N/A'}}
7. Image3 Pipeline#
In the Image3
stage of the pipeline, the individual *_cal.fits files for each of the dither positions are
combined to one single distortion corrected image. First, an
Association
needs to be created to inform the pipeline that these individual exposures are linked together.
By default, the Image3 stage of the pipeline performs the following steps on MIRI data:
tweakreg - creates source catalogs of pointlike sources for each input image. The source catalog for each input image is compared to each other to derive coordinate transforms to align the images relative to each other.
As of pipeline version 1.14.0, the default source finding algorithm is
IRAFStarFinder.
skymatch - measures the background level from the sky to use as input into the subsequent
outlier detectionandresamplesteps.outlier detection - flags any remaining cosmic rays, bad pixels, or other artifacts not already flagged during the
DETECTOR1stage of the pipeline, using all input images to create a median image so that outliers in individual images can be identified.resample - resamples each input image based on its WCS and distortion information and creates a single undistorted image.
source catalog - creates a catalog of detected sources along with measured photometries and morphologies (i.e., point-like vs extended). Useful for quicklooks, but optimization is likely needed for specific science cases. Users may wish to experiment with changing the
snr_thresholdanddeblendoptions. Modifications to the following parameters will not significantly improve data quality and it is advised to keep them at their default values:aperture_ee1,aperture_ee2,aperture_ee3,ci1_star_threshold,ci2_star_threshold.
Some values that have been shown to give good results for MIRI data are to set the outlier_detection’s parameter scale
to ‘1.0 0.8’ and to set the resample parameter weight_type to ‘exptime’, both currently set in the
parameter reference file
pars-outlierdetectionstep, but can be overridden as indicated below.
time_image3 = time.perf_counter()
# Set up a dictionary to define how the Image3 pipeline should be configured
# Boilerplate dictionary setup
image3dict = {}
image3dict['assign_mtwcs'], image3dict['tweakreg'], image3dict['skymatch'] = {}, {}, {}
image3dict['outlier_detection'], image3dict['resample'], image3dict['source_catalog'] = {}, {}, {}
# Overrides for whether or not certain steps should be skipped (example)
#image3dict['outlier_detection']['skip'] = True
# Overrides for various reference files
# Files should be in the base local directory or provide full path
#image3dict['source_catalog']['override_apcorr'] = 'myfile.fits' # Aperture correction parameters
#image3dict['source_catalog']['override_abvegaoffset'] = 'myfile.asdf' # Data to convert from AB to Vega magnitudes (ASDF file)
# Overrides for specific parameters in the step (examples)
#image3dict['resample']['weight_type'] = ['exptime']
#image3dict['outlier_detection']['scale'] = ['1.0 0.8']
Find and sort all of the input files, ensuring use of absolute paths
# Science Files need are the cal.fits files
sstring = os.path.join(image2_dir, 'jw*cal.fits')
cal_files = sorted(glob.glob(sstring))
for ii in range(0, len(cal_files)):
cal_files[ii] = os.path.abspath(cal_files[ii])
calfiles = np.array(cal_files)
print(f'Found {str(len(cal_files))} science files to process')
Found 5 science files to process
Create Association File#
An association file lists the exposures to calibrated together in Stage3
of the pipeline. Note that an association file is available for download
from MAST, with a filename of *_asn.json. Here we show how to create an
association file to point to the data products created when processing data
through the pipeline. Note that the output products will have a rootname
that is specified by the product_name in the association file. For
this tutorial, the rootname of the output products will be
image3_association.
# Create a Level 3 Association
if doimage3:
associations = afl.asn_from_list(cal_files, rule=DMS_Level3_Base, product_name='image3_association')
associations.data['asn_type'] = 'image3'
program = datamodels.open(cal_files[0]).meta.observation.program_number
associations.data['program'] = program
# Format association as .json file
asn_filename, serialized = associations.dump(format="json")
# Write out association file
association_im3 = os.path.join(sci_dir, asn_filename)
with open(association_im3, "w") as fd:
fd.write(serialized)
2025-05-13 13:53:43,869 - 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)
1822
Run Image3 stage of the pipeline#
Given the grouped exposures in the association file, the products if the
Image3 stage of the pipeline are:
a
*_crf.fitsfile produced by theoutlier_detectionstep, where theDQarray marks the pixels flagged as outliers.a final combined, rectified image with name
*_i2d.fits,a source catalog with name
*_cat.ecsv,a segmentation map file (
*_segm.fits) which has integer values at the pixel locations where a source is detected where the pixel values match the source ID number in the catalog.
# Run Stage 3
if doimage3:
i2d_result = Image3Pipeline.call(association_im3, output_dir=image3_dir, steps=image3dict, save_results=True)
else:
print('Skipping Spec3 processing')
2025-05-13 13:53:44,023 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-tweakregstep_0020.asdf 1.1 K bytes (1 / 1 files) (0 / 1.1 K bytes)
2025-05-13 13:53:44,069 - stpipe - INFO - PARS-TWEAKREGSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-tweakregstep_0020.asdf
2025-05-13 13:53:44,081 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-outlierdetectionstep_0096.asdf 1.3 K bytes (1 / 1 files) (0 / 1.3 K bytes)
2025-05-13 13:53:44,122 - stpipe - INFO - PARS-OUTLIERDETECTIONSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-outlierdetectionstep_0096.asdf
2025-05-13 13:53:44,130 - stpipe - INFO - PARS-RESAMPLESTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-resamplestep_0001.asdf
2025-05-13 13:53:44,139 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_pars-sourcecatalogstep_0018.asdf 1.0 K bytes (1 / 1 files) (0 / 1.0 K bytes)
2025-05-13 13:53:44,189 - stpipe - INFO - PARS-SOURCECATALOGSTEP parameters found: /home/runner/crds/references/jwst/miri/jwst_miri_pars-sourcecatalogstep_0018.asdf
2025-05-13 13:53:44,205 - stpipe.Image3Pipeline - INFO - Image3Pipeline instance created.
2025-05-13 13:53:44,206 - stpipe.Image3Pipeline.assign_mtwcs - INFO - AssignMTWcsStep instance created.
2025-05-13 13:53:44,208 - stpipe.Image3Pipeline.tweakreg - INFO - TweakRegStep instance created.
2025-05-13 13:53:44,209 - stpipe.Image3Pipeline.skymatch - INFO - SkyMatchStep instance created.
2025-05-13 13:53:44,210 - stpipe.Image3Pipeline.outlier_detection - INFO - OutlierDetectionStep instance created.
2025-05-13 13:53:44,212 - stpipe.Image3Pipeline.resample - INFO - ResampleStep instance created.
2025-05-13 13:53:44,213 - stpipe.Image3Pipeline.source_catalog - INFO - SourceCatalogStep instance created.
2025-05-13 13:53:44,339 - stpipe.Image3Pipeline - INFO - Step Image3Pipeline running with args ('./mir_im_demo_data/Obs001/jw01040-a3001_image3_00007_asn.json',).
2025-05-13 13:53:44,351 - stpipe.Image3Pipeline - INFO - Step Image3Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: ./mir_im_demo_data/Obs001/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: ''
in_memory: True
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: ''
tweakreg:
pre_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: ''
save_catalogs: False
use_custom_catalogs: False
catalog_format: ecsv
catfile: ''
starfinder: iraf
snr_threshold: 10.0
bkg_boxsize: 400
kernel_fwhm: 2.19
minsep_fwhm: 0.0
sigma_radius: 1.5
sharplo: 0.5
sharphi: 2.0
roundlo: 0.0
roundhi: 0.2
brightest: 200
peakmax: None
npixels: 10
connectivity: '8'
nlevels: 32
contrast: 0.001
multithresh_mode: exponential
localbkg_width: 0
apermask_method: correct
kron_params: None
enforce_user_order: False
expand_refcat: False
minobj: 15
fitgeometry: rshift
nclip: 3
sigma: 3
searchrad: 1.0
use2dhist: True
separation: 1.0
tolerance: 0.7
xoffset: 0.0
yoffset: 0.0
abs_refcat: ''
save_abs_catalog: False
abs_minobj: 15
abs_fitgeometry: rshift
abs_nclip: 3
abs_sigma: 3.0
abs_searchrad: 6.0
abs_use2dhist: True
abs_separation: 1.0
abs_tolerance: 0.7
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
in_memory: True
skymatch:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
skymethod: match
match_down: True
subtract: False
skylist: None
stepsize: None
skystat: mode
dqbits: ~DO_NOT_USE+NON_SCIENCE
lower: None
upper: None
nclip: 5
lsigma: 4.0
usigma: 4.0
binwidth: 0.1
in_memory: True
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: exptime
pixfrac: 1.0
kernel: square
fillval: NAN
maskpt: 0.7
snr: 4.0 3.0
scale: 1.0 0.8
backg: 0.0
kernel_size: 7 7
threshold_percent: 99.8
rolling_window_width: 25
ifu_second_check: False
save_intermediate_results: False
resample_data: True
good_bits: ~DO_NOT_USE+NON_SCIENCE
in_memory: True
resample:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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
crpix: None
crval: None
rotation: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
source_catalog:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: cat
search_output_file: True
input_dir: ''
bkg_boxsize: 1000
kernel_fwhm: 2.27
snr_threshold: 3.0
npixels: 5
deblend: False
aperture_ee1: 30
aperture_ee2: 50
aperture_ee3: 70
ci1_star_threshold: 2.0
ci2_star_threshold: 1.8
2025-05-13 13:53:44,361 - stpipe.Image3Pipeline - 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)
2025-05-13 13:53:44,467 - stpipe.Image3Pipeline - INFO - Prefetching reference files for dataset: 'jw01040001005_03103_00001_mirimage_cal.fits' reftypes = ['abvegaoffset', 'apcorr']
2025-05-13 13:53:44,471 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_abvegaoffset_0002.asdf 1.8 K bytes (1 / 2 files) (0 / 27.7 K bytes)
2025-05-13 13:53:44,517 - CRDS - INFO - Fetching /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0014.fits 25.9 K bytes (2 / 2 files) (1.8 K / 27.7 K bytes)
2025-05-13 13:53:44,566 - stpipe.Image3Pipeline - INFO - Prefetch for ABVEGAOFFSET reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_abvegaoffset_0002.asdf'.
2025-05-13 13:53:44,566 - stpipe.Image3Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0014.fits'.
2025-05-13 13:53:44,567 - stpipe.Image3Pipeline - INFO - Starting calwebb_image3 ...
2025-05-13 13:53:44,576 - stpipe.Image3Pipeline - 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)
2025-05-13 13:53:44,860 - stpipe.Image3Pipeline.tweakreg - INFO - Step tweakreg running with args (<jwst.datamodels.library.ModelLibrary object at 0x7fa551b995b0>,).
2025-05-13 13:53:45,233 - stpipe.Image3Pipeline.tweakreg - INFO - Detected 101 sources in jw01040001005_03103_00001_mirimage_cal.fits.
2025-05-13 13:53:45,718 - stpipe.Image3Pipeline.tweakreg - INFO - Detected 93 sources in jw01040001005_03103_00002_mirimage_cal.fits.
2025-05-13 13:53:46,203 - stpipe.Image3Pipeline.tweakreg - INFO - Detected 95 sources in jw01040001005_03103_00003_mirimage_cal.fits.
2025-05-13 13:53:46,688 - stpipe.Image3Pipeline.tweakreg - INFO - Detected 96 sources in jw01040001005_03103_00004_mirimage_cal.fits.
2025-05-13 13:53:47,170 - stpipe.Image3Pipeline.tweakreg - INFO - Detected 100 sources in jw01040001005_03103_00005_mirimage_cal.fits.
2025-05-13 13:53:47,191 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,192 - stpipe.Image3Pipeline.tweakreg - INFO - Number of image groups to be aligned: 5.
2025-05-13 13:53:47,193 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,193 - stpipe.Image3Pipeline.tweakreg - INFO - ***** tweakwcs.imalign.align_wcs() started on 2025-05-13 13:53:47.193010
2025-05-13 13:53:47,194 - stpipe.Image3Pipeline.tweakreg - INFO - Version 0.8.10
2025-05-13 13:53:47,194 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,528 - stpipe.Image3Pipeline.tweakreg - INFO - Selected image 'GROUP ID: jw01040001005_03103_1' as reference image
2025-05-13 13:53:47,532 - stpipe.Image3Pipeline.tweakreg - INFO - Aligning image catalog 'GROUP ID: jw01040001005_03103_2' to the reference catalog.
2025-05-13 13:53:47,580 - stpipe.Image3Pipeline.tweakreg - INFO - Matching sources from 'jw01040001005_03103_00002_mirimage_cal' catalog with sources from the reference 'jw01040001005_03103_00001_mirimage_cal' catalog.
2025-05-13 13:53:47,580 - stpipe.Image3Pipeline.tweakreg - INFO - Computing initial guess for X and Y shifts...
2025-05-13 13:53:47,582 - stpipe.Image3Pipeline.tweakreg - INFO - Found initial X and Y shifts of 0.1092, 0.1092 (arcsec) with significance of 74 and 74 matches.
2025-05-13 13:53:47,584 - stpipe.Image3Pipeline.tweakreg - INFO - Found 73 matches for 'GROUP ID: jw01040001005_03103_2'...
2025-05-13 13:53:47,584 - stpipe.Image3Pipeline.tweakreg - INFO - Performing 'rshift' fit
2025-05-13 13:53:47,586 - stpipe.Image3Pipeline.tweakreg - INFO - Computed 'rshift' fit for GROUP ID: jw01040001005_03103_2:
2025-05-13 13:53:47,586 - stpipe.Image3Pipeline.tweakreg - INFO - XSH: -0.00407686 YSH: -0.00199884 ROT: 0.00185935 SCALE: 1
2025-05-13 13:53:47,587 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,587 - stpipe.Image3Pipeline.tweakreg - INFO - FIT RMSE: 0.0149898 FIT MAE: 0.0137465
2025-05-13 13:53:47,588 - stpipe.Image3Pipeline.tweakreg - INFO - Final solution based on 73 objects.
2025-05-13 13:53:47,620 - stpipe.Image3Pipeline.tweakreg - INFO - Aligning image catalog 'GROUP ID: jw01040001005_03103_3' to the reference catalog.
2025-05-13 13:53:47,665 - stpipe.Image3Pipeline.tweakreg - INFO - Matching sources from 'jw01040001005_03103_00003_mirimage_cal' catalog with sources from the reference 'jw01040001005_03103_00001_mirimage_cal' catalog.
2025-05-13 13:53:47,666 - stpipe.Image3Pipeline.tweakreg - INFO - Computing initial guess for X and Y shifts...
2025-05-13 13:53:47,667 - stpipe.Image3Pipeline.tweakreg - INFO - Found initial X and Y shifts of 0.1092, 0.1092 (arcsec) with significance of 74 and 74 matches.
2025-05-13 13:53:47,669 - stpipe.Image3Pipeline.tweakreg - INFO - Found 73 matches for 'GROUP ID: jw01040001005_03103_3'...
2025-05-13 13:53:47,669 - stpipe.Image3Pipeline.tweakreg - INFO - Performing 'rshift' fit
2025-05-13 13:53:47,671 - stpipe.Image3Pipeline.tweakreg - INFO - Computed 'rshift' fit for GROUP ID: jw01040001005_03103_3:
2025-05-13 13:53:47,672 - stpipe.Image3Pipeline.tweakreg - INFO - XSH: -0.00597939 YSH: -0.00234982 ROT: 0.00229052 SCALE: 1
2025-05-13 13:53:47,672 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,673 - stpipe.Image3Pipeline.tweakreg - INFO - FIT RMSE: 0.0136662 FIT MAE: 0.0124186
2025-05-13 13:53:47,673 - stpipe.Image3Pipeline.tweakreg - INFO - Final solution based on 73 objects.
2025-05-13 13:53:47,704 - stpipe.Image3Pipeline.tweakreg - INFO - Aligning image catalog 'GROUP ID: jw01040001005_03103_4' to the reference catalog.
2025-05-13 13:53:47,752 - stpipe.Image3Pipeline.tweakreg - INFO - Matching sources from 'jw01040001005_03103_00004_mirimage_cal' catalog with sources from the reference 'jw01040001005_03103_00001_mirimage_cal' catalog.
2025-05-13 13:53:47,753 - stpipe.Image3Pipeline.tweakreg - INFO - Computing initial guess for X and Y shifts...
2025-05-13 13:53:47,754 - stpipe.Image3Pipeline.tweakreg - INFO - Found initial X and Y shifts of 0.1092, 0.1092 (arcsec) with significance of 63 and 63 matches.
2025-05-13 13:53:47,755 - stpipe.Image3Pipeline.tweakreg - INFO - Found 62 matches for 'GROUP ID: jw01040001005_03103_4'...
2025-05-13 13:53:47,756 - stpipe.Image3Pipeline.tweakreg - INFO - Performing 'rshift' fit
2025-05-13 13:53:47,757 - stpipe.Image3Pipeline.tweakreg - INFO - Computed 'rshift' fit for GROUP ID: jw01040001005_03103_4:
2025-05-13 13:53:47,758 - stpipe.Image3Pipeline.tweakreg - INFO - XSH: -0.00857461 YSH: -0.00305348 ROT: 0.00456085 SCALE: 1
2025-05-13 13:53:47,759 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,759 - stpipe.Image3Pipeline.tweakreg - INFO - FIT RMSE: 0.0140797 FIT MAE: 0.0121287
2025-05-13 13:53:47,760 - stpipe.Image3Pipeline.tweakreg - INFO - Final solution based on 62 objects.
2025-05-13 13:53:47,790 - stpipe.Image3Pipeline.tweakreg - INFO - Aligning image catalog 'GROUP ID: jw01040001005_03103_5' to the reference catalog.
2025-05-13 13:53:47,836 - stpipe.Image3Pipeline.tweakreg - INFO - Matching sources from 'jw01040001005_03103_00005_mirimage_cal' catalog with sources from the reference 'jw01040001005_03103_00001_mirimage_cal' catalog.
2025-05-13 13:53:47,836 - stpipe.Image3Pipeline.tweakreg - INFO - Computing initial guess for X and Y shifts...
2025-05-13 13:53:47,838 - stpipe.Image3Pipeline.tweakreg - INFO - Found initial X and Y shifts of 0.1092, 0.1092 (arcsec) with significance of 68 and 68 matches.
2025-05-13 13:53:47,839 - stpipe.Image3Pipeline.tweakreg - INFO - Found 66 matches for 'GROUP ID: jw01040001005_03103_5'...
2025-05-13 13:53:47,839 - stpipe.Image3Pipeline.tweakreg - INFO - Performing 'rshift' fit
2025-05-13 13:53:47,841 - stpipe.Image3Pipeline.tweakreg - INFO - Computed 'rshift' fit for GROUP ID: jw01040001005_03103_5:
2025-05-13 13:53:47,842 - stpipe.Image3Pipeline.tweakreg - INFO - XSH: -0.00664114 YSH: -0.00266732 ROT: 2.18219e-05 SCALE: 1
2025-05-13 13:53:47,842 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,843 - stpipe.Image3Pipeline.tweakreg - INFO - FIT RMSE: 0.011449 FIT MAE: 0.00975016
2025-05-13 13:53:47,843 - stpipe.Image3Pipeline.tweakreg - INFO - Final solution based on 66 objects.
2025-05-13 13:53:47,877 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,877 - stpipe.Image3Pipeline.tweakreg - INFO - ***** tweakwcs.imalign.align_wcs() ended on 2025-05-13 13:53:47.877175
2025-05-13 13:53:47,878 - stpipe.Image3Pipeline.tweakreg - INFO - ***** tweakwcs.imalign.align_wcs() TOTAL RUN TIME: 0:00:00.684165
2025-05-13 13:53:47,878 - stpipe.Image3Pipeline.tweakreg - INFO -
2025-05-13 13:53:47,944 - stpipe.Image3Pipeline.tweakreg - INFO - Update S_REGION to POLYGON ICRS 80.519756549 -69.441179116 80.538579401 -69.471754034 80.626144059 -69.465134886 80.607977860 -69.434458008
2025-05-13 13:53:47,983 - stpipe.Image3Pipeline.tweakreg - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:48,034 - stpipe.Image3Pipeline.tweakreg - INFO - Update S_REGION to POLYGON ICRS 80.517106891 -69.438899507 80.535923518 -69.469474745 80.623479797 -69.462857092 80.605319779 -69.432179904
2025-05-13 13:53:48,072 - stpipe.Image3Pipeline.tweakreg - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:48,125 - stpipe.Image3Pipeline.tweakreg - INFO - Update S_REGION to POLYGON ICRS 80.513331672 -69.439820483 80.532140219 -69.470396394 80.619702189 -69.463781875 80.601550295 -69.433104037
2025-05-13 13:53:48,164 - stpipe.Image3Pipeline.tweakreg - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:48,216 - stpipe.Image3Pipeline.tweakreg - INFO - Update S_REGION to POLYGON ICRS 80.515617170 -69.443456369 80.534439059 -69.474031510 80.622013654 -69.467413403 80.603848480 -69.436736310
2025-05-13 13:53:48,255 - stpipe.Image3Pipeline.tweakreg - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/gwcs/wcs/_wcs.py:1698: LinAlgWarning: Failed to achieve requested SIP approximation accuracy.
fit_inv_poly_u, fit_inv_poly_v, max_inv_resid = fit_2D_poly(
2025-05-13 13:53:48,272 - stpipe.Image3Pipeline.tweakreg - INFO - Step tweakreg done
2025-05-13 13:53:48,431 - stpipe.Image3Pipeline.skymatch - INFO - Step skymatch running with args (<jwst.datamodels.library.ModelLibrary object at 0x7fa551b995b0>,).
2025-05-13 13:53:48,524 - stpipe.Image3Pipeline.skymatch - INFO -
2025-05-13 13:53:48,525 - stpipe.Image3Pipeline.skymatch - INFO - ***** stcal.skymatch.skymatch.skymatch() started on 2025-05-13 13:53:48.524929
2025-05-13 13:53:48,525 - stpipe.Image3Pipeline.skymatch - INFO -
2025-05-13 13:53:48,526 - stpipe.Image3Pipeline.skymatch - INFO - Sky computation method: 'match'
2025-05-13 13:53:48,526 - stpipe.Image3Pipeline.skymatch - INFO - Sky matching direction: DOWN
2025-05-13 13:53:48,527 - stpipe.Image3Pipeline.skymatch - INFO - Sky subtraction from image data: OFF
2025-05-13 13:53:48,528 - stpipe.Image3Pipeline.skymatch - INFO -
2025-05-13 13:53:48,528 - stpipe.Image3Pipeline.skymatch - INFO - ---- Computing differences in sky values in overlapping regions.
2025-05-13 13:53:49,926 - stpipe.Image3Pipeline.skymatch - INFO - * Image ID=jw01040001005_03103_00001_mirimage_cal.fits. Sky background: 0.0552419
2025-05-13 13:53:49,927 - stpipe.Image3Pipeline.skymatch - INFO - * Image ID=jw01040001005_03103_00002_mirimage_cal.fits. Sky background: 0.035894
2025-05-13 13:53:49,927 - stpipe.Image3Pipeline.skymatch - INFO - * Image ID=jw01040001005_03103_00003_mirimage_cal.fits. Sky background: 0.0235521
2025-05-13 13:53:49,928 - stpipe.Image3Pipeline.skymatch - INFO - * Image ID=jw01040001005_03103_00004_mirimage_cal.fits. Sky background: 0.0461255
2025-05-13 13:53:49,928 - stpipe.Image3Pipeline.skymatch - INFO - * Image ID=jw01040001005_03103_00005_mirimage_cal.fits. Sky background: 0
2025-05-13 13:53:49,929 - stpipe.Image3Pipeline.skymatch - INFO -
2025-05-13 13:53:49,929 - stpipe.Image3Pipeline.skymatch - INFO - ***** stcal.skymatch.skymatch.skymatch() ended on 2025-05-13 13:53:49.929069
2025-05-13 13:53:49,929 - stpipe.Image3Pipeline.skymatch - INFO - ***** stcal.skymatch.skymatch.skymatch() TOTAL RUN TIME: 0:00:01.404140
2025-05-13 13:53:49,930 - stpipe.Image3Pipeline.skymatch - INFO -
2025-05-13 13:53:49,946 - stpipe.Image3Pipeline.skymatch - INFO - Step skymatch done
2025-05-13 13:53:50,109 - stpipe.Image3Pipeline.outlier_detection - INFO - Step outlier_detection running with args (<jwst.datamodels.library.ModelLibrary object at 0x7fa551b995b0>,).
2025-05-13 13:53:50,110 - stpipe.Image3Pipeline.outlier_detection - INFO - Outlier Detection mode: imaging
2025-05-13 13:53:50,111 - stpipe.Image3Pipeline.outlier_detection - INFO - Outlier Detection asn_id: a3001
2025-05-13 13:53:50,132 - stpipe.Image3Pipeline.outlier_detection - INFO - Pixel scale ratio (pscale_out/pscale_in): 1.0
2025-05-13 13:53:50,133 - stpipe.Image3Pipeline.outlier_detection - INFO - Computed output pixel scale: 0.1109170593250524 arcsec.
2025-05-13 13:53:50,148 - stpipe.Image3Pipeline.outlier_detection - INFO - Output pixel scale: 0.1109170593250524 arcsec.
2025-05-13 13:53:50,149 - stpipe.Image3Pipeline.outlier_detection - INFO - Driz parameter kernel: square
2025-05-13 13:53:50,150 - stpipe.Image3Pipeline.outlier_detection - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:53:50,150 - stpipe.Image3Pipeline.outlier_detection - INFO - Driz parameter fillval: NAN
2025-05-13 13:53:50,151 - stpipe.Image3Pipeline.outlier_detection - INFO - Driz parameter weight_type: exptime
2025-05-13 13:53:50,152 - stpipe.Image3Pipeline.outlier_detection - INFO - 1 exposures to drizzle together
2025-05-13 13:53:50,656 - stpipe.Image3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 13:53:50,958 - stpipe.Image3Pipeline.outlier_detection - INFO - Update S_REGION to POLYGON ICRS 80.512843884 -69.439087970 80.534017785 -69.474047004 80.629903387 -69.466866383 80.608580645 -69.431919026
2025-05-13 13:53:50,990 - stpipe.Image3Pipeline.outlier_detection - INFO - 1 exposures to drizzle together
2025-05-13 13:53:51,652 - stpipe.Image3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 13:53:51,962 - stpipe.Image3Pipeline.outlier_detection - INFO - Update S_REGION to POLYGON ICRS 80.512843884 -69.439087970 80.534017785 -69.474047004 80.629903387 -69.466866383 80.608580645 -69.431919026
2025-05-13 13:53:51,993 - stpipe.Image3Pipeline.outlier_detection - INFO - 1 exposures to drizzle together
2025-05-13 13:53:52,651 - stpipe.Image3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 13:53:52,949 - stpipe.Image3Pipeline.outlier_detection - INFO - Update S_REGION to POLYGON ICRS 80.512843884 -69.439087970 80.534017785 -69.474047004 80.629903387 -69.466866383 80.608580645 -69.431919026
2025-05-13 13:53:52,979 - stpipe.Image3Pipeline.outlier_detection - INFO - 1 exposures to drizzle together
2025-05-13 13:53:53,643 - stpipe.Image3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 13:53:53,943 - stpipe.Image3Pipeline.outlier_detection - INFO - Update S_REGION to POLYGON ICRS 80.512843884 -69.439087970 80.534017785 -69.474047004 80.629903387 -69.466866383 80.608580645 -69.431919026
2025-05-13 13:53:53,972 - stpipe.Image3Pipeline.outlier_detection - INFO - 1 exposures to drizzle together
2025-05-13 13:53:54,630 - stpipe.Image3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 13:53:54,929 - stpipe.Image3Pipeline.outlier_detection - INFO - Update S_REGION to POLYGON ICRS 80.512843884 -69.439087970 80.534017785 -69.474047004 80.629903387 -69.466866383 80.608580645 -69.431919026
2025-05-13 13:53:56,215 - stpipe.Image3Pipeline.outlier_detection - INFO - Blotting (1024, 1032) <-- (1160, 1116)
2025-05-13 13:53:56,293 - stpipe.Image3Pipeline.outlier_detection - INFO - 207 pixels marked as outliers
2025-05-13 13:53:56,979 - stpipe.Image3Pipeline.outlier_detection - INFO - Blotting (1024, 1032) <-- (1160, 1116)
2025-05-13 13:53:57,055 - stpipe.Image3Pipeline.outlier_detection - INFO - 194 pixels marked as outliers
2025-05-13 13:53:57,746 - stpipe.Image3Pipeline.outlier_detection - INFO - Blotting (1024, 1032) <-- (1160, 1116)
2025-05-13 13:53:57,822 - stpipe.Image3Pipeline.outlier_detection - INFO - 148 pixels marked as outliers
2025-05-13 13:53:58,515 - stpipe.Image3Pipeline.outlier_detection - INFO - Blotting (1024, 1032) <-- (1160, 1116)
2025-05-13 13:53:58,592 - stpipe.Image3Pipeline.outlier_detection - INFO - 194 pixels marked as outliers
2025-05-13 13:53:59,277 - stpipe.Image3Pipeline.outlier_detection - INFO - Blotting (1024, 1032) <-- (1160, 1116)
2025-05-13 13:53:59,356 - stpipe.Image3Pipeline.outlier_detection - INFO - 115 pixels marked as outliers
2025-05-13 13:53:59,509 - stpipe.Image3Pipeline.outlier_detection - INFO - Saved model in ./mir_im_demo_data/Obs001/stage3/jw01040001005_03103_00001_mirimage_a3001_crf.fits
2025-05-13 13:53:59,648 - stpipe.Image3Pipeline.outlier_detection - INFO - Saved model in ./mir_im_demo_data/Obs001/stage3/jw01040001005_03103_00002_mirimage_a3001_crf.fits
2025-05-13 13:53:59,786 - stpipe.Image3Pipeline.outlier_detection - INFO - Saved model in ./mir_im_demo_data/Obs001/stage3/jw01040001005_03103_00003_mirimage_a3001_crf.fits
2025-05-13 13:53:59,926 - stpipe.Image3Pipeline.outlier_detection - INFO - Saved model in ./mir_im_demo_data/Obs001/stage3/jw01040001005_03103_00004_mirimage_a3001_crf.fits
2025-05-13 13:54:00,065 - stpipe.Image3Pipeline.outlier_detection - INFO - Saved model in ./mir_im_demo_data/Obs001/stage3/jw01040001005_03103_00005_mirimage_a3001_crf.fits
2025-05-13 13:54:00,065 - stpipe.Image3Pipeline.outlier_detection - INFO - Step outlier_detection done
2025-05-13 13:54:00,224 - stpipe.Image3Pipeline.resample - INFO - Step resample running with args (<jwst.datamodels.library.ModelLibrary object at 0x7fa551b995b0>,).
2025-05-13 13:54:00,290 - stpipe.Image3Pipeline.resample - INFO - Pixel scale ratio (pscale_out/pscale_in): 1.0
2025-05-13 13:54:00,291 - stpipe.Image3Pipeline.resample - INFO - Computed output pixel scale: 0.1109170593250524 arcsec.
2025-05-13 13:54:00,307 - stpipe.Image3Pipeline.resample - INFO - Output pixel scale: 0.1109170593250524 arcsec.
2025-05-13 13:54:00,307 - stpipe.Image3Pipeline.resample - INFO - Driz parameter kernel: square
2025-05-13 13:54:00,308 - stpipe.Image3Pipeline.resample - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:54:00,309 - stpipe.Image3Pipeline.resample - INFO - Driz parameter fillval: NAN
2025-05-13 13:54:00,309 - stpipe.Image3Pipeline.resample - INFO - Driz parameter weight_type: exptime
2025-05-13 13:54:00,313 - stpipe.Image3Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:54:00,819 - stpipe.Image3Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:54:01,062 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:01,282 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:01,496 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:02,409 - stpipe.Image3Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:54:02,653 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:02,872 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:03,085 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:03,963 - stpipe.Image3Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:54:04,207 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:04,426 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:04,636 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:05,513 - stpipe.Image3Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:54:05,765 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:05,985 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:06,196 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:07,074 - stpipe.Image3Pipeline.resample - INFO - Resampling science and variance data
2025-05-13 13:54:07,318 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:07,537 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:07,748 - stpipe.Image3Pipeline.resample - INFO - Drizzling (1024, 1032) --> (1160, 1116)
2025-05-13 13:54:08,209 - stpipe.Image3Pipeline.resample - INFO - Update S_REGION to POLYGON ICRS 80.512843884 -69.439087970 80.534017785 -69.474047004 80.629903387 -69.466866383 80.608580645 -69.431919026
2025-05-13 13:54:08,423 - stpipe.Image3Pipeline.resample - INFO - Saved model in ./mir_im_demo_data/Obs001/stage3/image3_association_i2d.fits
2025-05-13 13:54:08,423 - stpipe.Image3Pipeline.resample - INFO - Step resample done
2025-05-13 13:54:08,575 - stpipe.Image3Pipeline.source_catalog - INFO - Step source_catalog running with args (<ImageModel(1160, 1116) from image3_association_i2d.fits>,).
2025-05-13 13:54:08,605 - stpipe.Image3Pipeline.source_catalog - INFO - Using APCORR reference file: /home/runner/crds/references/jwst/miri/jwst_miri_apcorr_0014.fits
2025-05-13 13:54:08,613 - stpipe.Image3Pipeline.source_catalog - INFO - Using ABVEGAOFFSET reference file: /home/runner/crds/references/jwst/miri/jwst_miri_abvegaoffset_0002.asdf
2025-05-13 13:54:08,613 - stpipe.Image3Pipeline.source_catalog - INFO - Instrument: MIRI
2025-05-13 13:54:08,614 - stpipe.Image3Pipeline.source_catalog - INFO - Detector: MIRIMAGE
2025-05-13 13:54:08,614 - stpipe.Image3Pipeline.source_catalog - INFO - Filter: F770W
2025-05-13 13:54:08,614 - stpipe.Image3Pipeline.source_catalog - INFO - Subarray: FULL
2025-05-13 13:54:08,654 - stpipe.Image3Pipeline.source_catalog - INFO - AB to Vega magnitude offset 4.38398
2025-05-13 13:54:08,773 - stpipe.Image3Pipeline.source_catalog - INFO - Background could not be estimated in meshes. Using the entire unmasked array for background estimation: bkg_boxsize=(1160, 1116).
2025-05-13 13:54:09,156 - stpipe.Image3Pipeline.source_catalog - INFO - Detected 739 sources
2025-05-13 13:54:09,728 - stpipe.Image3Pipeline.source_catalog - INFO - Wrote source catalog: ./mir_im_demo_data/Obs001/stage3/image3_association_cat.ecsv
2025-05-13 13:54:09,819 - stpipe.Image3Pipeline.source_catalog - INFO - Saved model in ./mir_im_demo_data/Obs001/stage3/image3_association_segm.fits
2025-05-13 13:54:09,820 - stpipe.Image3Pipeline.source_catalog - INFO - Wrote segmentation map: image3_association_segm.fits
2025-05-13 13:54:09,822 - stpipe.Image3Pipeline.source_catalog - INFO - Step source_catalog done
2025-05-13 13:54:09,830 - stpipe.Image3Pipeline - INFO - Step Image3Pipeline done
2025-05-13 13:54:09,830 - stpipe - INFO - Results used jwst version: 1.18.0
# Print out the time benchmark
time1 = time.perf_counter()
print(f"Runtime so far: {time1 - time0:0.0f} seconds")
print(f"Runtime for Image3: {time1 - time_image3:0.0f} seconds")
Runtime so far: 337 seconds
Runtime for Image3: 26 seconds
Verify which pipeline steps were run and reference files used#
if doimage3:
# Identify *_i2d file and open as datamodel
i2d = glob.glob(os.path.join(image3_dir, "*_i2d.fits"))[0]
i2d_f = datamodels.open(i2d)
# Check which steps were run
i2d_f.meta.cal_step.instance
# Check which reference files were used to calibrate the dataset
i2d_f.meta.ref_file.instance
{'assign_wcs': 'COMPLETE',
'charge_migration': 'SKIPPED',
'clean_flicker_noise': 'SKIPPED',
'dark_sub': 'COMPLETE',
'dq_init': 'COMPLETE',
'emicorr': 'COMPLETE',
'firstframe': 'COMPLETE',
'flat_field': 'COMPLETE',
'gain_scale': 'SKIPPED',
'group_scale': 'SKIPPED',
'ipc': 'SKIPPED',
'jump': 'COMPLETE',
'lastframe': 'COMPLETE',
'linearity': 'COMPLETE',
'outlier_detection': 'COMPLETE',
'photom': 'COMPLETE',
'ramp_fit': 'COMPLETE',
'refpix': 'SKIPPED',
'resample': 'COMPLETE',
'reset': 'COMPLETE',
'rscd': 'COMPLETE',
'saturation': 'COMPLETE',
'skymatch': 'COMPLETE',
'tweakreg': 'COMPLETE'}
{'area': {'name': 'crds://jwst_miri_area_0006.fits'},
'camera': {'name': 'N/A'},
'collimator': {'name': 'N/A'},
'crds': {'context_used': 'jwst_1364.pmap', 'sw_version': '12.1.5'},
'dark': {'name': 'crds://jwst_miri_dark_0103.fits'},
'dflat': {'name': 'N/A'},
'disperser': {'name': 'N/A'},
'distortion': {'name': 'crds://jwst_miri_distortion_0047.asdf'},
'emicorr': {'name': 'crds://jwst_miri_emicorr_0002.asdf'},
'fflat': {'name': 'N/A'},
'filteroffset': {'name': 'crds://jwst_miri_filteroffset_0008.asdf'},
'flat': {'name': 'crds://jwst_miri_flat_0785.fits'},
'fore': {'name': 'N/A'},
'fpa': {'name': 'N/A'},
'gain': {'name': 'crds://jwst_miri_gain_0034.fits'},
'ifufore': {'name': 'N/A'},
'ifupost': {'name': 'N/A'},
'ifuslicer': {'name': 'N/A'},
'linearity': {'name': 'crds://jwst_miri_linearity_0032.fits'},
'mask': {'name': 'crds://jwst_miri_mask_0036.fits'},
'msa': {'name': 'N/A'},
'ote': {'name': 'N/A'},
'photom': {'name': 'crds://jwst_miri_photom_0218.fits'},
'readnoise': {'name': 'crds://jwst_miri_readnoise_0085.fits'},
'regions': {'name': 'N/A'},
'reset': {'name': 'crds://jwst_miri_reset_0077.fits'},
'rscd': {'name': 'crds://jwst_miri_rscd_0017.fits'},
'saturation': {'name': 'crds://jwst_miri_saturation_0034.fits'},
'sflat': {'name': 'N/A'},
'specwcs': {'name': 'N/A'},
'wavelengthrange': {'name': 'N/A'}}
8. Visualize the drizzle-combined image#
We will use matplotlib routines for visualizing the data. Display the combined i2d image.
if doviz:
# Look at the final i2d image (combined mosaic)
sstring = os.path.join(image3_dir, '*i2d.fits')
miri_mosaic_file = glob.glob(sstring)
print(miri_mosaic_file)
# Read your mosaic image into an ImageModel datamodel
miri_mosaic = ImageModel(miri_mosaic_file[0])
# Autoscale the stretch
display_vals = [np.nanpercentile(miri_mosaic.data, 1), np.nanpercentile(miri_mosaic.data, 99)]
plt.figure(figsize=(8, 8))
fig, ax = plt.subplots(figsize=(8, 8))
# Set up image
cax = ax.imshow(miri_mosaic.data, cmap='Greys', origin='lower', vmin=display_vals[0], vmax=display_vals[1])
# Set up colorbar
cb = fig.colorbar(cax, fraction=0.046)
cb.ax.set_ylabel('MJy/str', fontsize=14)
# Set labels
ax.set_xlabel('X', fontsize=16)
ax.set_ylabel('Y', fontsize=16)
ax.set_title('Final MIRI mosaic', fontsize=16)
plt.tight_layout()
['./mir_im_demo_data/Obs001/stage3/image3_association_i2d.fits']
<Figure size 800x800 with 0 Axes>
Text(0, 0.5, 'MJy/str')
Text(0.5, 0, 'X')
Text(0, 0.5, 'Y')
Text(0.5, 1.0, 'Final MIRI mosaic')
<Figure size 800x800 with 0 Axes>
display_vals
[np.float32(4.006327), np.float32(5.483154)]
Visualize Detected Sources#
Using the source catalog created by the IMAGE3 stage of the pipeline,
mark the detected sources, using different markers for point sources
and extended sources. The source catalog is saved in
image3/image3_association_cat.ecsv file.
Read in catalog file and identify point/extended sources#
if doviz:
catalog_file = glob.glob(os.path.join(image3_dir, "*_cat.ecsv"))[0]
catalog = Table.read(catalog_file)
# find where sources are considered extended or point sources
pt_src, = np.where(~catalog['is_extended'])
ext_src, = np.where(catalog['is_extended'])
# Get x and y coordinates of the objects found
miri_x = catalog['xcentroid'][pt_src]
miri_y = catalog['ycentroid'][pt_src]
ext_x = catalog['xcentroid'][ext_src]
ext_y = catalog['ycentroid'][ext_src]
# Show catalog
catalog
Table length=739
| label | xcentroid | ycentroid | sky_centroid | aper_bkg_flux | aper_bkg_flux_err | aper30_flux | aper30_flux_err | aper50_flux | aper50_flux_err | aper70_flux | aper70_flux_err | aper_total_flux | aper_total_flux_err | aper30_abmag | aper30_abmag_err | aper50_abmag | aper50_abmag_err | aper70_abmag | aper70_abmag_err | aper_total_abmag | aper_total_abmag_err | aper30_vegamag | aper30_vegamag_err | aper50_vegamag | aper50_vegamag_err | aper70_vegamag | aper70_vegamag_err | aper_total_vegamag | aper_total_vegamag_err | CI_50_30 | CI_70_50 | CI_70_30 | is_extended | sharpness | roundness | nn_label | nn_dist | isophotal_flux | isophotal_flux_err | isophotal_abmag | isophotal_abmag_err | isophotal_vegamag | isophotal_vegamag_err | isophotal_area | semimajor_sigma | semiminor_sigma | ellipticity | orientation | sky_orientation | sky_bbox_ll | sky_bbox_ul | sky_bbox_lr | sky_bbox_ur |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| deg,deg | Jy | Jy | Jy | Jy | Jy | Jy | Jy | Jy | Jy | Jy | pix | Jy | Jy | pix2 | pix | pix | deg | deg | deg,deg | deg,deg | deg,deg | deg,deg | |||||||||||||||||||||||||||||||
| int32 | float64 | float64 | SkyCoord | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | bool | float64 | float32 | int32 | float64 | float64 | float32 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | float64 | SkyCoord | SkyCoord | SkyCoord | SkyCoord |
| 1 | 565.5772 | 13.8621 | 80.56167582487912,-69.43589096022993 | -1.792434e-09 | 4.063509e-09 | 1.018060e-05 | 2.362820e-07 | 2.209045e-05 | 3.594889e-07 | 4.583332e-05 | 6.524137e-07 | 6.610559e-05 | 9.409790e-07 | 21.380567 | 0.024911 | 20.539488 | 0.017526 | 19.747047 | 0.015346 | 19.349405 | 0.015346 | 16.996587 | 0.024911 | 16.155509 | 0.017526 | 15.363067 | 0.015346 | 14.965425 | 0.015346 | 2.1699 | 2.0748 | 4.5020 | True | 0.412044 | 0.252461 | 4 | 25.050965 | 6.125196e-05 | 8.643762e-07 | 19.432200 | 0.015215 | 15.048220 | 0.015215 | 103.0 | 3.310685 | 2.004696 | 0.394477 | 88.113995 | 346.070158 | 80.5609832583757,-69.43564789247372 | 80.56127587694084,-69.43613002279469 | 80.5620126880845,-69.43557080243825 | 80.56230532869286,-69.43605293102986 |
| 2 | 791.3872 | 14.0897 | 80.58105021767125,-69.43444607962323 | -9.146866e-09 | 4.463530e-09 | 5.162222e-06 | 2.078388e-07 | 8.553984e-06 | 3.106942e-07 | 1.253839e-05 | 5.842468e-07 | 1.808418e-05 | 8.426617e-07 | 22.117908 | 0.042856 | 21.569579 | 0.038736 | 21.154395 | 0.049448 | 20.756753 | 0.049448 | 17.733929 | 0.042856 | 17.185599 | 0.038736 | 16.770415 | 0.049448 | 16.372773 | 0.049448 | 1.6570 | 1.4658 | 2.4289 | False | 0.635086 | -0.166275 | 6 | 11.107157 | 1.044460e-05 | 4.194403e-07 | 21.352770 | 0.042749 | 16.968790 | 0.042749 | 27.0 | 1.328549 | 1.167515 | 0.121210 | -16.755215 | 241.200947 | 80.58075513698023,-69.43438662577921 | 80.58086502727205,-69.43456741224165 | 80.58135556190653,-69.43434158918343 | 80.58146545701823,-69.434522375267 |
| 3 | 1065.8198 | 17.6783 | 80.60465366413567,-69.43278696506695 | 5.710087e-09 | 5.234549e-09 | 3.663608e-06 | 2.089476e-07 | 5.762887e-06 | 3.125485e-07 | nan | nan | nan | nan | 22.490227 | 0.060222 | 21.998400 | 0.057343 | nan | nan | nan | nan | 18.106248 | 0.060222 | 17.614420 | 0.057343 | nan | nan | nan | nan | 1.5730 | nan | nan | False | 0.632754 | nan | 10 | 22.088503 | 6.333273e-06 | 3.514970e-07 | 21.895929 | 0.058646 | 17.511950 | 0.058646 | 18.0 | 1.083827 | 1.017501 | 0.061196 | -17.241282 | 240.714880 | 80.60441475171305,-69.43273628921447 | 80.6045248325417,-69.43291706073215 | 80.60492931974434,-69.43269761665447 | 80.60503940470213,-69.43287838784676 |
| 4 | 541.8024 | 21.7555 | 80.55978058254186,-69.43628153804646 | -1.158791e-08 | 3.986661e-09 | 1.077337e-06 | 1.817691e-07 | 2.328907e-06 | 2.817500e-07 | 5.758253e-06 | 5.694627e-07 | 8.305152e-06 | 8.213385e-07 | 23.819121 | 0.169277 | 22.982119 | 0.123994 | 21.999273 | 0.102391 | 21.601631 | 0.102391 | 19.435141 | 0.169277 | 18.598140 | 0.123994 | 17.615293 | 0.102391 | 17.217651 | 0.102391 | 2.1617 | 2.4725 | 5.3449 | True | 0.393676 | -0.700242 | 1 | 25.050965 | 3.171737e-06 | 3.022352e-07 | 22.646757 | 0.098823 | 18.262777 | 0.098823 | 16.0 | 1.973988 | 0.710603 | 0.640017 | 12.263362 | 270.219524 | 80.55945603197334,-69.43623478542604 | 80.55954746565533,-69.43638545200628 | 80.56014234165772,-69.43618339876095 | 80.56023377993236,-69.43633406498095 |
| 5 | 658.0748 | 22.3194 | 80.5697654527583,-69.43555138977563 | -3.326341e-08 | 3.170654e-09 | 4.100851e-06 | 2.025240e-07 | 6.424979e-06 | 2.930157e-07 | 9.858449e-06 | 5.373963e-07 | 1.421888e-05 | 7.750889e-07 | 22.367815 | 0.052338 | 21.880321 | 0.048420 | 21.415478 | 0.057628 | 21.017836 | 0.057628 | 17.983835 | 0.052338 | 17.496341 | 0.048420 | 17.031499 | 0.057628 | 16.633856 | 0.057628 | 1.5667 | 1.5344 | 2.4040 | False | 0.604802 | 0.627010 | 18 | 51.898954 | 6.624784e-06 | 3.396166e-07 | 21.847071 | 0.054280 | 17.463091 | 0.054280 | 19.0 | 1.127921 | 1.034247 | 0.083050 | 5.881611 | 263.837773 | 80.56949298408757,-69.43548298609313 | 80.5696027852525,-69.43566377965921 | 80.5700076806516,-69.43544441669452 | 80.57011748594898,-69.43562520993612 |
| 6 | 789.4885 | 25.0333 | 80.5810877947193,-69.4347880396943 | -1.149787e-08 | 3.466949e-09 | 6.318319e-06 | 1.641652e-07 | 1.043786e-05 | 2.451976e-07 | 1.532913e-05 | 4.776107e-07 | 2.210927e-05 | 6.888599e-07 | 21.898496 | 0.027850 | 21.353471 | 0.025210 | 20.936206 | 0.033312 | 20.538564 | 0.033312 | 17.514516 | 0.027850 | 16.969491 | 0.025210 | 16.552226 | 0.033312 | 16.154584 | 0.033312 | 1.6520 | 1.4686 | 2.4261 | False | 0.649055 | 0.309257 | 2 | 11.107157 | 1.399352e-05 | 3.828865e-07 | 21.035183 | 0.029308 | 16.651203 | 0.029308 | 34.0 | 1.610915 | 1.220451 | 0.242387 | -42.147436 | 215.808726 | 80.58076673575725,-69.43470080391077 | 80.58091325882894,-69.43494185250313 | 80.58145294547005,-69.43464933330071 | 80.58159947588652,-69.43489038131571 |
| 7 | 944.0429 | 27.9675 | 80.59439813467013,-69.4338815649351 | -5.986270e-09 | 3.112147e-09 | 1.372000e-06 | 1.363989e-07 | 2.238518e-06 | 2.094340e-07 | 3.159673e-06 | 4.148111e-07 | 4.557210e-06 | 5.982838e-07 | 23.556615 | 0.102905 | 23.025098 | 0.097106 | 22.650895 | 0.133928 | 22.253252 | 0.133928 | 19.172635 | 0.102905 | 18.641119 | 0.097106 | 18.266915 | 0.133928 | 17.869273 | 0.133928 | 1.6316 | 1.4115 | 2.3030 | False | 0.563399 | 0.302522 | 16 | 32.327101 | 1.277864e-06 | 1.276885e-07 | 23.633788 | 0.103406 | 19.249809 | 0.103406 | 5.0 | 0.621686 | 0.609388 | 0.019782 | 5.314419 | 263.270581 | 80.59423889813218,-69.43384728784697 | 80.59431223188611,-69.43396780648791 | 80.5945819736313,-69.43382152634787 | 80.59465530922088,-69.43394204484433 |
| 8 | 1040.4774 | 36.4312 | 80.6028242573723,-69.43351529827265 | 3.040333e-08 | 4.799268e-09 | 3.167745e-06 | 2.062966e-07 | 5.777754e-06 | 3.216661e-07 | 8.793054e-06 | 6.020373e-07 | 1.268226e-05 | 8.683210e-07 | 22.648124 | 0.068501 | 21.995602 | 0.058824 | 21.539651 | 0.071903 | 21.142008 | 0.071903 | 18.264145 | 0.068501 | 17.611623 | 0.058824 | 17.155671 | 0.071903 | 16.758029 | 0.071903 | 1.8239 | 1.5219 | 2.7758 | False | 0.345988 | 0.852507 | 10 | 23.340710 | 8.936639e-06 | 4.546117e-07 | 21.522065 | 0.053873 | 17.138085 | 0.053873 | 30.0 | 1.519687 | 1.225685 | 0.193462 | 42.505395 | 300.461557 | 80.60251512986834,-69.43344617131892 | 80.60264354328528,-69.43365707281878 | 80.60311548287397,-69.43340105973006 | 80.60324390191172,-69.43361196078708 |
| 9 | 825.7692 | 36.4838 | 80.58440957056901,-69.43489960009276 | -1.781155e-08 | 2.762766e-09 | 4.267015e-06 | 1.464886e-07 | 6.632902e-06 | 2.183378e-07 | 9.030790e-06 | 4.198831e-07 | 1.302515e-05 | 6.055991e-07 | 22.324690 | 0.036648 | 21.845741 | 0.035164 | 21.510686 | 0.049342 | 21.113043 | 0.049342 | 17.940710 | 0.036648 | 17.461761 | 0.035164 | 17.126706 | 0.049342 | 16.729064 | 0.049342 | 1.5545 | 1.3615 | 2.1164 | False | 0.594707 | -0.253770 | 15 | 23.240473 | 6.839685e-06 | 2.453777e-07 | 21.812410 | 0.038269 | 17.428430 | 0.038269 | 18.0 | 1.117432 | 0.975735 | 0.126807 | -2.798229 | 255.157933 | 80.58417858498389,-69.43485442924208 | 80.58427018608747,-69.43500508283299 | 80.584693240125,-69.43481581645854 | 80.58478484467129,-69.43496646977871 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 731 | 616.9605 | 1152.6357 | 80.58695131663895,-69.46987379790059 | 9.393466e-08 | 6.351908e-09 | 6.428060e-07 | 1.917124e-07 | 8.322333e-07 | 2.956629e-07 | nan | nan | nan | nan | 24.379800 | 0.283390 | 24.099387 | 0.330060 | nan | nan | nan | nan | 19.995820 | 0.283390 | 19.715407 | 0.330060 | nan | nan | nan | nan | 1.2947 | nan | nan | False | 0.647643 | nan | 732 | 5.342098 | 1.696792e-06 | 2.254954e-07 | 23.325928 | 0.135474 | 18.941948 | 0.135474 | 8.0 | 1.193440 | 0.481213 | 0.596785 | 0.240469 | 258.196631 | 80.58671907880537,-69.46985541622202 | 80.5867741396604,-69.46994580758098 | 80.5872345688177,-69.46981679592076 | 80.587289631745,-69.469907187117 |
| 732 | 622.3023 | 1152.5782 | 80.58740920186159,-69.46983768234674 | 8.960722e-08 | 5.383633e-09 | 4.525977e-07 | 1.951658e-07 | 8.003159e-07 | 2.963134e-07 | 8.126754e-07 | 5.874423e-07 | 1.172125e-06 | 8.472705e-07 | 24.760719 | 0.389260 | 24.141846 | 0.341996 | 24.125207 | 0.590619 | 23.727565 | 0.590619 | 20.376739 | 0.389260 | 19.757867 | 0.341996 | 19.741227 | 0.590619 | 19.343585 | 0.590619 | 1.7683 | 1.0154 | 1.7956 | False | -0.324542 | 0.182219 | 731 | 5.342098 | 1.173332e-06 | 2.147188e-07 | 23.726448 | 0.182461 | 19.342468 | 0.182461 | 7.0 | 1.030094 | 0.472917 | 0.540899 | 8.941238 | 266.897400 | 80.5872345688177,-69.46981679592076 | 80.587289631745,-69.469907187117 | 80.58766414241029,-69.46978461117281 | 80.58771920706448,-69.46987500223347 |
| 733 | 627.7883 | 1155.0304 | 80.58792554570209,-69.46987625319353 | 1.078113e-07 | 6.694492e-09 | 2.341071e-07 | 1.960717e-07 | 4.042966e-07 | 2.982068e-07 | nan | nan | nan | nan | 25.476463 | 0.660586 | 24.883250 | 0.599871 | nan | nan | nan | nan | 21.092484 | 0.660586 | 20.499270 | 0.599871 | nan | nan | nan | nan | 1.7270 | nan | nan | False | 1.423499 | nan | 732 | 6.009165 | 2.577129e-06 | 3.017500e-07 | 22.872160 | 0.120218 | 18.488180 | 0.120218 | 14.0 | 2.023443 | 0.868146 | 0.570956 | -66.554684 | 191.401478 | 80.58757822779486,-69.46979104820701 | 80.58770671190372,-69.47000196071801 | 80.58809371471403,-69.46975242536709 | 80.58822220365818,-69.46996333749846 |
| 734 | 964.1164 | 1153.3828 | 80.61678790669298,-69.46765921806484 | 1.089227e-07 | 5.252529e-09 | 4.455572e-07 | 1.933316e-07 | 7.974072e-07 | 2.992629e-07 | nan | nan | nan | nan | 24.777741 | 0.391304 | 24.145800 | 0.345990 | nan | nan | nan | nan | 20.393761 | 0.391304 | 19.761820 | 0.345990 | nan | nan | nan | nan | 1.7897 | nan | nan | False | -0.676120 | nan | 728 | 5.179332 | 2.033250e-06 | 2.682646e-07 | 23.129523 | 0.134557 | 18.745543 | 0.134557 | 11.0 | 1.084746 | 0.752988 | 0.305840 | 75.689351 | 333.645513 | 80.61661442952222,-69.46761292121438 | 80.61670639812688,-69.46776355772423 | 80.61695801789638,-69.46758711562997 | 80.61704998880205,-69.46773775195861 |
| 735 | 478.6819 | 1153.8086 | 80.57509210148523,-69.47079879241485 | 2.478914e-08 | 4.960245e-09 | 8.484562e-07 | 1.899387e-07 | 1.792417e-06 | 2.918713e-07 | 4.121250e-06 | 5.815341e-07 | 5.944096e-06 | 8.387491e-07 | 24.078426 | 0.219333 | 23.266403 | 0.163797 | 22.362428 | 0.143315 | 21.964785 | 0.143315 | 19.694447 | 0.219333 | 18.882423 | 0.163797 | 17.978448 | 0.143315 | 17.580806 | 0.143315 | 2.1126 | 2.2993 | 4.8574 | True | 0.651124 | -0.143288 | 699 | 36.184571 | 1.137534e-06 | 1.937183e-07 | 23.760089 | 0.170740 | 19.376110 | 0.170740 | 6.0 | 0.752359 | 0.663020 | 0.118746 | -24.467100 | 233.489062 | 80.57496655650841,-69.47076696365187 | 80.57503990819225,-69.47088749040276 | 80.57531024542021,-69.47074124010544 | 80.57538359894659,-69.47086176671186 |
| 736 | 577.8803 | 1154.4982 | 80.58362787308106,-69.47018143135209 | 8.224251e-08 | 4.640034e-09 | 4.629541e-07 | 1.878862e-07 | 9.764451e-07 | 2.920392e-07 | nan | nan | nan | nan | 24.736155 | 0.369841 | 23.925880 | 0.284093 | nan | nan | nan | nan | 20.352175 | 0.369841 | 19.541901 | 0.284093 | nan | nan | nan | nan | 2.1092 | nan | nan | False | 0.646516 | 0.934725 | 727 | 8.360562 | 1.453133e-06 | 2.226885e-07 | 23.494237 | 0.154806 | 19.110257 | 0.154806 | 8.0 | 1.325016 | 0.563937 | 0.574392 | 82.773365 | 340.729527 | 80.58347261482685,-69.47013010688951 | 80.58358271105968,-69.47031089163875 | 80.58381628333645,-69.47010436658645 | 80.58392638233256,-69.47028515111882 |
| 737 | 742.4447 | 1154.7956 | 80.59777158187215,-69.4691308354995 | 9.766017e-08 | 1.100970e-08 | 8.861377e-07 | 1.947222e-07 | 1.698463e-06 | 3.022326e-07 | nan | nan | nan | nan | 24.031247 | 0.215670 | 23.324860 | 0.177812 | nan | nan | nan | nan | 19.647267 | 0.215670 | 18.940880 | 0.177812 | nan | nan | nan | nan | 1.9167 | nan | nan | False | 0.516379 | nan | 730 | 6.340521 | 5.155949e-06 | 4.134313e-07 | 22.119228 | 0.083746 | 17.735249 | 0.083746 | 26.0 | 1.756211 | 1.097792 | 0.374909 | -25.987727 | 231.968436 | 80.5974764385076,-69.46908064126312 | 80.59758664732676,-69.4692614171703 | 80.59816370746027,-69.4690291048092 | 80.59827392180419,-69.46920988028214 |
| 738 | 588.3587 | 1155.9769 | 80.58455528011976,-69.4701585556248 | 9.936698e-08 | 5.960312e-09 | 3.286612e-07 | 1.850256e-07 | nan | nan | nan | nan | nan | nan | 25.108129 | 0.484875 | nan | nan | nan | nan | nan | nan | 20.724149 | 0.484875 | nan | nan | nan | nan | nan | nan | nan | nan | nan | False | nan | nan | 736 | 10.582194 | 2.312021e-06 | 2.732106e-07 | 22.990021 | 0.121269 | 18.606041 | 0.121269 | 12.0 | 1.436127 | 0.719363 | 0.499095 | 12.281541 | 270.237703 | 80.58428256842443,-69.4701324516838 | 80.58435597026403,-69.4702529745169 | 80.58479806947808,-69.47009383858205 | 80.58487147408091,-69.47021436119825 |
| 739 | 734.1859 | 1155.7786 | 80.59708013042236,-69.46921365506797 | 1.085662e-07 | 7.200338e-09 | 3.511228e-07 | 1.932242e-07 | nan | nan | nan | nan | nan | nan | 25.036352 | 0.476042 | nan | nan | nan | nan | nan | nan | 20.652373 | 0.476042 | nan | nan | nan | nan | nan | nan | nan | nan | nan | False | nan | nan | 737 | 8.317101 | 9.432173e-07 | 1.806442e-07 | 23.963471 | 0.190253 | 19.579491 | 0.190253 | 5.0 | 0.994006 | 0.347426 | 0.650479 | 45.071935 | 303.028098 | 80.59691180992077,-69.46918599220943 | 80.59698527945035,-69.4693065097264 | 80.59725544717521,-69.46916022543307 | 80.59732891854644,-69.46928074280532 |
Mark the extended and point sources on the image#
Display combined image with point sources marked with red dots and extended sources marked with blue triangles. You will see that there are a grouping of sources near the top edge of the MIRI image, several of which may be spurious sources, which tend to be found near image edges.
if doviz:
# Look at mosaic data and sources found with source_catalog
fig, ax = plt.subplots(figsize=(8, 8))
# Set up image
cax = ax.imshow(miri_mosaic.data, cmap='Greys', origin='lower', vmin=display_vals[0], vmax=display_vals[1])
ax.scatter(miri_x, miri_y, lw=1, s=10, color='red') # overplot point source positions
ax.scatter(ext_x, ext_y, lw=1, s=20, color='blue', marker='v') # overplot extended source positions
# Set up colorbar
cb = fig.colorbar(cax, fraction=0.046)
cb.ax.set_ylabel('MJy/str', fontsize=14)
# Set labels
ax.set_xlabel('X', fontsize=16)
ax.set_ylabel('Y', fontsize=16)
ax.set_title('Final MIRI mosaic', fontsize=16)
plt.tight_layout()
<matplotlib.collections.PathCollection at 0x7fa58471a7b0>
<matplotlib.collections.PathCollection at 0x7fa55100f750>
Text(0, 0.5, 'MJy/str')
Text(0.5, 0, 'X')
Text(0, 0.5, 'Y')
Text(0.5, 1.0, 'Final MIRI mosaic')
