NIRSpec MOS Pipeline Notebook#
Authors: Dan Coe (dcoe@stsci.edu), Kayli Glidic (kglidic@stsci.edu), NIRSpec branch, with contributions from the NIRSpec team, including Elena Manjavacas, Peter Zeidler, Melanie Clarke, James Muzerolle, Nikolay Nikolov, Chris Hayes, and Alaina Henry, who designed the ERO NIRSpec observations.
Last Updated: April 16, 2025
Pipeline Version: 1.18.1 (Build 11.3, Context jwst_1364.pmap)
Purpose:
End-to-end calibration with the James Webb Space Telescope (JWST) pipeline is divided into three main processing stages. This notebook provides a framework for processing generic Near-Infrared Spectrograph (NIRSpec) multi-object spectroscopy (MOS) data through stages 1-3 of the JWST pipeline, including how to use associations for multi-exposure observations and how to interact and work with JWST datamodels. In most cases, editing cells outside the Configuration section is unnecessary unless the standard pipeline processing options or plot parameters need to be modified.
Data:
This notebook is set up to use observations of galaxy cluster SMACS0723 with the G395M grism obtained by Proposal ID (PID) 2736, Observation 7. The demo data will automatically download unless disabled (i.e., to use local files instead).
JWST pipeline version and CRDS context:
This notebook was written for the above-specified pipeline version and associated build context for this version of the JWST Calibration Pipeline. Information about this and 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.
Please note that pipeline software development is a continuous process, so results in some cases may be slightly different if a subsequent version is used. For optimal results, users are strongly encouraged to reprocess their data using the most recent pipeline version and associated CRDS context, taking advantage of bug fixes and algorithm improvements. Any known issues for this build are noted in the notebook.
Updates:
This notebook is regularly updated to incorporate the latest pipeline improvements. Find the most up-to-date version of this notebook here.
Recent Changes:
October 15, 2024: Converted notebook to follow standard template (original).
November 4, 2024: Notebook updated to JWST pipeline version 1.16.0 (Build 11.1).
January 12, 2024: Added an example for association file creation.
February 19, 2025: Updated JWST pipeline version 1.17.1 (Build 11.2). Changed code to create all associations instead of using the MAST downloads.
April 16, 2025: Updated JWST pipeline version 1.18.0 (Build 11.3) and added Jdaviz plotting options.
Table of Contents#
1. Configuration
2. Package Imports
3. Demo Mode Setup
4. Directory Setup
5. Stage 1:
Detector1Pipeline(calwebb_detector1)5.1 Configure
Detector1Pipeline5.2 Run
Detector1Pipeline
6. Stage 2:
Spec2Pipeline(calwebb_spec2)6.1 Configure
Spec2Pipeline6.2 Create
Spec2PipelineAssociation Files6.3 MSA Metadata File
6.4 Run
Spec2Pipeline
7. Stage 3:
Spec3Pipeline(calwebb_spec3)7.1 Configure
Spec3Pipeline7.2 Create
Spec3PipelineAssociation Files7.3 Run
Spec3Pipeline
8. Visualize the Data
8.1 Display
Detector1PipelineProducts8.2 Display
Spec2PipelineProducts8.3 Display
Spec3PipelineProducts
9. Modifying the EXTRACT1D Reference File (as needed)
1. Configuration#
Install dependencies and parameters#
To make sure that the pipeline version is compatible with the steps discussed below and that the required dependencies and packages get installed, you can create a fresh conda environment and install the provided requirements.txt file before starting this notebook:
conda create -n nirspec_mos_pipeline python=3.12
conda activate nirspec_mos_pipeline
pip install -r requirements.txt
Set the basic parameters to configure the notebook#
These parameters determine what data gets used, where data is located (if already on disk), and the type of background subtraction (if any). The list of parameters includes:
demo_mode:True: Downloads example data from the Barbara A. Mikulski Archive for Space Telescopes (MAST) and processes it through the pipeline. All processing will occur in a local directory unless modified in Section 3 below.False: Process your own downloaded data; provide its location.
Directories with data:
sci_dir: Directory where science observation data is stored.
Backgroud subtraction methods (
True= run,False= skip):master_bg: Apply master-background subtraction incalwebb_spec2? Uses “blank sky” shutters defined in the observation.pixel_bg: Apply pixel-to-pixel background subtraction incalwebb_spec2. This is the default pipeline setting. Uses nodded observations.
# Basic import necessary for configuration.
# Uncomment logging to hide log information.
import os
import warnings
#import logging
# Control logging level: INFO, WARNING, ERROR
# Run command logging.disable if want to hide logging
# ERROR messages.
#logging.disable(logging.ERROR)
warnings.simplefilter("ignore", RuntimeWarning)
Note that demo_mode must be set appropriately below.
# Set parameters for demo_mode, data mode directories, and processing steps.
# -------------------------------DEMO MODE-----------------------------------
demo_mode = True
if demo_mode:
print('Running in demonstration mode using online example data!')
# --------------------------User Mode Directories----------------------------
else: # If demo_mode = False, look for user data in these paths.
# Set directory paths for processing specific data; adjust to your local
# directory setup (examples provided below).
basedir = os.path.abspath(os.path.join(os.getcwd(), ''))
# Directory to science observation data; expects uncalibrated data in
# sci_dir/uncal/ and results in stage1, stage2, and stage3 directories.
sci_dir = os.path.join(basedir, 'mos_data_02736/Obs007', '')
# --------------------------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
dospec2 = True # calwebb_spec2
dospec3 = True # calwebb_spec3
doviz = True # Visualize calwebb outputs
# ---------------------------Set Processing Steps----------------------------
# How should background subtraction be done?
# If none are selected, data will not be background subtracted.
# pixel_bg - True for nodded observations.
# master_bg - True if using "blank sky" sutters in the science observation.
master_bg = False # Master-background subtraction in spec2.
pixel_bg = True # Pixel-based background subtraction in spec2.
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 local CRDS cache directory has not been set, it will automatically be created in the home directory.
Build Context Table
# ------------------------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.
#os.environ['CRDS_CONTEXT'] = 'jwst_1364.pmap' # CRDS context for 1.18.0
# Set CRDS cache directory to user home if not already set.
if os.getenv('CRDS_PATH') is None:
os.environ['CRDS_PATH'] = os.path.join(os.path.expanduser('~'), 'crds_cache')
# 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'
# Output the current CRDS path and server URL in use.
print('CRDS local filepath:', os.environ['CRDS_PATH'])
print('CRDS file server:', os.environ['CRDS_SERVER_URL'])
CRDS local filepath: /home/runner/crds_cache
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, JSON
display(HTML("<style>.container { width:95% !important; }</style>"))
# ----------------------General Imports----------------------
import time
import glob
import json
import itertools
import numpy as np
# ----------------------Astropy Imports----------------------
# Astropy utilities for opening FITS files, downloading demo files, etc.
from astropy.io import fits
from astropy.stats import sigma_clip
from astropy.visualization import ImageNormalize, ManualInterval, LogStretch
from astropy.visualization import LinearStretch, AsinhStretch, simple_norm
# -------------------- Astroquery Imports ----------------------
from astroquery.mast import Observations
# ----------------------Plotting Imports---------------------
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
from matplotlib.collections import PatchCollection
from jdaviz import Mosviz
Installation instructions for the JWST pipeline found here: JDox • ReadtheDocs • Github
# ----------------------JWST Calibration Pipeline Imports----------------------
import jwst # Import the base JWST and CRDS packages.
import crds
from crds.client import api
from stpipe import crds_client
# JWST pipelines (each encompassing many steps).
from jwst.pipeline import Detector1Pipeline # calwebb_detector1
from jwst.pipeline import Spec2Pipeline # calwebb_spec2
from jwst.pipeline import Spec3Pipeline # calwebb_spec3
from jwst.extract_1d import Extract1dStep # Extract1D Step
# JWST pipeline utilities
from jwst import datamodels # JWST pipeline utilities: datamodels.
from jwst.associations import asn_from_list as afl # Tools for creating association files.
from jwst.associations.lib.rules_level2_base import DMSLevel2bBase # Define Lvl2 ASN.
from jwst.associations.lib.rules_level3_base import DMS_Level3_Base # Define Lvl3 ASN.
default_context = crds.get_default_context('jwst', state='build')
print("JWST Calibration Pipeline Version = {}".format(jwst.__version__))
print(f"Default CRDS Context for JWST Version {jwst.__version__}: {default_context}")
print(f"Using CRDS Context: {os.environ.get('CRDS_CONTEXT', default_context)}")
CRDS - INFO - Calibration SW Found: jwst 1.18.0 (/usr/share/miniconda/lib/python3.13/site-packages/jwst-1.18.0.dist-info)
JWST Calibration Pipeline Version = 1.18.0
Default CRDS Context for JWST Version 1.18.0: jwst_1364.pmap
Using CRDS Context: jwst_1364.pmap
Define Convience Functions#
Define a function that identifies unique MSA files.
# Find unique files to download.
def unique_files_to_array(files):
"""
Checks for unique files and adds them to an array.
Parameters
----------
files : list of lists
The input files.
Returns
-------
list : An array of unique files.
"""
unique_files = set()
for row in files:
for element in row:
if isinstance(element, str):
unique_files.add(element)
return list(unique_files)
Define a function that filters files based on detector, filter, and grating.
def get_matching(files, detector, filt, grating, exp_type):
"""
Filters a list of FITS files to find those with matching
detector, filter, and grating for a specified exposure type.
Parameters
----------
files : list of str
Paths to FITS files to check.
detector : str
Expected value of the DETECTOR keyword.
filt : str
Expected value of the FILTER keyword.
grating : str
Expected value of the GRATING keyword.
exp_type : str, optional
The exposure type to match.
Returns
-------
files_regular : list of str
Files with matching configuration and IS_IMPRT == False or missing.
files_imprint : list of str)
Files with matching configuration and IS_IMPRT == True.
"""
files_regular, files_imprint = [], []
for file in files:
# Skip if EXP_TYPE doesn't match the provided one.
if fits.getval(file, 'EXP_TYPE') != exp_type:
files_regular.append(file)
continue
# Check if DETECTOR, FILTER, and GRATING match
if (fits.getval(file, 'DETECTOR') == detector and fits.getval(file, 'FILTER') == filt and fits.getval(file, 'GRATING') == grating):
try:
is_imprt = fits.getval(file, 'IS_IMPRT') # Only IFU and MOS observations have imprint exposures.
except KeyError:
is_imprt = None
(files_imprint if is_imprt else files_regular).append(file)
return files_regular, files_imprint
# Start a timer to keep track of runtime.
time0 = time.perf_counter()
3. Demo Mode Setup (ignore if not using demo data)#
The data in this notebook is public and does not require a token. For other data sets, you may need to provide a token. For more infomation visit the astroquery documentation.
If running in demonstration mode, set up the program information to retrieve the uncalibrated data (_uncal.fits) automatically from MAST using astroquery. MAST provides flexibility by allowing searches based on proposal ID and observation ID, rather than relying solely on filenames. More information about the JWST file naming conventions can be found here.
The MOS demo data in this notebook is from “JWST’s First Deep Field”, JWST Early Release Observation (ERO) program 2736 and features observations of galaxy cluster SMACS0723 with NIRCam, NIRSpec, and MIRI. This program includes two identical MOS observations (7 and 8) with confirmation images taken after target acquisition (20 groups | NRSIRS2RAPID | 306 [s]). More of the program setup is briefly summarized in the table below.
Demo Target: SMACS0723 |
||
|---|---|---|
PROGRAM |
02736 |
Program number |
OBSERVTN |
007 |
Observation number |
G395M/F290LP |
λ: 2.87–5.10 μm (a medium resolution, R ~ 1000) |
|
G235M/F170LP |
λ: 1.66–3.07 μm (a medium resolution, R ~ 1000) |
|
SUBARRAY |
FULL |
Subarray used (2048 x 2048) |
NINTS |
2 |
Number of integrations in exposure |
NGROUPS |
20 |
Number of groups in integration |
READPATT |
NRSIRS2 |
Readout pattern |
NOD_TYPE |
3-SHUTTER-SLITLET |
Nod pattern type |
NUMDTHPT |
3 |
Total number of points in pattern |
SRCTYAPT |
UNKNOWN |
Source type selected in APT |
TOTAL DURATION |
NOD_TYPE x NINTS x NGROUPS = 8841 [s] (~2.5 hrs) |
Total duration (per grating and observation) |
Note: The presence of a physical gap between detectors affects all MOS observations (any resolution) because the spectra can be long enough to span both NIRSpec detectors. More Info …
# Set up the program information and directories to collect
# the data in demo_mode.
if demo_mode:
print('Running in demonstration mode. '
'Example data will be downloaded from MAST!')
# NOTE:
# For non public data sets, you may need to provide a token.
# However, for security it is not recommended to enter tokens into
# a terminal or Jupyter notebook.
#Observations.login(token="your-token")
# --------------Program and observation information--------------
program = "02736"
sci_observtn = "007"
filters = ["F290LP;G395M"]
# ----------Define the base and observation directories----------
basedir = os.path.abspath(os.path.join(os.getcwd(), ''))
sci_dir = os.path.join(basedir, f'mos_data_{program}')
sci_dir = os.path.join(sci_dir, f'Obs{sci_observtn}')
uncal_dir = os.path.join(sci_dir, 'uncal/')
asn_dir = os.path.join(sci_dir, 'asn/') # Keep MSA files in the association directory.
# ----Ensure directories for downloading MAST data exists--------
os.makedirs(uncal_dir, exist_ok=True)
os.makedirs(asn_dir, exist_ok=True)
Running in demonstration mode. Example data will be downloaded from MAST!
Click on the following links to learn more about querying and downloading data:
• Downloading data
• Observations Class
• Products Field Descriptions
Compile a table of files from MAST associated with the science (SCI) observation.
# Obtain a list of observation IDs for the specified demo program.
if demo_mode:
# --------------------SCIENCE Observation--------------------
sci_obs_id_table = Observations.query_criteria(instrument_name=['NIRSPEC/MSA'],
provenance_name=["CALJWST"],
obs_id=[f'*{program}*{sci_observtn}*'])
Filter these tables to identify uncalibrated and metadata files to download from MAST.
The demo dataset consists of six _uncal.fits files, each approximately 500 MB in size.
# Convert visits into a list of uncalibrated data and ASN files.
if demo_mode:
file_criteria = {'filters': filters, 'calib_level': [1],
'productSubGroupDescription': 'UNCAL'}
# Initialize lists for science and metadata files.
sci_downloads, msa_downloads = [], []
pfilter = Observations.filter_products # Alias for filter_products method.
# ----Identify uncalibrated SCIENCE files associated with each visit-----
for exposure in sci_obs_id_table:
sci_products = Observations.get_product_list(exposure)
# Filter for full-size science files (exclude smaller confirmation images).
avg_sci_size = np.nanmean(sci_products['size'])
sci_products_avg = sci_products[sci_products['size'] > avg_sci_size]
sci_downloads.extend(pfilter(sci_products_avg, **file_criteria)['dataURI'])
# Identifies association metadata files.
msa_files = {
f['productFilename'] for f in sci_products
if 'AUXILIARY' in f['productType'] and 'metadata' in f['description']}
msa_downloads.append(msa_files)
# Filter out other observations and remove duplicates.
msa_downloads = unique_files_to_array(msa_downloads)
sci_downloads = {f for f in sci_downloads if f"jw{program}{sci_observtn}" in f}
msa_mast_downloads = [
f"mast:JWST/product/{f}" for f in msa_downloads
if f"jw{program}{sci_observtn}" in f
]
print(f"Science files selected for downloading: {len(sci_downloads)}")
print(f"MSA files selected for downloading: {len(msa_mast_downloads)}")
Science files selected for downloading: 6
MSA files selected for downloading: 1
Download the data.
Warning: If this notebook is halted during this step, the downloaded file may be incomplete, and cause crashes later on!
# Download data and place them into the appropriate directories.
if demo_mode:
for file in sci_downloads:
sci_manifest = Observations.download_file(file, local_path=uncal_dir)
for file in msa_mast_downloads:
msa_manifest = Observations.download_file(file, local_path=asn_dir)
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw02736007001_03103_00003_nrs2_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00003_nrs2_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw02736007001_03103_00003_nrs1_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00003_nrs1_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw02736007001_03103_00002_nrs2_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00002_nrs2_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw02736007001_03103_00001_nrs2_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00001_nrs2_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw02736007001_03103_00002_nrs1_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00002_nrs1_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw02736007001_03103_00001_nrs1_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00001_nrs1_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw02736007001_01_msa.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_01_msa.fits ...
[Done]
Galaxies of Interest#
There are several galaxies of interest in the demo data. Here we will look at some of them (source_ids provided below).
6355: z = 7.665 (13.0 Gyr ago)
We’ll look at this galaxy in this notebook.
Excellent spectrum with bright lines.
5-shutter slitlet (rather than standard 3-shutter slitlet), so 1D extraction can be improved significantly.
Not a multiple image of 10612 (described below), which has a similar redshift.
5144: z = 6.383 (12.8 Gyr ago)
The following galaxies have been featured in the press release:
4590: z = 8.498 (13.1 Gyr ago)
10612: z = 7.663 (13.0 Gyr ago)
8140: z = 5.275 (12.6 Gyr ago)
9922: z = 2.743 (11.3 Gyr ago)
and presented and studied in papers including Katz et al. 2023, Curti et al. 2023, Carnall et al. 2023.
4. Directory Setup#
Set up detailed paths to input/output stages here.
# Define/create output subdirectories to keep data products organized.
# -----------------------------Science Directories------------------------------
uncal_dir = os.path.join(sci_dir, 'uncal/') # Uncalibrated pipeline inputs.
det1_dir = os.path.join(sci_dir, 'stage1/') # calwebb_detector1 pipeline outputs.
spec2_dir = os.path.join(sci_dir, 'stage2/') # calwebb_spec2 pipeline outputs.
spec3_dir = os.path.join(sci_dir, 'stage3/') # calwebb_spec3 pipeline outputs.
asn_dir = os.path.join(sci_dir, 'asn/') # Associations directory.
# Creates the directories if target directory does not exist.
os.makedirs(det1_dir, exist_ok=True)
os.makedirs(spec2_dir, exist_ok=True)
os.makedirs(spec3_dir, exist_ok=True)
os.makedirs(asn_dir, exist_ok=True)
# Print out the time benchmark.
time1 = time.perf_counter()
print(f"Runtime so far: {round((time1 - time0) / 60.0, 1):0.4f} min")
Runtime so far: 36.7000 min
5. Stage 1: Detector1Pipeline (calwebb_detector1)#
In this section, we process the data through the calwebb_detector1 pipeline to create Stage 1 data products.
Input: Raw exposure (
_uncal.fits) containing original data from all detector readouts (ncols x nrows x ngroups x nintegrations).Output: Uncalibrated countrate (slope) image in units of DN/s:
_rate.fits: A single countrate image averaged over multiple integrations (if available)._rateints.fits: Countrate images for each integration, saved in multiple extensions.
The Detector1Pipeline applies basic detector-level corrections on a group-by-group basis, followed by ramp fitting for all exposure types, commonly referred to as “ramps-to-slopes” processing.
5.1 Configure Detector1Pipeline#
The Detector1Pipeline has the following steps available for NIRSpec MOS:
group_scale: Rescales pixel values to correct for improper onboard frame averaging.dq_init: Initializes the data quality (DQ) flags for the input data.saturation: Flags pixels at or below the A/D floor or above the saturation threshold.superbias: Subtracts the superbias reference file from the input data.refpix: Use reference pixels to correct bias drifts.linearity: Applies a correction for non-linear detector response.dark_current: Subtracts the dark current reference file from the input data.jump: Performs CR/jump detection on each ramp integration within an exposure.clean_flicker_noise: Removes flicker (1/f) noise from calibrated ramp images (similar tonscleanin spec2).ramp_fit: Determines the mean count rate (counts per second) for each pixel by performing a linear fit to the input data.gain_scale: Corrects pixel values for non-standard gain settings, primarily in NIRSpec subarray data.
For more information about each step and a full list of step arguments, please refer to the official documentation: JDox and ReadtheDocs
Below, we set up a dictionary that defines how the Detector1Pipeline should be configured for MOS data. We follow the CEERS NIRSpec reduction parameters to improve the rejection of cosmic rays and snowballs during the jump step.
To override specific steps and reference files, use the examples below.
# Set up a dictionary to define how the Detector1 pipeline should be configured.
# -------------------------Boilerplate dictionary setup-------------------------
det1dict = {}
det1dict['group_scale'], det1dict['dq_init'], det1dict['saturation'] = {}, {}, {}
det1dict['superbias'], det1dict['refpix'] = {}, {}
det1dict['linearity'], det1dict['dark_current'], det1dict['jump'] = {}, {}, {}
det1dict['clean_flicker_noise'], det1dict['ramp_fit'] = {}, {}
det1dict['gain_scale'] = {}
# ---------------------------Override reference files---------------------------
# Overrides for various reference files (example).
# Files should be in the base local directory or provide full path.
#det1dict['dq_init']['override_mask'] = 'myfile.fits' # Bad pixel mask
#det1dict['superbias']['override_superbias'] = 'myfile.fits' # Bias subtraction
#det1dict['dark_current']['override_dark'] = 'myfile.fits' # Dark current subtraction
# -----------------------------Set step parameters------------------------------
# Overrides for whether or not certain steps should be skipped (example).
det1dict['linearity']['skip'] = False # This is the default.
# Turn on multi-core processing (off by default).
# Choose what fraction of cores to use (quarter, half, or all).
det1dict['jump']['maximum_cores'] = 'half'
#det1dict['ramp_fit']['maximum_cores'] = 'half'
# Turn on detection of cosmic ray snowballs (on by default)
# and change some parameters.
det1dict['jump']['expand_large_events'] = True
det1dict['jump']['expand_factor'] = 3 # (default 2)
det1dict['jump']['min_sat_area'] = 15 # (default 1)
det1dict['jump']['min_jump_area'] = 15 # (default 5)
Many exposures are affected by artifacts known as snowballs caused by large cosmic ray events. These artifacts are particularly significant in deep exposures with long integration times, with an estimated rate of one snowball per detector (FULL FRAME) per 20 seconds. To expand the number of pixels flagged as jumps around large cosmic ray events, set expand_large_events to True. An expand_factor of 3 works well for NIRSpec observations to cover most snowballs.
# Turn on 1/f noise correction in Stage 1? (off by default).
#det1dict['clean_flicker_noise']['skip'] = False
JWST detector readout electronics (a.k.a. SIDECAR ASICs) generate significant 1/f noise during detector operations and signal digitization. This noise manifests as faint banding along the detector’s slow axis and varies from column to column. For NIRSpec data, the primary pipeline algorithm to address 1/f noise is nsclean in the Spec2Pipeline (Rauscher 2023) but is off by default.
An additional 1/f noise-cleaning algorithm, clean_flicker_noise, has been implemented at the group stage in the Detector1Pipeline. This step is also off by default.
5.2 Run Detector1Pipeline#
Run the science files through the calwebb_detector1 pipeline using the .call() method.
We use .call() instead of .run() to ensure that the latest default parameters set via reference files in CRDS are applied (ReadtheDocs).
This stage takes approximately 25 minutes to process six _uncal.fits files (~4 minutes per file) and generate _rate.fits files.
# Final list of UNCAL files ready for Stage 1 processing.
uncal_sci = sorted(glob.glob(uncal_dir + '*uncal.fits'))
print(f"Science UNCAL Files:\n{'-' * 20}\n" + "\n".join(uncal_sci))
Science UNCAL Files:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00001_nrs1_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00001_nrs2_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00002_nrs1_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00002_nrs2_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00003_nrs1_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00003_nrs2_uncal.fits
time_det1 = time.perf_counter() # Tracks runtime for Stage 1.
# Run Stage 1 pipeline using the custom det1dict dictionary.
if dodet1:
# --------------------------Science UNCAL files--------------------------
for uncal_file in uncal_sci:
print(f"Applying Stage 1 Corrections & Calibrations to: "
f"{os.path.basename(uncal_file)}")
det1_result = Detector1Pipeline.call(uncal_file,
save_results=True,
steps=det1dict,
output_dir=det1_dir)
print("Stage 1 has been completed! \n")
else:
print('Skipping Detector1 processing for SCI data.')
Applying Stage 1 Corrections & Calibrations to: jw02736007001_03103_00001_nrs1_uncal.fits
2025-05-13 14:26:26,456 - 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 14:26:26,810 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_system_datalvl_0002.rmap 694 bytes (1 / 204 files) (0 / 741.0 K bytes)
2025-05-13 14:26:26,886 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_system_calver_0048.rmap 5.3 K bytes (2 / 204 files) (694 / 741.0 K bytes)
2025-05-13 14:26:26,934 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_system_0047.imap 385 bytes (3 / 204 files) (6.0 K / 741.0 K bytes)
2025-05-13 14:26:26,981 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_wavelengthrange_0024.rmap 1.4 K bytes (4 / 204 files) (6.4 K / 741.0 K bytes)
2025-05-13 14:26:27,052 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_wavecorr_0005.rmap 884 bytes (5 / 204 files) (7.8 K / 741.0 K bytes)
2025-05-13 14:26:27,112 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_superbias_0079.rmap 36.0 K bytes (6 / 204 files) (8.6 K / 741.0 K bytes)
2025-05-13 14:26:27,170 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_sirskernel_0001.rmap 630 bytes (7 / 204 files) (44.6 K / 741.0 K bytes)
2025-05-13 14:26:27,230 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_sflat_0026.rmap 20.6 K bytes (8 / 204 files) (45.3 K / 741.0 K bytes)
2025-05-13 14:26:27,357 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_saturation_0018.rmap 2.0 K bytes (9 / 204 files) (65.9 K / 741.0 K bytes)
2025-05-13 14:26:27,427 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_refpix_0015.rmap 1.6 K bytes (10 / 204 files) (67.9 K / 741.0 K bytes)
2025-05-13 14:26:27,525 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_readnoise_0025.rmap 2.6 K bytes (11 / 204 files) (69.5 K / 741.0 K bytes)
2025-05-13 14:26:27,574 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pictureframe_0001.rmap 675 bytes (12 / 204 files) (72.0 K / 741.0 K bytes)
2025-05-13 14:26:27,625 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_photom_0013.rmap 958 bytes (13 / 204 files) (72.7 K / 741.0 K bytes)
2025-05-13 14:26:27,672 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pathloss_0008.rmap 1.2 K bytes (14 / 204 files) (73.7 K / 741.0 K bytes)
2025-05-13 14:26:27,746 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-whitelightstep_0001.rmap 777 bytes (15 / 204 files) (74.9 K / 741.0 K bytes)
2025-05-13 14:26:27,793 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-spec2pipeline_0013.rmap 2.1 K bytes (16 / 204 files) (75.6 K / 741.0 K bytes)
2025-05-13 14:26:27,840 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-resamplespecstep_0002.rmap 709 bytes (17 / 204 files) (77.8 K / 741.0 K bytes)
2025-05-13 14:26:27,893 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-outlierdetectionstep_0005.rmap 1.1 K bytes (18 / 204 files) (78.5 K / 741.0 K bytes)
2025-05-13 14:26:27,957 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-jumpstep_0005.rmap 810 bytes (19 / 204 files) (79.6 K / 741.0 K bytes)
2025-05-13 14:26:28,075 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-image2pipeline_0008.rmap 1.0 K bytes (20 / 204 files) (80.4 K / 741.0 K bytes)
2025-05-13 14:26:28,139 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-detector1pipeline_0003.rmap 1.1 K bytes (21 / 204 files) (81.4 K / 741.0 K bytes)
2025-05-13 14:26:28,213 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-darkpipeline_0003.rmap 872 bytes (22 / 204 files) (82.5 K / 741.0 K bytes)
2025-05-13 14:26:28,269 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_pars-darkcurrentstep_0003.rmap 1.8 K bytes (23 / 204 files) (83.4 K / 741.0 K bytes)
2025-05-13 14:26:28,331 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_ote_0030.rmap 1.3 K bytes (24 / 204 files) (85.2 K / 741.0 K bytes)
2025-05-13 14:26:28,382 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_msaoper_0016.rmap 1.5 K bytes (25 / 204 files) (86.4 K / 741.0 K bytes)
2025-05-13 14:26:28,464 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_msa_0027.rmap 1.3 K bytes (26 / 204 files) (87.9 K / 741.0 K bytes)
2025-05-13 14:26:28,511 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_mask_0043.rmap 3.5 K bytes (27 / 204 files) (89.2 K / 741.0 K bytes)
2025-05-13 14:26:28,558 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_linearity_0017.rmap 1.6 K bytes (28 / 204 files) (92.7 K / 741.0 K bytes)
2025-05-13 14:26:28,676 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_ipc_0006.rmap 876 bytes (29 / 204 files) (94.3 K / 741.0 K bytes)
2025-05-13 14:26:28,723 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_ifuslicer_0017.rmap 1.5 K bytes (30 / 204 files) (95.2 K / 741.0 K bytes)
2025-05-13 14:26:28,782 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_ifupost_0019.rmap 1.5 K bytes (31 / 204 files) (96.7 K / 741.0 K bytes)
2025-05-13 14:26:28,830 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_ifufore_0017.rmap 1.5 K bytes (32 / 204 files) (98.2 K / 741.0 K bytes)
2025-05-13 14:26:28,922 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_gain_0023.rmap 1.8 K bytes (33 / 204 files) (99.7 K / 741.0 K bytes)
2025-05-13 14:26:28,987 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_fpa_0028.rmap 1.3 K bytes (34 / 204 files) (101.5 K / 741.0 K bytes)
2025-05-13 14:26:29,033 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_fore_0026.rmap 5.0 K bytes (35 / 204 files) (102.7 K / 741.0 K bytes)
2025-05-13 14:26:29,101 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_flat_0015.rmap 3.8 K bytes (36 / 204 files) (107.7 K / 741.0 K bytes)
2025-05-13 14:26:29,147 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_fflat_0026.rmap 7.2 K bytes (37 / 204 files) (111.5 K / 741.0 K bytes)
2025-05-13 14:26:29,216 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_extract1d_0018.rmap 2.3 K bytes (38 / 204 files) (118.7 K / 741.0 K bytes)
2025-05-13 14:26:29,283 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_disperser_0028.rmap 5.7 K bytes (39 / 204 files) (121.0 K / 741.0 K bytes)
2025-05-13 14:26:29,355 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_dflat_0007.rmap 1.1 K bytes (40 / 204 files) (126.7 K / 741.0 K bytes)
2025-05-13 14:26:29,409 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_dark_0074.rmap 34.2 K bytes (41 / 204 files) (127.9 K / 741.0 K bytes)
2025-05-13 14:26:29,510 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_cubepar_0015.rmap 966 bytes (42 / 204 files) (162.1 K / 741.0 K bytes)
2025-05-13 14:26:29,557 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_collimator_0026.rmap 1.3 K bytes (43 / 204 files) (163.1 K / 741.0 K bytes)
2025-05-13 14:26:29,603 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_camera_0026.rmap 1.3 K bytes (44 / 204 files) (164.4 K / 741.0 K bytes)
2025-05-13 14:26:29,655 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_barshadow_0007.rmap 1.8 K bytes (45 / 204 files) (165.7 K / 741.0 K bytes)
2025-05-13 14:26:29,700 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_area_0018.rmap 6.3 K bytes (46 / 204 files) (167.5 K / 741.0 K bytes)
2025-05-13 14:26:29,753 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_apcorr_0009.rmap 5.6 K bytes (47 / 204 files) (173.8 K / 741.0 K bytes)
2025-05-13 14:26:29,799 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nirspec_0398.imap 5.8 K bytes (48 / 204 files) (179.3 K / 741.0 K bytes)
2025-05-13 14:26:29,919 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_wfssbkg_0010.rmap 3.1 K bytes (49 / 204 files) (185.1 K / 741.0 K bytes)
2025-05-13 14:26:30,058 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_wavelengthrange_0006.rmap 862 bytes (50 / 204 files) (188.2 K / 741.0 K bytes)
2025-05-13 14:26:30,116 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_trappars_0004.rmap 753 bytes (51 / 204 files) (189.1 K / 741.0 K bytes)
2025-05-13 14:26:30,171 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_trapdensity_0005.rmap 705 bytes (52 / 204 files) (189.9 K / 741.0 K bytes)
2025-05-13 14:26:30,229 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_throughput_0005.rmap 1.3 K bytes (53 / 204 files) (190.6 K / 741.0 K bytes)
2025-05-13 14:26:30,276 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_superbias_0030.rmap 7.4 K bytes (54 / 204 files) (191.8 K / 741.0 K bytes)
2025-05-13 14:26:30,322 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_specwcs_0014.rmap 3.1 K bytes (55 / 204 files) (199.2 K / 741.0 K bytes)
2025-05-13 14:26:30,370 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_specprofile_0008.rmap 2.4 K bytes (56 / 204 files) (202.4 K / 741.0 K bytes)
2025-05-13 14:26:30,415 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_speckernel_0006.rmap 1.0 K bytes (57 / 204 files) (204.7 K / 741.0 K bytes)
2025-05-13 14:26:30,474 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_sirskernel_0001.rmap 627 bytes (58 / 204 files) (205.8 K / 741.0 K bytes)
2025-05-13 14:26:30,532 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_saturation_0015.rmap 829 bytes (59 / 204 files) (206.4 K / 741.0 K bytes)
2025-05-13 14:26:30,578 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_readnoise_0011.rmap 987 bytes (60 / 204 files) (207.2 K / 741.0 K bytes)
2025-05-13 14:26:30,624 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_photom_0036.rmap 1.3 K bytes (61 / 204 files) (208.2 K / 741.0 K bytes)
2025-05-13 14:26:30,671 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_persat_0007.rmap 674 bytes (62 / 204 files) (209.5 K / 741.0 K bytes)
2025-05-13 14:26:30,727 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_pathloss_0003.rmap 758 bytes (63 / 204 files) (210.1 K / 741.0 K bytes)
2025-05-13 14:26:30,772 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_pastasoss_0004.rmap 818 bytes (64 / 204 files) (210.9 K / 741.0 K bytes)
2025-05-13 14:26:30,825 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_pars-undersamplecorrectionstep_0001.rmap 904 bytes (65 / 204 files) (211.7 K / 741.0 K bytes)
2025-05-13 14:26:30,882 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:30,927 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_pars-spec2pipeline_0008.rmap 984 bytes (67 / 204 files) (215.8 K / 741.0 K bytes)
2025-05-13 14:26:30,973 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:31,022 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_pars-resamplestep_0002.rmap 687 bytes (69 / 204 files) (219.1 K / 741.0 K bytes)
2025-05-13 14:26:31,070 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:31,127 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:31,182 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:31,238 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:31,290 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_pars-darkpipeline_0002.rmap 868 bytes (74 / 204 files) (230.8 K / 741.0 K bytes)
2025-05-13 14:26:31,335 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_pars-darkcurrentstep_0001.rmap 591 bytes (75 / 204 files) (231.7 K / 741.0 K bytes)
2025-05-13 14:26:31,381 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:31,437 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_nrm_0005.rmap 663 bytes (77 / 204 files) (237.9 K / 741.0 K bytes)
2025-05-13 14:26:31,489 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_mask_0022.rmap 1.3 K bytes (78 / 204 files) (238.6 K / 741.0 K bytes)
2025-05-13 14:26:31,536 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_linearity_0022.rmap 961 bytes (79 / 204 files) (239.9 K / 741.0 K bytes)
2025-05-13 14:26:31,584 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_ipc_0007.rmap 651 bytes (80 / 204 files) (240.9 K / 741.0 K bytes)
2025-05-13 14:26:31,631 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_gain_0011.rmap 797 bytes (81 / 204 files) (241.5 K / 741.0 K bytes)
2025-05-13 14:26:31,679 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_flat_0023.rmap 5.9 K bytes (82 / 204 files) (242.3 K / 741.0 K bytes)
2025-05-13 14:26:31,743 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_filteroffset_0010.rmap 853 bytes (83 / 204 files) (248.2 K / 741.0 K bytes)
2025-05-13 14:26:31,800 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_extract1d_0007.rmap 905 bytes (84 / 204 files) (249.0 K / 741.0 K bytes)
2025-05-13 14:26:31,859 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_drizpars_0004.rmap 519 bytes (85 / 204 files) (249.9 K / 741.0 K bytes)
2025-05-13 14:26:31,904 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_distortion_0025.rmap 3.4 K bytes (86 / 204 files) (250.4 K / 741.0 K bytes)
2025-05-13 14:26:31,958 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_dark_0034.rmap 7.5 K bytes (87 / 204 files) (253.9 K / 741.0 K bytes)
2025-05-13 14:26:32,013 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_bkg_0002.rmap 2.9 K bytes (88 / 204 files) (261.4 K / 741.0 K bytes)
2025-05-13 14:26:32,069 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_area_0014.rmap 2.7 K bytes (89 / 204 files) (264.3 K / 741.0 K bytes)
2025-05-13 14:26:32,115 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_apcorr_0010.rmap 4.3 K bytes (90 / 204 files) (267.0 K / 741.0 K bytes)
2025-05-13 14:26:32,161 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_abvegaoffset_0004.rmap 1.4 K bytes (91 / 204 files) (271.3 K / 741.0 K bytes)
2025-05-13 14:26:32,219 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_niriss_0272.imap 5.8 K bytes (92 / 204 files) (272.7 K / 741.0 K bytes)
2025-05-13 14:26:32,266 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_wfssbkg_0004.rmap 7.2 K bytes (93 / 204 files) (278.5 K / 741.0 K bytes)
2025-05-13 14:26:32,320 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_wavelengthrange_0010.rmap 996 bytes (94 / 204 files) (285.7 K / 741.0 K bytes)
2025-05-13 14:26:32,384 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_tsophot_0003.rmap 896 bytes (95 / 204 files) (286.7 K / 741.0 K bytes)
2025-05-13 14:26:32,430 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_trappars_0003.rmap 1.6 K bytes (96 / 204 files) (287.6 K / 741.0 K bytes)
2025-05-13 14:26:32,476 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_trapdensity_0003.rmap 1.6 K bytes (97 / 204 files) (289.2 K / 741.0 K bytes)
2025-05-13 14:26:32,537 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_superbias_0019.rmap 18.9 K bytes (98 / 204 files) (290.8 K / 741.0 K bytes)
2025-05-13 14:26:32,603 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_specwcs_0022.rmap 7.1 K bytes (99 / 204 files) (309.7 K / 741.0 K bytes)
2025-05-13 14:26:32,650 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_sirskernel_0002.rmap 671 bytes (100 / 204 files) (316.8 K / 741.0 K bytes)
2025-05-13 14:26:32,708 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_saturation_0011.rmap 2.8 K bytes (101 / 204 files) (317.5 K / 741.0 K bytes)
2025-05-13 14:26:32,754 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_readnoise_0026.rmap 25.9 K bytes (102 / 204 files) (320.3 K / 741.0 K bytes)
2025-05-13 14:26:32,824 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_psfmask_0008.rmap 28.4 K bytes (103 / 204 files) (346.2 K / 741.0 K bytes)
2025-05-13 14:26:32,894 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_photom_0028.rmap 3.4 K bytes (104 / 204 files) (374.6 K / 741.0 K bytes)
2025-05-13 14:26:32,939 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_persat_0005.rmap 1.6 K bytes (105 / 204 files) (377.9 K / 741.0 K bytes)
2025-05-13 14:26:32,999 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:33,047 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:33,103 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_pars-spec2pipeline_0008.rmap 984 bytes (108 / 204 files) (386.0 K / 741.0 K bytes)
2025-05-13 14:26:33,156 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:33,214 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_pars-resamplestep_0002.rmap 687 bytes (110 / 204 files) (391.6 K / 741.0 K bytes)
2025-05-13 14:26:33,271 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_pars-outlierdetectionstep_0003.rmap 940 bytes (111 / 204 files) (392.3 K / 741.0 K bytes)
2025-05-13 14:26:33,327 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_pars-jumpstep_0005.rmap 806 bytes (112 / 204 files) (393.2 K / 741.0 K bytes)
2025-05-13 14:26:33,380 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:33,425 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:33,473 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_pars-darkpipeline_0002.rmap 868 bytes (115 / 204 files) (396.4 K / 741.0 K bytes)
2025-05-13 14:26:33,522 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_pars-darkcurrentstep_0001.rmap 618 bytes (116 / 204 files) (397.3 K / 741.0 K bytes)
2025-05-13 14:26:33,578 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_mask_0012.rmap 4.1 K bytes (117 / 204 files) (397.9 K / 741.0 K bytes)
2025-05-13 14:26:33,625 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_linearity_0011.rmap 2.4 K bytes (118 / 204 files) (402.1 K / 741.0 K bytes)
2025-05-13 14:26:33,686 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_ipc_0003.rmap 2.0 K bytes (119 / 204 files) (404.5 K / 741.0 K bytes)
2025-05-13 14:26:33,731 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_gain_0016.rmap 2.1 K bytes (120 / 204 files) (406.4 K / 741.0 K bytes)
2025-05-13 14:26:33,777 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_flat_0028.rmap 51.7 K bytes (121 / 204 files) (408.6 K / 741.0 K bytes)
2025-05-13 14:26:33,848 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_filteroffset_0004.rmap 1.4 K bytes (122 / 204 files) (460.2 K / 741.0 K bytes)
2025-05-13 14:26:33,904 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_extract1d_0005.rmap 1.2 K bytes (123 / 204 files) (461.7 K / 741.0 K bytes)
2025-05-13 14:26:33,955 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_drizpars_0001.rmap 519 bytes (124 / 204 files) (462.9 K / 741.0 K bytes)
2025-05-13 14:26:34,001 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_distortion_0033.rmap 53.4 K bytes (125 / 204 files) (463.4 K / 741.0 K bytes)
2025-05-13 14:26:34,079 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_dark_0047.rmap 29.0 K bytes (126 / 204 files) (516.7 K / 741.0 K bytes)
2025-05-13 14:26:34,137 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_area_0012.rmap 33.5 K bytes (127 / 204 files) (545.7 K / 741.0 K bytes)
2025-05-13 14:26:34,198 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_apcorr_0008.rmap 4.3 K bytes (128 / 204 files) (579.2 K / 741.0 K bytes)
2025-05-13 14:26:34,243 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_abvegaoffset_0003.rmap 1.3 K bytes (129 / 204 files) (583.5 K / 741.0 K bytes)
2025-05-13 14:26:34,289 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_nircam_0314.imap 5.6 K bytes (130 / 204 files) (584.8 K / 741.0 K bytes)
2025-05-13 14:26:34,345 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_wavelengthrange_0027.rmap 929 bytes (131 / 204 files) (590.4 K / 741.0 K bytes)
2025-05-13 14:26:34,393 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_tsophot_0004.rmap 882 bytes (132 / 204 files) (591.3 K / 741.0 K bytes)
2025-05-13 14:26:34,455 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_straymask_0009.rmap 987 bytes (133 / 204 files) (592.2 K / 741.0 K bytes)
2025-05-13 14:26:34,517 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_specwcs_0043.rmap 5.8 K bytes (134 / 204 files) (593.2 K / 741.0 K bytes)
2025-05-13 14:26:34,565 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_saturation_0015.rmap 1.2 K bytes (135 / 204 files) (599.0 K / 741.0 K bytes)
2025-05-13 14:26:34,622 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_rscd_0008.rmap 1.0 K bytes (136 / 204 files) (600.1 K / 741.0 K bytes)
2025-05-13 14:26:34,669 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_resol_0006.rmap 790 bytes (137 / 204 files) (601.2 K / 741.0 K bytes)
2025-05-13 14:26:34,714 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_reset_0026.rmap 3.9 K bytes (138 / 204 files) (602.0 K / 741.0 K bytes)
2025-05-13 14:26:34,759 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_regions_0034.rmap 5.2 K bytes (139 / 204 files) (605.8 K / 741.0 K bytes)
2025-05-13 14:26:34,806 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_readnoise_0023.rmap 1.6 K bytes (140 / 204 files) (611.0 K / 741.0 K bytes)
2025-05-13 14:26:34,853 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_psfmask_0009.rmap 2.1 K bytes (141 / 204 files) (612.7 K / 741.0 K bytes)
2025-05-13 14:26:34,911 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_psf_0003.rmap 839 bytes (142 / 204 files) (614.8 K / 741.0 K bytes)
2025-05-13 14:26:34,969 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_photom_0056.rmap 3.7 K bytes (143 / 204 files) (615.6 K / 741.0 K bytes)
2025-05-13 14:26:35,014 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pathloss_0005.rmap 866 bytes (144 / 204 files) (619.4 K / 741.0 K bytes)
2025-05-13 14:26:35,060 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pars-whitelightstep_0003.rmap 912 bytes (145 / 204 files) (620.2 K / 741.0 K bytes)
2025-05-13 14:26:35,119 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:35,188 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pars-spec3pipeline_0009.rmap 816 bytes (147 / 204 files) (623.0 K / 741.0 K bytes)
2025-05-13 14:26:35,234 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:35,293 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:35,345 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pars-resamplestep_0002.rmap 677 bytes (150 / 204 files) (627.0 K / 741.0 K bytes)
2025-05-13 14:26:35,405 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pars-resamplespecstep_0002.rmap 706 bytes (151 / 204 files) (627.7 K / 741.0 K bytes)
2025-05-13 14:26:35,450 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:35,498 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:35,556 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:35,612 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pars-extract1dstep_0003.rmap 807 bytes (155 / 204 files) (634.5 K / 741.0 K bytes)
2025-05-13 14:26:35,658 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pars-emicorrstep_0003.rmap 796 bytes (156 / 204 files) (635.3 K / 741.0 K bytes)
2025-05-13 14:26:35,706 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:35,763 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pars-darkpipeline_0002.rmap 860 bytes (158 / 204 files) (637.7 K / 741.0 K bytes)
2025-05-13 14:26:35,819 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_pars-darkcurrentstep_0002.rmap 683 bytes (159 / 204 files) (638.5 K / 741.0 K bytes)
2025-05-13 14:26:35,865 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_mrsxartcorr_0002.rmap 2.2 K bytes (160 / 204 files) (639.2 K / 741.0 K bytes)
2025-05-13 14:26:35,914 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_mrsptcorr_0005.rmap 2.0 K bytes (161 / 204 files) (641.4 K / 741.0 K bytes)
2025-05-13 14:26:35,961 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_mask_0026.rmap 4.3 K bytes (162 / 204 files) (643.3 K / 741.0 K bytes)
2025-05-13 14:26:36,008 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_linearity_0018.rmap 2.8 K bytes (163 / 204 files) (647.6 K / 741.0 K bytes)
2025-05-13 14:26:36,053 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_ipc_0008.rmap 700 bytes (164 / 204 files) (650.4 K / 741.0 K bytes)
2025-05-13 14:26:36,101 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_gain_0013.rmap 3.9 K bytes (165 / 204 files) (651.1 K / 741.0 K bytes)
2025-05-13 14:26:36,148 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_fringefreq_0003.rmap 1.4 K bytes (166 / 204 files) (655.0 K / 741.0 K bytes)
2025-05-13 14:26:36,195 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_fringe_0019.rmap 3.9 K bytes (167 / 204 files) (656.5 K / 741.0 K bytes)
2025-05-13 14:26:36,252 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_flat_0066.rmap 15.7 K bytes (168 / 204 files) (660.4 K / 741.0 K bytes)
2025-05-13 14:26:36,306 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_filteroffset_0025.rmap 2.5 K bytes (169 / 204 files) (676.1 K / 741.0 K bytes)
2025-05-13 14:26:36,373 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_extract1d_0020.rmap 1.4 K bytes (170 / 204 files) (678.6 K / 741.0 K bytes)
2025-05-13 14:26:36,417 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_emicorr_0003.rmap 663 bytes (171 / 204 files) (679.9 K / 741.0 K bytes)
2025-05-13 14:26:36,463 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_drizpars_0002.rmap 511 bytes (172 / 204 files) (680.6 K / 741.0 K bytes)
2025-05-13 14:26:36,509 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_distortion_0040.rmap 4.9 K bytes (173 / 204 files) (681.1 K / 741.0 K bytes)
2025-05-13 14:26:36,568 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_dark_0036.rmap 4.4 K bytes (174 / 204 files) (686.0 K / 741.0 K bytes)
2025-05-13 14:26:36,633 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_cubepar_0017.rmap 800 bytes (175 / 204 files) (690.4 K / 741.0 K bytes)
2025-05-13 14:26:36,689 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_area_0015.rmap 866 bytes (176 / 204 files) (691.2 K / 741.0 K bytes)
2025-05-13 14:26:36,735 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_apcorr_0019.rmap 5.0 K bytes (177 / 204 files) (692.0 K / 741.0 K bytes)
2025-05-13 14:26:36,783 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_abvegaoffset_0003.rmap 1.3 K bytes (178 / 204 files) (697.0 K / 741.0 K bytes)
2025-05-13 14:26:36,831 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_miri_0437.imap 5.8 K bytes (179 / 204 files) (698.3 K / 741.0 K bytes)
2025-05-13 14:26:36,878 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_trappars_0004.rmap 903 bytes (180 / 204 files) (704.1 K / 741.0 K bytes)
2025-05-13 14:26:36,923 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_trapdensity_0006.rmap 930 bytes (181 / 204 files) (705.0 K / 741.0 K bytes)
2025-05-13 14:26:36,967 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_superbias_0017.rmap 3.8 K bytes (182 / 204 files) (706.0 K / 741.0 K bytes)
2025-05-13 14:26:37,021 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_saturation_0009.rmap 779 bytes (183 / 204 files) (709.7 K / 741.0 K bytes)
2025-05-13 14:26:37,066 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_readnoise_0014.rmap 1.3 K bytes (184 / 204 files) (710.5 K / 741.0 K bytes)
2025-05-13 14:26:37,112 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_photom_0014.rmap 1.1 K bytes (185 / 204 files) (711.8 K / 741.0 K bytes)
2025-05-13 14:26:37,169 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_persat_0006.rmap 884 bytes (186 / 204 files) (712.9 K / 741.0 K bytes)
2025-05-13 14:26:37,225 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_pars-tweakregstep_0002.rmap 850 bytes (187 / 204 files) (713.8 K / 741.0 K bytes)
2025-05-13 14:26:37,270 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_pars-sourcecatalogstep_0001.rmap 636 bytes (188 / 204 files) (714.6 K / 741.0 K bytes)
2025-05-13 14:26:37,321 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_pars-outlierdetectionstep_0001.rmap 654 bytes (189 / 204 files) (715.3 K / 741.0 K bytes)
2025-05-13 14:26:37,383 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_pars-image2pipeline_0005.rmap 974 bytes (190 / 204 files) (715.9 K / 741.0 K bytes)
2025-05-13 14:26:37,436 - CRDS - INFO - Fetching /home/runner/crds_cache/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 14:26:37,482 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_pars-darkpipeline_0002.rmap 856 bytes (192 / 204 files) (717.9 K / 741.0 K bytes)
2025-05-13 14:26:37,528 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_mask_0023.rmap 1.1 K bytes (193 / 204 files) (718.8 K / 741.0 K bytes)
2025-05-13 14:26:37,575 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_linearity_0015.rmap 925 bytes (194 / 204 files) (719.8 K / 741.0 K bytes)
2025-05-13 14:26:37,631 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_ipc_0003.rmap 614 bytes (195 / 204 files) (720.8 K / 741.0 K bytes)
2025-05-13 14:26:37,678 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_gain_0010.rmap 890 bytes (196 / 204 files) (721.4 K / 741.0 K bytes)
2025-05-13 14:26:37,725 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_flat_0009.rmap 1.1 K bytes (197 / 204 files) (722.3 K / 741.0 K bytes)
2025-05-13 14:26:37,770 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_distortion_0011.rmap 1.2 K bytes (198 / 204 files) (723.4 K / 741.0 K bytes)
2025-05-13 14:26:37,818 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_dark_0017.rmap 4.3 K bytes (199 / 204 files) (724.6 K / 741.0 K bytes)
2025-05-13 14:26:37,876 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_area_0010.rmap 1.2 K bytes (200 / 204 files) (728.9 K / 741.0 K bytes)
2025-05-13 14:26:37,922 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_apcorr_0004.rmap 4.0 K bytes (201 / 204 files) (730.1 K / 741.0 K bytes)
2025-05-13 14:26:37,968 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_abvegaoffset_0002.rmap 1.3 K bytes (202 / 204 files) (734.0 K / 741.0 K bytes)
2025-05-13 14:26:38,014 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_fgs_0123.imap 5.1 K bytes (203 / 204 files) (735.3 K / 741.0 K bytes)
2025-05-13 14:26:38,061 - CRDS - INFO - Fetching /home/runner/crds_cache/mappings/jwst/jwst_1364.pmap 580 bytes (204 / 204 files) (740.4 K / 741.0 K bytes)
2025-05-13 14:26:38,451 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-darkcurrentstep_0005.asdf 1.4 K bytes (1 / 1 files) (0 / 1.4 K bytes)
2025-05-13 14:26:38,497 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-darkcurrentstep_0005.asdf
2025-05-13 14:26:38,507 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf 1.7 K bytes (1 / 1 files) (0 / 1.7 K bytes)
2025-05-13 14:26:38,554 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 14:26:38,566 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf 1.2 K bytes (1 / 1 files) (0 / 1.2 K bytes)
2025-05-13 14:26:38,615 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 14:26:38,633 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 14:26:38,634 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 14:26:38,634 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 14:26:38,635 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 14:26:38,636 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 14:26:38,637 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 14:26:38,640 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 14:26:38,641 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 14:26:38,643 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 14:26:38,644 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 14:26:38,645 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 14:26:38,646 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 14:26:38,647 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 14:26:38,647 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 14:26:38,648 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 14:26:38,649 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 14:26:38,651 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 14:26:38,652 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 14:26:38,653 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 14:26:38,654 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 14:26:38,782 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00001_nrs1_uncal.fits',).
2025-05-13 14:26:38,802 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: sequential
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
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: 0.0082
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: 0
after_jump_flag_time1: 0
after_jump_flag_dn2: 0
after_jump_flag_time2: 0
expand_large_events: True
min_sat_area: 15
min_jump_area: 15
expand_factor: 3
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: False
max_shower_amplitude: 4.0
extend_snr_threshold: 0.0
extend_min_area: 0
extend_inner_radius: 0
extend_outer_radius: 0.0
extend_ellipse_expand_ratio: 0.0
time_masked_after_shower: 0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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 14:26:39,183 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00001_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 14:26:39,187 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0351.fits 8.3 G bytes (1 / 8 files) (0 / 8.8 G bytes)
2025-05-13 14:28:07,145 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits 16.8 M bytes (2 / 8 files) (8.3 G / 8.8 G bytes)
2025-05-13 14:28:07,419 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0022.fits 117.5 M bytes (3 / 8 files) (8.4 G / 8.8 G bytes)
2025-05-13 14:28:08,701 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0048.fits 26.2 M bytes (4 / 8 files) (8.5 G / 8.8 G bytes)
2025-05-13 14:28:09,031 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits 33.6 M bytes (5 / 8 files) (8.5 G / 8.8 G bytes)
2025-05-13 14:28:09,409 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0019.fits 93.3 M bytes (6 / 8 files) (8.5 G / 8.8 G bytes)
2025-05-13 14:28:10,143 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0031.fits 50.4 M bytes (7 / 8 files) (8.6 G / 8.8 G bytes)
2025-05-13 14:28:10,525 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0254.fits 78.7 M bytes (8 / 8 files) (8.7 G / 8.8 G bytes)
2025-05-13 14:28:11,841 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0351.fits'.
2025-05-13 14:28:11,842 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits'.
2025-05-13 14:28:11,842 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0022.fits'.
2025-05-13 14:28:11,843 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0048.fits'.
2025-05-13 14:28:11,843 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 14:28:11,843 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits'.
2025-05-13 14:28:11,844 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0019.fits'.
2025-05-13 14:28:11,844 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 14:28:11,845 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 14:28:11,845 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0031.fits'.
2025-05-13 14:28:11,845 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 14:28:11,846 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0254.fits'.
2025-05-13 14:28:11,847 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 14:28:11,848 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 14:28:11,851 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 14:28:13,350 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:28:14,622 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES=5, FRMDIVSR=8
2025-05-13 14:28:14,623 - stpipe.Detector1Pipeline.group_scale - INFO - Rescaling all groups by 8/5
2025-05-13 14:28:16,180 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 14:28:16,366 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:28:16,383 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0048.fits
2025-05-13 14:28:16,894 - 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 14:28:16,961 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 14:28:17,098 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:28:17,115 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0031.fits
2025-05-13 14:28:17,339 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 5
2025-05-13 14:28:21,578 - stpipe.Detector1Pipeline.saturation - INFO - Detected 54143 saturated pixels
2025-05-13 14:28:21,665 - stpipe.Detector1Pipeline.saturation - INFO - Detected 2 A/D floor pixels
2025-05-13 14:28:21,678 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 14:28:21,813 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:28:21,814 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 14:28:21,940 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:28:21,961 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0254.fits
2025-05-13 14:28:22,951 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 14:28:23,090 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:28:23,414 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels flagged: 50
2025-05-13 14:28:23,546 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels replaced: 50
2025-05-13 14:28:23,557 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0019.fits
2025-05-13 14:28:23,860 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1 out of 2
2025-05-13 14:28:51,979 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 2 out of 2
2025-05-13 14:29:20,121 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 14:29:20,260 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:29:20,327 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0022.fits
2025-05-13 14:29:20,370 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 14:29:21,684 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 14:29:21,819 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:29:21,896 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0351.fits
2025-05-13 14:29:28,551 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 0.0082 e-/sec
2025-05-13 14:29:28,551 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=20, nframes=5, groupgap=0
2025-05-13 14:29:28,552 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=245, nframes=1, groupgap=0
2025-05-13 14:29:31,294 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 14:29:31,429 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:29:31,430 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 14:29:31,551 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:29:31,573 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 14:29:31,574 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 14:29:31,732 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits
2025-05-13 14:29:31,770 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits
2025-05-13 14:29:32,140 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 14:29:32,141 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 14:29:41,132 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 14:29:42,367 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 804
2025-05-13 14:29:42,368 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 10.2269 sec
2025-05-13 14:29:42,577 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 11.003953
2025-05-13 14:29:42,581 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 14:29:42,737 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:29:42,737 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 14:29:42,856 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:29:43,094 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits
2025-05-13 14:29:43,095 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits
2025-05-13 14:29:43,124 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 14:29:43,124 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 14:29:44,606 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 14:29:56,487 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 11.876186609268188
2025-05-13 14:29:56,543 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 14:29:56,672 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:29:56,692 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:29:56,698 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:29:56,846 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 2048, 2048) from jw02736007001_03103_00001_nrs1_uncal.fits>,).
2025-05-13 14:29:56,869 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:29:56,878 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:29:57,051 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rateints.fits
2025-05-13 14:29:57,052 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 14:29:57,053 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:29:57,163 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits
2025-05-13 14:29:57,164 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 14:29:57,164 - stpipe - INFO - Results used jwst version: 1.18.0
Applying Stage 1 Corrections & Calibrations to: jw02736007001_03103_00001_nrs2_uncal.fits
2025-05-13 14:29:58,417 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-darkcurrentstep_0003.asdf 1.4 K bytes (1 / 1 files) (0 / 1.4 K bytes)
2025-05-13 14:29:58,467 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-darkcurrentstep_0003.asdf
2025-05-13 14:29:58,476 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 14:29:58,487 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 14:29:58,512 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 14:29:58,513 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 14:29:58,514 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 14:29:58,515 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 14:29:58,516 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 14:29:58,517 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 14:29:58,517 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 14:29:58,518 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 14:29:58,519 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 14:29:58,520 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 14:29:58,521 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 14:29:58,522 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 14:29:58,523 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 14:29:58,524 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 14:29:58,525 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 14:29:58,526 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 14:29:58,527 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 14:29:58,528 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 14:29:58,529 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 14:29:58,530 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 14:29:58,658 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00001_nrs2_uncal.fits',).
2025-05-13 14:29:58,679 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: sequential
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
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: 0.0048
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: 0
after_jump_flag_time1: 0
after_jump_flag_dn2: 0
after_jump_flag_time2: 0
expand_large_events: True
min_sat_area: 15
min_jump_area: 15
expand_factor: 3
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: False
max_shower_amplitude: 4.0
extend_snr_threshold: 0.0
extend_min_area: 0
extend_inner_radius: 0
extend_outer_radius: 0.0
extend_ellipse_expand_ratio: 0.0
time_masked_after_shower: 0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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 14:29:59,016 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00001_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 14:29:59,020 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0350.fits 8.3 G bytes (1 / 8 files) (0 / 8.8 G bytes)
2025-05-13 14:31:18,243 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits 16.8 M bytes (2 / 8 files) (8.3 G / 8.8 G bytes)
2025-05-13 14:31:18,465 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0025.fits 117.5 M bytes (3 / 8 files) (8.4 G / 8.8 G bytes)
2025-05-13 14:31:19,607 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0050.fits 26.2 M bytes (4 / 8 files) (8.5 G / 8.8 G bytes)
2025-05-13 14:31:19,915 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits 33.6 M bytes (5 / 8 files) (8.5 G / 8.8 G bytes)
2025-05-13 14:31:20,280 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0018.fits 186.7 M bytes (6 / 8 files) (8.5 G / 8.8 G bytes)
2025-05-13 14:31:21,710 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0030.fits 50.4 M bytes (7 / 8 files) (8.7 G / 8.8 G bytes)
2025-05-13 14:31:22,211 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0256.fits 78.7 M bytes (8 / 8 files) (8.8 G / 8.8 G bytes)
2025-05-13 14:31:22,809 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0350.fits'.
2025-05-13 14:31:22,809 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits'.
2025-05-13 14:31:22,810 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0025.fits'.
2025-05-13 14:31:22,810 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0050.fits'.
2025-05-13 14:31:22,811 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 14:31:22,811 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits'.
2025-05-13 14:31:22,812 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0018.fits'.
2025-05-13 14:31:22,813 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 14:31:22,813 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 14:31:22,814 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0030.fits'.
2025-05-13 14:31:22,814 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 14:31:22,815 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0256.fits'.
2025-05-13 14:31:22,816 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 14:31:22,816 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 14:31:22,820 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 14:31:23,822 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:31:24,382 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES=5, FRMDIVSR=8
2025-05-13 14:31:24,383 - stpipe.Detector1Pipeline.group_scale - INFO - Rescaling all groups by 8/5
2025-05-13 14:31:25,858 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 14:31:26,022 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:31:26,037 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0050.fits
2025-05-13 14:31:26,535 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 14:31:26,688 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:31:26,703 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0030.fits
2025-05-13 14:31:26,920 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 5
2025-05-13 14:31:30,697 - stpipe.Detector1Pipeline.saturation - INFO - Detected 36567 saturated pixels
2025-05-13 14:31:30,785 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2025-05-13 14:31:30,793 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 14:31:30,930 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:31:30,931 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 14:31:31,051 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:31:31,067 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0256.fits
2025-05-13 14:31:32,056 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 14:31:32,207 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:31:32,552 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels flagged: 50
2025-05-13 14:31:32,685 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels replaced: 50
2025-05-13 14:31:32,694 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0018.fits
2025-05-13 14:31:33,008 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1 out of 2
2025-05-13 14:32:01,113 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 2 out of 2
2025-05-13 14:32:29,391 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 14:32:29,544 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:32:29,560 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0025.fits
2025-05-13 14:32:29,600 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 14:32:30,895 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 14:32:31,040 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:32:31,114 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0350.fits
2025-05-13 14:32:50,072 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 0.0048 e-/sec
2025-05-13 14:32:50,072 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=20, nframes=5, groupgap=0
2025-05-13 14:32:50,073 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=245, nframes=1, groupgap=0
2025-05-13 14:32:53,343 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 14:32:53,568 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:32:53,568 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 14:32:53,696 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:32:53,732 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 14:32:53,733 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 14:32:53,892 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits
2025-05-13 14:32:53,930 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits
2025-05-13 14:32:54,310 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 14:32:54,311 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 14:33:03,195 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 14:33:04,405 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 624
2025-05-13 14:33:04,406 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 10.0947 sec
2025-05-13 14:33:04,612 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 10.879266
2025-05-13 14:33:04,616 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 14:33:04,779 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:33:04,779 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 14:33:04,912 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:33:05,143 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits
2025-05-13 14:33:05,144 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits
2025-05-13 14:33:05,175 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 14:33:05,175 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 14:33:06,626 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 14:33:18,522 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 11.890422582626343
2025-05-13 14:33:18,569 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 14:33:18,700 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:33:18,720 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:33:18,727 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:33:18,857 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 2048, 2048) from jw02736007001_03103_00001_nrs2_uncal.fits>,).
2025-05-13 14:33:18,880 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:33:18,889 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:33:19,064 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rateints.fits
2025-05-13 14:33:19,064 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 14:33:19,065 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:33:19,177 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits
2025-05-13 14:33:19,178 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 14:33:19,178 - stpipe - INFO - Results used jwst version: 1.18.0
Applying Stage 1 Corrections & Calibrations to: jw02736007001_03103_00002_nrs1_uncal.fits
2025-05-13 14:33:20,424 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-darkcurrentstep_0005.asdf
2025-05-13 14:33:20,432 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 14:33:20,443 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 14:33:20,461 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 14:33:20,462 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 14:33:20,462 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 14:33:20,464 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 14:33:20,464 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 14:33:20,465 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 14:33:20,466 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 14:33:20,467 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 14:33:20,468 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 14:33:20,469 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 14:33:20,470 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 14:33:20,471 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 14:33:20,472 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 14:33:20,473 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 14:33:20,474 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 14:33:20,475 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 14:33:20,476 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 14:33:20,477 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 14:33:20,478 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 14:33:20,481 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 14:33:20,614 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00002_nrs1_uncal.fits',).
2025-05-13 14:33:20,634 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: sequential
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
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: 0.0082
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: 0
after_jump_flag_time1: 0
after_jump_flag_dn2: 0
after_jump_flag_time2: 0
expand_large_events: True
min_sat_area: 15
min_jump_area: 15
expand_factor: 3
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: False
max_shower_amplitude: 4.0
extend_snr_threshold: 0.0
extend_min_area: 0
extend_inner_radius: 0
extend_outer_radius: 0.0
extend_ellipse_expand_ratio: 0.0
time_masked_after_shower: 0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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 14:33:20,972 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00002_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 14:33:20,976 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0351.fits'.
2025-05-13 14:33:20,976 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits'.
2025-05-13 14:33:20,977 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0022.fits'.
2025-05-13 14:33:20,977 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0048.fits'.
2025-05-13 14:33:20,978 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 14:33:20,978 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits'.
2025-05-13 14:33:20,979 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0019.fits'.
2025-05-13 14:33:20,980 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 14:33:20,980 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 14:33:20,980 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0031.fits'.
2025-05-13 14:33:20,981 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 14:33:20,982 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0254.fits'.
2025-05-13 14:33:20,982 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 14:33:20,983 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 14:33:20,986 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 14:33:21,644 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:33:21,834 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES=5, FRMDIVSR=8
2025-05-13 14:33:21,834 - stpipe.Detector1Pipeline.group_scale - INFO - Rescaling all groups by 8/5
2025-05-13 14:33:22,293 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 14:33:22,433 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:33:22,449 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0048.fits
2025-05-13 14:33:22,964 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 14:33:23,105 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:33:23,121 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0031.fits
2025-05-13 14:33:23,355 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 5
2025-05-13 14:33:27,090 - stpipe.Detector1Pipeline.saturation - INFO - Detected 54921 saturated pixels
2025-05-13 14:33:27,177 - stpipe.Detector1Pipeline.saturation - INFO - Detected 4 A/D floor pixels
2025-05-13 14:33:27,185 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 14:33:27,321 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:33:27,322 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 14:33:27,443 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:33:27,459 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0254.fits
2025-05-13 14:33:28,417 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 14:33:28,558 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:33:28,881 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels flagged: 54
2025-05-13 14:33:29,016 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels replaced: 54
2025-05-13 14:33:29,026 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0019.fits
2025-05-13 14:33:29,351 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1 out of 2
2025-05-13 14:33:57,455 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 2 out of 2
2025-05-13 14:34:25,731 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 14:34:25,877 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:34:25,896 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0022.fits
2025-05-13 14:34:25,982 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 14:34:27,292 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 14:34:27,431 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:34:27,503 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0351.fits
2025-05-13 14:34:45,273 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 0.0082 e-/sec
2025-05-13 14:34:45,274 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=20, nframes=5, groupgap=0
2025-05-13 14:34:45,274 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=245, nframes=1, groupgap=0
2025-05-13 14:34:48,589 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 14:34:48,803 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:34:48,804 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 14:34:48,935 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:34:48,972 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 14:34:48,973 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 14:34:49,134 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits
2025-05-13 14:34:49,172 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits
2025-05-13 14:34:49,530 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 14:34:49,531 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 14:34:58,391 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 14:34:59,608 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 806
2025-05-13 14:34:59,609 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 10.078 sec
2025-05-13 14:34:59,815 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 10.843019
2025-05-13 14:34:59,819 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 14:34:59,985 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:34:59,986 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 14:35:00,114 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:35:00,348 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits
2025-05-13 14:35:00,349 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits
2025-05-13 14:35:00,380 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 14:35:00,380 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 14:35:01,874 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 14:35:13,907 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 12.027709007263184
2025-05-13 14:35:13,954 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 14:35:14,095 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:35:14,114 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:35:14,121 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:35:14,256 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 2048, 2048) from jw02736007001_03103_00002_nrs1_uncal.fits>,).
2025-05-13 14:35:14,280 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:35:14,289 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:35:14,465 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rateints.fits
2025-05-13 14:35:14,466 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 14:35:14,467 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:35:14,583 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits
2025-05-13 14:35:14,583 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 14:35:14,584 - stpipe - INFO - Results used jwst version: 1.18.0
Applying Stage 1 Corrections & Calibrations to: jw02736007001_03103_00002_nrs2_uncal.fits
2025-05-13 14:35:15,829 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-darkcurrentstep_0003.asdf
2025-05-13 14:35:15,837 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 14:35:15,848 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 14:35:15,865 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 14:35:15,866 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 14:35:15,867 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 14:35:15,868 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 14:35:15,869 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 14:35:15,870 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 14:35:15,871 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 14:35:15,872 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 14:35:15,873 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 14:35:15,874 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 14:35:15,875 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 14:35:15,876 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 14:35:15,877 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 14:35:15,878 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 14:35:15,879 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 14:35:15,880 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 14:35:15,881 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 14:35:15,882 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 14:35:15,884 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 14:35:15,884 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 14:35:16,024 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00002_nrs2_uncal.fits',).
2025-05-13 14:35:16,044 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: sequential
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
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: 0.0048
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: 0
after_jump_flag_time1: 0
after_jump_flag_dn2: 0
after_jump_flag_time2: 0
expand_large_events: True
min_sat_area: 15
min_jump_area: 15
expand_factor: 3
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: False
max_shower_amplitude: 4.0
extend_snr_threshold: 0.0
extend_min_area: 0
extend_inner_radius: 0
extend_outer_radius: 0.0
extend_ellipse_expand_ratio: 0.0
time_masked_after_shower: 0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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 14:35:16,387 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00002_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 14:35:16,390 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0350.fits'.
2025-05-13 14:35:16,391 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits'.
2025-05-13 14:35:16,391 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0025.fits'.
2025-05-13 14:35:16,392 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0050.fits'.
2025-05-13 14:35:16,393 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 14:35:16,393 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits'.
2025-05-13 14:35:16,393 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0018.fits'.
2025-05-13 14:35:16,394 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 14:35:16,394 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 14:35:16,394 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0030.fits'.
2025-05-13 14:35:16,395 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 14:35:16,396 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0256.fits'.
2025-05-13 14:35:16,396 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 14:35:16,396 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 14:35:16,399 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 14:35:17,064 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:35:17,255 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES=5, FRMDIVSR=8
2025-05-13 14:35:17,255 - stpipe.Detector1Pipeline.group_scale - INFO - Rescaling all groups by 8/5
2025-05-13 14:35:17,722 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 14:35:17,872 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:35:17,887 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0050.fits
2025-05-13 14:35:18,432 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 14:35:18,572 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:35:18,588 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0030.fits
2025-05-13 14:35:18,821 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 5
2025-05-13 14:35:22,951 - stpipe.Detector1Pipeline.saturation - INFO - Detected 34881 saturated pixels
2025-05-13 14:35:23,038 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2025-05-13 14:35:23,048 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 14:35:23,188 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:35:23,188 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 14:35:23,313 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:35:23,329 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0256.fits
2025-05-13 14:35:24,211 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 14:35:24,352 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:35:24,681 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels flagged: 52
2025-05-13 14:35:24,815 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels replaced: 52
2025-05-13 14:35:24,824 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0018.fits
2025-05-13 14:35:25,256 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1 out of 2
2025-05-13 14:35:52,712 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 2 out of 2
2025-05-13 14:36:20,101 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 14:36:20,246 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:36:20,262 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0025.fits
2025-05-13 14:36:20,337 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 14:36:21,619 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 14:36:21,756 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:36:21,827 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0350.fits
2025-05-13 14:36:41,874 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 0.0048 e-/sec
2025-05-13 14:36:41,875 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=20, nframes=5, groupgap=0
2025-05-13 14:36:41,875 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=245, nframes=1, groupgap=0
2025-05-13 14:36:44,537 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 14:36:44,753 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:36:44,754 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 14:36:44,892 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:36:44,928 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 14:36:44,929 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 14:36:45,089 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits
2025-05-13 14:36:45,126 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits
2025-05-13 14:36:45,504 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 14:36:45,505 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 14:36:54,265 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 14:36:55,460 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 590
2025-05-13 14:36:55,461 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 9.956 sec
2025-05-13 14:36:55,666 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 10.738285
2025-05-13 14:36:55,670 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 14:36:55,835 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:36:55,835 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 14:36:55,972 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:36:56,203 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits
2025-05-13 14:36:56,204 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits
2025-05-13 14:36:56,234 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 14:36:56,235 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 14:36:57,659 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 14:37:09,541 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 11.876774311065674
2025-05-13 14:37:09,589 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 14:37:09,728 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:37:09,747 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:37:09,754 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:37:09,887 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 2048, 2048) from jw02736007001_03103_00002_nrs2_uncal.fits>,).
2025-05-13 14:37:09,910 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:37:09,919 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:37:10,095 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rateints.fits
2025-05-13 14:37:10,096 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 14:37:10,097 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:37:10,211 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits
2025-05-13 14:37:10,212 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 14:37:10,212 - stpipe - INFO - Results used jwst version: 1.18.0
Applying Stage 1 Corrections & Calibrations to: jw02736007001_03103_00003_nrs1_uncal.fits
2025-05-13 14:37:11,478 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-darkcurrentstep_0005.asdf
2025-05-13 14:37:11,486 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 14:37:11,498 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 14:37:11,515 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 14:37:11,516 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 14:37:11,517 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 14:37:11,518 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 14:37:11,519 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 14:37:11,519 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 14:37:11,521 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 14:37:11,522 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 14:37:11,523 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 14:37:11,523 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 14:37:11,524 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 14:37:11,525 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 14:37:11,527 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 14:37:11,528 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 14:37:11,529 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 14:37:11,529 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 14:37:11,531 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 14:37:11,532 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 14:37:11,533 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 14:37:11,534 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 14:37:11,674 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00003_nrs1_uncal.fits',).
2025-05-13 14:37:11,695 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: sequential
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
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: 0.0082
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: 0
after_jump_flag_time1: 0
after_jump_flag_dn2: 0
after_jump_flag_time2: 0
expand_large_events: True
min_sat_area: 15
min_jump_area: 15
expand_factor: 3
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: False
max_shower_amplitude: 4.0
extend_snr_threshold: 0.0
extend_min_area: 0
extend_inner_radius: 0
extend_outer_radius: 0.0
extend_ellipse_expand_ratio: 0.0
time_masked_after_shower: 0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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 14:37:12,038 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00003_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 14:37:12,042 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0351.fits'.
2025-05-13 14:37:12,042 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits'.
2025-05-13 14:37:12,043 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0022.fits'.
2025-05-13 14:37:12,043 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0048.fits'.
2025-05-13 14:37:12,044 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 14:37:12,044 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits'.
2025-05-13 14:37:12,045 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0019.fits'.
2025-05-13 14:37:12,045 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 14:37:12,045 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 14:37:12,046 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0031.fits'.
2025-05-13 14:37:12,047 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 14:37:12,047 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0254.fits'.
2025-05-13 14:37:12,047 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 14:37:12,048 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 14:37:12,050 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 14:37:12,727 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:37:12,925 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES=5, FRMDIVSR=8
2025-05-13 14:37:12,925 - stpipe.Detector1Pipeline.group_scale - INFO - Rescaling all groups by 8/5
2025-05-13 14:37:13,388 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 14:37:13,527 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:37:13,542 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0048.fits
2025-05-13 14:37:14,040 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 14:37:14,181 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:37:14,196 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0031.fits
2025-05-13 14:37:14,424 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 5
2025-05-13 14:37:18,586 - stpipe.Detector1Pipeline.saturation - INFO - Detected 54462 saturated pixels
2025-05-13 14:37:18,672 - stpipe.Detector1Pipeline.saturation - INFO - Detected 3 A/D floor pixels
2025-05-13 14:37:18,682 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 14:37:18,826 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:37:18,827 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 14:37:18,956 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:37:18,972 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0254.fits
2025-05-13 14:37:19,858 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 14:37:20,001 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:37:20,324 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels flagged: 48
2025-05-13 14:37:20,456 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels replaced: 48
2025-05-13 14:37:20,466 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0019.fits
2025-05-13 14:37:20,789 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1 out of 2
2025-05-13 14:37:48,339 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 2 out of 2
2025-05-13 14:38:16,115 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 14:38:16,255 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:38:16,271 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0022.fits
2025-05-13 14:38:16,364 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 14:38:17,664 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 14:38:17,811 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:38:17,890 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0351.fits
2025-05-13 14:38:35,678 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 0.0082 e-/sec
2025-05-13 14:38:35,678 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=20, nframes=5, groupgap=0
2025-05-13 14:38:35,679 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=245, nframes=1, groupgap=0
2025-05-13 14:38:38,897 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 14:38:39,114 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:38:39,115 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 14:38:39,272 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:38:39,314 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 14:38:39,315 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 14:38:39,497 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits
2025-05-13 14:38:39,535 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits
2025-05-13 14:38:39,902 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 14:38:39,903 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 14:38:48,914 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 14:38:50,113 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 854
2025-05-13 14:38:50,113 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 10.211 sec
2025-05-13 14:38:50,323 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 11.009353
2025-05-13 14:38:50,327 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 14:38:50,506 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:38:50,507 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 14:38:50,641 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:38:50,873 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0038.fits
2025-05-13 14:38:50,874 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0023.fits
2025-05-13 14:38:50,905 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 14:38:50,906 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 14:38:52,378 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 14:39:04,390 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 12.00613808631897
2025-05-13 14:39:04,437 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 14:39:04,581 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:39:04,601 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:39:04,608 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:39:04,752 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 2048, 2048) from jw02736007001_03103_00003_nrs1_uncal.fits>,).
2025-05-13 14:39:04,775 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:39:04,786 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:39:04,966 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rateints.fits
2025-05-13 14:39:04,967 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 14:39:04,967 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:39:05,090 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits
2025-05-13 14:39:05,091 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 14:39:05,091 - stpipe - INFO - Results used jwst version: 1.18.0
Applying Stage 1 Corrections & Calibrations to: jw02736007001_03103_00003_nrs2_uncal.fits
2025-05-13 14:39:06,335 - stpipe - INFO - PARS-DARKCURRENTSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-darkcurrentstep_0003.asdf
2025-05-13 14:39:06,344 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 14:39:06,355 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 14:39:06,372 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 14:39:06,373 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 14:39:06,374 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 14:39:06,375 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 14:39:06,376 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 14:39:06,377 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 14:39:06,377 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 14:39:06,378 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 14:39:06,379 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 14:39:06,380 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 14:39:06,381 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 14:39:06,382 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 14:39:06,383 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 14:39:06,384 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 14:39:06,385 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 14:39:06,386 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 14:39:06,388 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 14:39:06,389 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 14:39:06,390 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 14:39:06,391 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 14:39:06,550 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/uncal/jw02736007001_03103_00003_nrs2_uncal.fits',).
2025-05-13 14:39:06,571 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_calibrated_ramp: False
steps:
group_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
dq_init:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
emicorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: sequential
nints_to_phase: None
nbins: None
scale_reference: True
onthefly_corr_freq: None
use_n_cycles: 3
fit_ints_separately: False
user_supplied_reffile: None
save_intermediate_results: False
saturation:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
n_pix_grow_sat: 1
use_readpatt: True
ipc:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
superbias:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
refpix:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
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: 0.0048
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: 0
after_jump_flag_time1: 0
after_jump_flag_dn2: 0
after_jump_flag_time2: 0
expand_large_events: True
min_sat_area: 15
min_jump_area: 15
expand_factor: 3
use_ellipses: False
sat_required_snowball: True
min_sat_radius_extend: 2.5
sat_expand: 2
edge_size: 25
mask_snowball_core_next_int: True
snowball_time_masked_next_int: 4000
find_showers: False
max_shower_amplitude: 4.0
extend_snr_threshold: 0.0
extend_min_area: 0
extend_inner_radius: 0
extend_outer_radius: 0.0
extend_ellipse_expand_ratio: 0.0
time_masked_after_shower: 0
min_diffs_single_pass: 10
max_extended_radius: 200
minimum_groups: 3
minimum_sigclip_groups: 100
only_use_ints: True
clean_flicker_noise:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: median
fit_by_channel: False
background_method: median
background_box_size: None
mask_science_regions: False
apply_flat_field: False
n_sigma: 2.0
fit_histogram: False
single_mask: True
user_mask: None
save_mask: False
save_background: False
save_noise: False
ramp_fit:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
algorithm: OLS_C
int_name: ''
save_opt: False
opt_name: ''
suppress_one_group: True
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
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 14:39:06,938 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00003_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 14:39:06,942 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0350.fits'.
2025-05-13 14:39:06,942 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits'.
2025-05-13 14:39:06,943 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0025.fits'.
2025-05-13 14:39:06,943 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0050.fits'.
2025-05-13 14:39:06,944 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 14:39:06,944 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits'.
2025-05-13 14:39:06,945 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0018.fits'.
2025-05-13 14:39:06,946 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 14:39:06,946 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 14:39:06,947 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0030.fits'.
2025-05-13 14:39:06,947 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 14:39:06,948 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0256.fits'.
2025-05-13 14:39:06,948 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 14:39:06,949 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 14:39:06,951 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 14:39:07,631 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:39:07,835 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES=5, FRMDIVSR=8
2025-05-13 14:39:07,835 - stpipe.Detector1Pipeline.group_scale - INFO - Rescaling all groups by 8/5
2025-05-13 14:39:08,299 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 14:39:08,454 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:39:08,469 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0050.fits
2025-05-13 14:39:08,962 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 14:39:09,106 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:39:09,121 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0030.fits
2025-05-13 14:39:09,356 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 5
2025-05-13 14:39:13,531 - stpipe.Detector1Pipeline.saturation - INFO - Detected 35981 saturated pixels
2025-05-13 14:39:13,615 - stpipe.Detector1Pipeline.saturation - INFO - Detected 2 A/D floor pixels
2025-05-13 14:39:13,625 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 14:39:13,768 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:39:13,769 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 14:39:13,904 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:39:13,920 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0256.fits
2025-05-13 14:39:14,816 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 14:39:14,962 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:39:15,291 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels flagged: 54
2025-05-13 14:39:15,427 - stpipe.Detector1Pipeline.refpix - INFO - Total bad reference pixels replaced: 54
2025-05-13 14:39:15,437 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_refpix_0018.fits
2025-05-13 14:39:15,827 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1 out of 2
2025-05-13 14:39:43,377 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 2 out of 2
2025-05-13 14:40:10,934 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 14:40:11,076 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:40:11,092 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0025.fits
2025-05-13 14:40:11,177 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 14:40:12,457 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 14:40:12,599 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:40:12,678 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0350.fits
2025-05-13 14:40:32,726 - stpipe.Detector1Pipeline.dark_current - INFO - Using Poisson noise from average dark current 0.0048 e-/sec
2025-05-13 14:40:32,727 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=20, nframes=5, groupgap=0
2025-05-13 14:40:32,727 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=245, nframes=1, groupgap=0
2025-05-13 14:40:35,377 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 14:40:35,617 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:40:35,618 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 14:40:35,761 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:40:35,798 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 14:40:35,799 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 14:40:35,959 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits
2025-05-13 14:40:35,997 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits
2025-05-13 14:40:36,381 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 14:40:36,382 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 14:40:45,238 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 14:40:46,443 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 644
2025-05-13 14:40:46,444 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 10.0623 sec
2025-05-13 14:40:46,651 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 10.853275
2025-05-13 14:40:46,655 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 14:40:46,819 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:40:46,819 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 14:40:46,954 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 20, 3200, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:40:47,182 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0042.fits
2025-05-13 14:40:47,182 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0020.fits
2025-05-13 14:40:47,213 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 14:40:47,213 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 14:40:48,658 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 14:41:00,510 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 11.846368074417114
2025-05-13 14:41:00,557 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 14:41:00,700 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:41:00,719 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:41:00,726 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:41:00,866 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 2048, 2048) from jw02736007001_03103_00003_nrs2_uncal.fits>,).
2025-05-13 14:41:00,889 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2025-05-13 14:41:00,899 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 14:41:01,075 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rateints.fits
2025-05-13 14:41:01,076 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 14:41:01,077 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:41:01,191 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits
2025-05-13 14:41:01,192 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 14:41:01,192 - stpipe - INFO - Results used jwst version: 1.18.0
Stage 1 has been completed!
# Print output result details:
#det1_result.__dict__ # View entire contents.
#det1_result.meta.filename
#det1_result.data.shape
# Print out the time benchmark.
time2 = time.perf_counter()
print(f"Runtime so far: {round((time2 - time0) / 60.0, 1):0.4f} min")
print(f"Runtime for Stage 1: {round((time2 - time_det1) / 60.0, 1):0.4f} min")
Runtime so far: 51.3000 min
Runtime for Stage 1: 14.6000 min
# Final list of RATE[INTS] files ready for Stage 2 processing.
rate_sci = sorted(glob.glob(det1_dir + '*_rate.fits'))
rateints_sci = sorted(glob.glob(det1_dir + '*_rateints.fits'))
print(f"SCIENCE | RATE[INTS] Files:\n{'-'*20}\n" + "\n".join(rate_sci + rateints_sci))
SCIENCE | RATE[INTS] Files:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rateints.fits
6. Stage 2: Spec2Pipeline (calwebb_spec2)#
In this section, we process our countrate (slope) image products from Stage 1 (calwebb_detector1) through the Spec2 (calwebb_spec2) pipeline to create Stage 2 data products.
Input: A single countrate (slope) image (
_rate[ints].fits) or an association file listing multiple inputs.Output: Calibrated products (rectified and unrectified) and 1D spectra.
_cal[ints].fits: Calibrated 2D (unrectified) spectra (ncols x nrows).
_s2d.fits: Resampled (rectified) 2D spectra (ncols x nrows).
_x1d[ints].fits: Extracted 1D spectroscopic data (wavelength vs. flux).
In Stage 2, each exposure (or association) and detector produces a single file, with multiple extensions corresponding to each source.
The Spec2Pipeline applies additional instrumental corrections and calibrations (e.g., slit loss, path loss, etc.,) to countrate products that result in a fully calibrated individual exposure (per nod/dither position). The Spec2Pipeline also converts countrate products from units of DN/s to flux (Jy) for point sources and surface brightness (MJy/sr) for extended sources.
6.1 Configure Spec2Pipeline#
The Spec2Pipeline has the following steps available for NIRSpec MOS:
assign_wcs: Associates a WCS object with each exposure.badpix_selfcal: Flags bad pixels in the input data using a self-calibration technique based on median filtering along the spectral axis.msaflagopen: Flags pixels in NIRSpec exposures affected by MSA shutters stuck in the open position.nsclean: Cleans 1/f noise.imprint: Removes patterns caused by the MSA structure in NIRSpec MOS and IFU exposures.bkg_subtract: Performs image subtraction for background removal.extract_2d: Extracts 2D arrays from spectral images.srctype: Determines whether a spectroscopic source should be classified as a point or extended object.master_background: Subtracts background signal from 2D spectroscopic data using a 1D master background spectrum.wavecorr: Updates wavelength assignments for FS and MOS point sources that are offset in the dispersion direction within their slit.flat_field: Applies flat-field corrections to the input science dataset.pathloss: Calculates and applies corrections for signal loss in spectroscopic data.barshadow: Calculates the correction to NIRSpec MOS data for extended sources affected by the bar that separates adjacent microshutters.photom: Applies photometric calibrations to convert data from countrate to surface brightness or flux density.pixel_replace: Interpolates and estimates flux values for pixels flagged as DO_NOT_USE in 2D extracted spectra.resample_spec: Resamples each input 2D spectral image using WCS and distortion information.extract_1d: Extracts a 1D signal from 2D or 3D datasets.
For more information about each step and a full list of step arguments, please refer to the official documentation: JDox and ReadtheDocs
Below, we set up a dictionary that defines how the Spec2Pipeline should be configured for MOS data.
If pixel-to-pixel or master background subtraction was chosen above, it will be applied during this stage.
To override specific steps and reference files, use the examples below.
# Select source to inspect.
# Set None to proccess all sources.
source_ids, slit_names = None, None
if demo_mode:
# The pipeline will accept a list of source IDs or slit names.
# Galaxies of interest:
source_ids = [
6355,
# 5144, 4590, 10612, 8140, 9922
]
slit_names = [
'72',
# '51', '55', '69', '16', '64'
]
# If running master background subtraction,
# make sure we don't restrict to one slit.
elif not master_bg:
source_ids, slit_names = None, None
# Set up a dictionary to define how the Spec2 pipeline should be configured.
# -------------------------Boilerplate dictionary setup-------------------------
spec2dict = {}
spec2dict['assign_wcs'], spec2dict['badpix_selfcal'] = {}, {}
spec2dict['nsclean'], spec2dict['master_background_mos'] = {}, {}
spec2dict['barshadow'], spec2dict['extract_2d'] = {}, {}
spec2dict['bkg_subtract'], spec2dict['srctype'], spec2dict['wavecorr'] = {}, {}, {}
spec2dict['flat_field'], spec2dict['pathloss'] = {}, {}
spec2dict['photom'], spec2dict['pixel_replace'] = {}, {}
spec2dict['resample_spec'], spec2dict['extract_1d'] = {}, {}
# ---------------------------Override reference files---------------------------
# Overrides for various reference files (example).
# Files should be in the base local directory or provide full path.
#spec2dict['extract_1d']['override_extract1d'] = 'myfile.json'
# -----------------------------Set step parameters------------------------------
# Overrides for whether or not certain steps should be skipped (example).
spec2dict['bkg_subtract']['skip'] = not pixel_bg # Runs if pixel-to-pixel bkg selected.
spec2dict['master_background_mos']['skip'] = not master_bg # Runs if masterbg selected.
# Run pixel replacement code to extrapolate values for otherwise bad pixels
# This can help mitigate 5-10% negative dips in spectra of bright sources.
# Use the 'fit_profile' algorithm.
#spec2dict['pixel_replace']['skip'] = False
#spec2dict['pixel_replace']['n_adjacent_cols'] = 5
#spec2dict['pixel_replace']['algorithm'] = 'fit_profile'
# Extract specific sources; saves on processing time.
if slit_names or source_ids is not None:
spec2dict['extract_2d']['slit_names'] = slit_names or source_ids
# Turn on bad pixel self-calibration, where all exposures on a given detector
# are used to find and flag bad pixels that may have been missed by the bad pixel mask.
# This step is experimental, and works best when dedicated background observations are included.
#spec2dict['badpix_selfcal']['skip'] = False
#spec2dict['badpix_selfcal']['flagfrac_upper'] = 0.005 # Fraction of pixels to flag.
# Resample weight_type.
spec2dict['resample_spec']['weight_type'] = 'ivm'
Resampling 2D spectra (resample_spec step)can sometimes introduce artificial noise and reduce the signal-to-noise ratio (SNR) in the resulting 1D spectra when using weight_type='ivm' (known issue). The default is now set to ‘exptime’. Consider the following when selecting a weight_type:
‘ivm’: Inverse variant scaling based on read noise (VAR_RNOISE), ideal for rejecting outliers and better suited for faint sources.
‘exptime’: Uses exposure time for scaling, improving SNR for bright sources.
# Run nsclean for 1/f noise.
#spec2dict['nsclean']['skip'] = False
#spec2dict['nsclean']['n_sigma'] = 2
To correct for 1/f noise with nsclean in Stage 2, see the MOS_NSClean_example demo notebook for MOS data here.
6.2 Create Spec2Pipeline Association Files#
Association (ASN) files define the relationships between multiple exposures, allowing them to get processed as a set rather than individually. Processing an ASN file enables the exposures to be calibrated, archived, retrieved, and reprocessed as a set rather than as individual objects.
Stage 2 ASN files for MOS data can include science, background, and selfcal exposure types. A Stage 2 ASN file requires at least one science file but can contain multiple background and selfcal files that enable pixel-to-pixel background subtraction and bad pixel self-calibration in calwebb_spec2.
Below we create these Stage 2 ASN files.
Background subtraction may not be correctly applied if more than one science file is included in the association.
Define a function that associates background, imprint, and selfcal exposures for nodded observations.
def asn_nod(asn, onescifile, sci, sci_imprint, pattnum):
"""
Associate background, imprint, and selfcal exposures for nodded observations.
Parameters
----------
asn : dict
The association dictionary to update.
onescifile : str
Path to the primary science file.
sci : list of str
List of science exposure file paths.
sci_imprint : list of str
List of science imprint exposure file paths.
pattnum : int
Dither position.
Returns
-------
asn : dict
Updated association dictionary with members for applicable background, imprint, and selfcal.
"""
members = asn['products'][0]['members']
# Assign background exposures.
for file in sci:
# If dither position is different from the input position, use it as a background.
if fits.getval(file, 'PATT_NUM') != pattnum:
members.append({'expname': file, 'exptype': 'background'})
# Assign imprint exposures (pipeline handles figuring out which one is best).
for file in sci_imprint:
# Only IFU and MOS observations have imprint exposures.
if fits.getval(file, 'EXP_TYPE') == 'NRS_IFU' or 'NRS_MSASPEC':
if match_gwa(onescifile, file):
members.append({'expname': file, 'exptype': 'imprint'})
# Assign selfcal exposures.
for file in sci + sci_imprint:
members.append({'expname': file, 'exptype': 'selfcal'})
return asn
Define a function that creates a Level 2 ASN file.
def writel2asn(onescifile, allscifiles, asnfile, product_name, exp_type):
"""
Create a Level 2 association file for each science exposure.
Parameters
----------
onescifile : str
Path to the primary science exposure file.
allscifiles : list of str
List of all science exposure files.
asnfile : str
Path to write the output association file.
product_name : str
Name of the product for the association.
exp_type : str, optional
Exposure type to match against.
Returns
-------
True if the association was written successfully, and False otherwise
"""
# Define a basic association with the science file.
# Wrap in array since input was single exposure.
asn = afl.asn_from_list([onescifile], rule=DMSLevel2bBase, product_name=product_name)
asn.data['program'] = program if 'program' in globals() else "9999"
# Grab header information from the science file.
exp_type = fits.getval(onescifile, 'EXP_TYPE')
if (exp_type == exp_type):
detector = fits.getval(onescifile, 'DETECTOR')
grating = fits.getval(onescifile, 'GRATING')
filt = fits.getval(onescifile, 'FILTER')
patttype = fits.getval(onescifile, 'PATTTYPE') # Dither pattern type.
pattnum = fits.getval(onescifile, 'PATT_NUM') # Dither pattern number.
imprint = fits.getval(onescifile, 'IS_IMPRT') # Imprint exposure?
# If this is an imprint exposure, fail out since those shouldn't be processed alone.
if imprint:
return False
# If the exposure type does not match, fail out
# to ensure TA images don't get processed by accident.
else:
return False
# Find all files matching the input configuration and split into regular/imprint.
use_sci, use_sci_imprint = get_matching(allscifiles, detector, filt, grating, exp_type)
# If this uses nodded exposures set up pixel-based background subtraction accordingly.
is_nod = 'NOD' in patttype.split('-') or fits.getval(onescifile, 'NOD_TYPE')
if is_nod:
asn = asn_nod(asn, onescifile, use_sci, use_sci_imprint, pattnum)
# Write the association to a json file.
_, serialized = asn.dump()
with open(asnfile, 'w') as outfile:
outfile.write(serialized)
return True
6.3 MSA Metadata File#
While it doesn’t contain actual science data, the NIRSpec MSA metadata file is a crucial component of calibration processing for NIRSpec MOS exposures through the calwebb_spec2 pipeline. The MSA metadata contains:
Information on which MSA shutters (slitlets) are open, which sources they observe (if any), and whether they should be used for science or background in each dithered exposure.
Source details, including RA, Dec, and whether they should be treated as point sources (stellarity > 0.75) or extended (uniform illumination) for path loss corrections.
All MSA configurations for an observing program may be stored in a single MSA metadata file.
The MSA metadata file is stored in the ASN directory.
If you wish to edit the MSA metafile, a detailed example notebook is forthcoming (draft) …
6.4 Run Spec2Pipeline#
Run the science files and, if available, any background files through the calwebb_spec2 pipeline using the .call() method.
Perform pixel-to-pixel or master background subtraction (if desired) here in Stage 2.
time_spec2 = time.perf_counter() # Tracks runtime for Stage 2.
# To save on runtime turns off creation of quicklook 2d/1d spectra for science data.
#spec2dict['resample_spec']['skip'] = True # S2D products.
#spec2dict['extract_1d']['skip'] = True # X1D products.
# Run Stage 2 pipeline using the custom spec2dict dictionary.
if dospec2:
# ------------------Execute using Science ASN files-------------------
for file in rate_sci:
try: # Create ASN files.
asnfile = os.path.join(asn_dir, os.path.basename(file).replace('rate.fits', 'l2asn.json'))
if writel2asn(file, rate_sci, asnfile, 'Level2', 'NRS_MSASPEC'):
print(f"Applying Stage 2 Corrections & Calibrations to: {file}")
spec2sci_result = Spec2Pipeline.call(asnfile,
save_results=True,
steps=spec2dict,
output_dir=spec2_dir)
except Exception as e:
# A handle for when no slits fall on NRS1/2.
print(f"Skipped processing {os.path.basename(asnfile)}: {e}")
print("Stage 2 has been completed! \n")
else:
print('Skipping Spec2 processing for SCI data.')
2025-05-13 14:41:01,276 - 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)
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits
2025-05-13 14:41:01,484 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf 1.0 K bytes (1 / 1 files) (0 / 1.0 K bytes)
2025-05-13 14:41:01,611 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:41:01,638 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:41:01,666 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 14:41:01,667 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 14:41:01,668 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 14:41:01,669 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 14:41:01,671 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 14:41:01,672 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 14:41:01,673 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 14:41:01,674 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 14:41:01,678 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 14:41:01,679 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:41:01,680 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:41:01,681 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:41:01,682 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 14:41:01,683 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:41:01,684 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:41:01,685 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:41:01,686 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 14:41:01,687 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:41:01,688 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 14:41:01,690 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 14:41:01,691 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 14:41:01,692 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 14:41:01,693 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:41:01,694 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:41:01,695 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 14:41:01,696 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 14:41:01,697 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:41:01,698 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:41:01,699 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 14:41:01,700 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:41:01,857 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_03103_00001_nrs1_l2asn.json',).
2025-05-13 14:41:01,890 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names:
- '72'
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: none
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: ivm
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
2025-05-13 14:41:01,899 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:41:01,947 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00001_nrs1_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange', 'wfssbkg']
2025-05-13 14:41:01,953 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits 1.6 M bytes (1 / 19 files) (0 / 1.1 G bytes)
2025-05-13 14:41:02,102 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits 2.5 M bytes (2 / 19 files) (1.6 M / 1.1 G bytes)
2025-05-13 14:41:02,317 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits 3.3 M bytes (3 / 19 files) (4.1 M / 1.1 G bytes)
2025-05-13 14:41:02,529 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf 5.8 K bytes (4 / 19 files) (7.4 M / 1.1 G bytes)
2025-05-13 14:41:02,607 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf 5.9 K bytes (5 / 19 files) (7.4 M / 1.1 G bytes)
2025-05-13 14:41:02,665 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits 688.9 M bytes (6 / 19 files) (7.4 M / 1.1 G bytes)
2025-05-13 14:41:07,082 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf 2.4 K bytes (7 / 19 files) (696.3 M / 1.1 G bytes)
2025-05-13 14:41:07,187 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json 527 bytes (8 / 19 files) (696.3 M / 1.1 G bytes)
2025-05-13 14:41:07,256 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits 12.1 M bytes (9 / 19 files) (696.3 M / 1.1 G bytes)
2025-05-13 14:41:07,503 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf 12.8 K bytes (10 / 19 files) (708.4 M / 1.1 G bytes)
2025-05-13 14:41:07,578 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf 4.3 K bytes (11 / 19 files) (708.4 M / 1.1 G bytes)
2025-05-13 14:41:07,638 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf 5.0 M bytes (12 / 19 files) (708.4 M / 1.1 G bytes)
2025-05-13 14:41:07,788 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json 7.3 M bytes (13 / 19 files) (713.4 M / 1.1 G bytes)
2025-05-13 14:41:07,993 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf 7.6 K bytes (14 / 19 files) (720.8 M / 1.1 G bytes)
2025-05-13 14:41:08,081 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits 1.3 M bytes (15 / 19 files) (720.8 M / 1.1 G bytes)
2025-05-13 14:41:08,212 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits 25.9 K bytes (16 / 19 files) (722.1 M / 1.1 G bytes)
2025-05-13 14:41:08,281 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0177.fits 336.6 M bytes (17 / 19 files) (722.1 M / 1.1 G bytes)
2025-05-13 14:41:10,518 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf 16.5 K bytes (18 / 19 files) (1.1 G / 1.1 G bytes)
2025-05-13 14:41:10,647 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf 3.4 K bytes (19 / 19 files) (1.1 G / 1.1 G bytes)
2025-05-13 14:41:10,700 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits'.
2025-05-13 14:41:10,701 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits'.
2025-05-13 14:41:10,701 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits'.
2025-05-13 14:41:10,702 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 14:41:10,702 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 14:41:10,703 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 14:41:10,703 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits'.
2025-05-13 14:41:10,704 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf'.
2025-05-13 14:41:10,705 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 14:41:10,705 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json'.
2025-05-13 14:41:10,705 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits'.
2025-05-13 14:41:10,706 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 14:41:10,707 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 14:41:10,707 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf'.
2025-05-13 14:41:10,708 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 14:41:10,708 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 14:41:10,709 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 14:41:10,709 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 14:41:10,710 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 14:41:10,710 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 14:41:10,711 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 14:41:10,711 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json'.
2025-05-13 14:41:10,711 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 14:41:10,713 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 14:41:10,713 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits'.
2025-05-13 14:41:10,714 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits'.
2025-05-13 14:41:10,714 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 14:41:10,715 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 14:41:10,715 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0177.fits'.
2025-05-13 14:41:10,715 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 14:41:10,716 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 14:41:10,716 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 14:41:10,716 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf'.
2025-05-13 14:41:10,717 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 14:41:10,717 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 14:41:10,718 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 14:41:10,725 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:41:10,726 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1
2025-05-13 14:41:10,726 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits ...
2025-05-13 14:41:10,912 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:11,142 - stpipe.Spec2Pipeline.assign_wcs - INFO - Retrieving open MSA slitlets for msa_metadata_id = 76 and dither_index = 1
2025-05-13 14:41:11,149 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 2 contains virtual source, with source_id=-32
2025-05-13 14:41:11,152 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 3 contains virtual source, with source_id=-33
2025-05-13 14:41:11,154 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 4 contains virtual source, with source_id=-34
2025-05-13 14:41:11,157 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 5 contains virtual source, with source_id=-35
2025-05-13 14:41:11,160 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 6 contains virtual source, with source_id=-36
2025-05-13 14:41:11,162 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 7 contains virtual source, with source_id=-37
2025-05-13 14:41:11,167 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 9 contains virtual source, with source_id=-38
2025-05-13 14:41:11,181 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 15 contains virtual source, with source_id=-39
2025-05-13 14:41:11,191 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 19 contains virtual source, with source_id=-40
2025-05-13 14:41:11,196 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 21 contains virtual source, with source_id=-41
2025-05-13 14:41:11,205 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 25 contains virtual source, with source_id=-42
2025-05-13 14:41:11,213 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 28 contains virtual source, with source_id=-43
2025-05-13 14:41:11,215 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 29 contains virtual source, with source_id=-44
2025-05-13 14:41:11,220 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 31 contains virtual source, with source_id=-45
2025-05-13 14:41:11,223 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 32 contains virtual source, with source_id=-46
2025-05-13 14:41:11,235 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 37 contains virtual source, with source_id=-47
2025-05-13 14:41:11,242 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 40 contains virtual source, with source_id=-48
2025-05-13 14:41:11,245 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 41 contains virtual source, with source_id=-49
2025-05-13 14:41:11,259 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 47 contains virtual source, with source_id=-50
2025-05-13 14:41:11,266 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 50 contains virtual source, with source_id=-51
2025-05-13 14:41:11,272 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 52 contains virtual source, with source_id=-52
2025-05-13 14:41:11,281 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 56 contains virtual source, with source_id=-53
2025-05-13 14:41:11,288 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 59 contains virtual source, with source_id=-54
2025-05-13 14:41:11,291 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 60 contains virtual source, with source_id=-55
2025-05-13 14:41:11,299 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 63 contains virtual source, with source_id=-56
2025-05-13 14:41:11,306 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 66 contains virtual source, with source_id=-57
2025-05-13 14:41:11,308 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 67 contains virtual source, with source_id=-58
2025-05-13 14:41:11,318 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 71 contains virtual source, with source_id=-59
2025-05-13 14:41:11,323 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 73 contains virtual source, with source_id=-60
2025-05-13 14:41:11,325 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 74 contains virtual source, with source_id=-61
2025-05-13 14:41:11,328 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 75 contains virtual source, with source_id=-62
2025-05-13 14:41:11,358 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:41:11,358 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:41:11,359 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:41:11,360 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:41:11,557 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,577 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,596 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,616 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,635 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 10 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,654 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 11 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,673 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 12 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,692 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 13 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,712 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 14 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,730 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 16 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,914 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,933 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,952 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 5 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,971 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 9 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:11,991 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 15 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:12,891 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS1: [np.int16(17), np.int16(18), np.int16(19), np.int16(20), np.int16(21), np.int16(22), np.int16(23), np.int16(24), np.int16(25), np.int16(26), np.int16(27), np.int16(28), np.int16(29), np.int16(30), np.int16(31), np.int16(32), np.int16(33), np.int16(34), np.int16(35), np.int16(36), np.int16(37), np.int16(38), np.int16(39), np.int16(40), np.int16(41), np.int16(42), np.int16(43), np.int16(44), np.int16(45), np.int16(46), np.int16(47), np.int16(48), np.int16(49), np.int16(50), np.int16(51), np.int16(52), np.int16(53), np.int16(54), np.int16(55), np.int16(56), np.int16(57), np.int16(58), np.int16(59), np.int16(60), np.int16(61), np.int16(62), np.int16(63), np.int16(64), np.int16(65), np.int16(66), np.int16(67), np.int16(68), np.int16(69), np.int16(70), np.int16(71), np.int16(72), np.int16(73), np.int16(74), np.int16(75)]
2025-05-13 14:41:12,891 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 59 open slitlets
2025-05-13 14:41:12,917 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:41:12,918 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:41:12,919 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:41:12,919 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:41:12,931 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:41:13,027 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999883916038974
2025-05-13 14:41:13,055 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 9 open slits in quadrant 1
2025-05-13 14:41:13,110 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 21 open slits in quadrant 2
2025-05-13 14:41:13,235 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 15 open slits in quadrant 3
2025-05-13 14:41:13,325 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 14 open slits in quadrant 4
2025-05-13 14:41:13,585 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:41:13,744 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf', 'camera': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf', 'collimator': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf', 'disperser': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf', 'fpa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf', 'msa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf', 'ote': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_01_msa.fits'}
2025-05-13 14:41:14,833 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 14:41:14,840 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 14:41:15,023 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits']).
2025-05-13 14:41:15,024 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 14:41:15,207 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:15,282 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json
2025-05-13 14:41:15,382 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:41:15,382 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:41:15,383 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:41:15,384 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:41:15,396 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:41:15,490 - stpipe.Spec2Pipeline.msa_flagging - INFO - Applied Barycentric velocity correction : 0.9999883916038974
2025-05-13 14:41:15,518 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 6 open slits in quadrant 1
2025-05-13 14:41:15,555 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2025-05-13 14:41:15,573 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 12 open slits in quadrant 3
2025-05-13 14:41:15,646 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2025-05-13 14:41:15,664 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:41:19,419 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2025-05-13 14:41:19,711 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:19,712 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 14:41:19,895 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs1_rate.fits>, []).
2025-05-13 14:41:19,896 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:41:20,080 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits', []).
2025-05-13 14:41:20,081 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:41:20,263 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits', []).
2025-05-13 14:41:20,263 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:41:20,451 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits']).
2025-05-13 14:41:20,670 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits
2025-05-13 14:41:20,760 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits
2025-05-13 14:41:20,852 - stpipe.Spec2Pipeline.bkg_subtract - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:327: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
2025-05-13 14:41:21,241 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw02736007001_03103_00001_nrs1_rate.fits
2025-05-13 14:41:22,169 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 14:41:22,417 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:22,443 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_MSASPEC
2025-05-13 14:41:22,444 - stpipe.Spec2Pipeline.extract_2d - INFO - Slits selected:
2025-05-13 14:41:22,445 - stpipe.Spec2Pipeline.extract_2d - INFO - Name: 72, source_id: 6355
2025-05-13 14:41:23,409 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 72
2025-05-13 14:41:23,410 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1014 2048
2025-05-13 14:41:23,410 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1586 1624
2025-05-13 14:41:23,568 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 14:41:23,577 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 110.843614826 -73.434854652 110.845969148 -73.435400859 110.846091091 -73.435357606 110.843736796 -73.434811390
2025-05-13 14:41:23,578 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 110.843614826 -73.434854652 110.845969148 -73.435400859 110.846091091 -73.435357606 110.843736796 -73.434811390
2025-05-13 14:41:23,622 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 14:41:23,915 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:23,921 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_MSASPEC
2025-05-13 14:41:23,922 - stpipe.Spec2Pipeline.srctype - INFO - source_id=6355, stellarity=0.1000, type=EXTENDED
2025-05-13 14:41:23,923 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 14:41:24,277 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:24,277 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 14:41:24,278 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:41:24,529 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:24,655 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf
2025-05-13 14:41:24,763 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 72
2025-05-13 14:41:24,765 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 14:41:25,022 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:25,062 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 14:41:25,121 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits
2025-05-13 14:41:25,332 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0177.fits
2025-05-13 14:41:25,477 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits
2025-05-13 14:41:25,574 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 72
2025-05-13 14:41:25,833 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 14:41:26,090 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:26,110 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits
2025-05-13 14:41:26,137 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_MSASPEC
2025-05-13 14:41:26,233 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit 0
2025-05-13 14:41:26,234 - stpipe.Spec2Pipeline.pathloss - INFO - Shutter state = 1x111, using MOS1x3 entry in ref file
2025-05-13 14:41:26,249 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 14:41:26,506 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:26,524 - stpipe.Spec2Pipeline.barshadow - INFO - Using BARSHADOW reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits
2025-05-13 14:41:26,638 - stpipe.Spec2Pipeline.barshadow - INFO - Working on slitlet 72
2025-05-13 14:41:26,664 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow done
2025-05-13 14:41:26,928 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs1_rate.fits>,).
2025-05-13 14:41:26,952 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits
2025-05-13 14:41:26,953 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits
2025-05-13 14:41:27,059 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 14:41:27,060 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS1
2025-05-13 14:41:27,060 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_MSASPEC
2025-05-13 14:41:27,061 - stpipe.Spec2Pipeline.photom - INFO - filter: F290LP
2025-05-13 14:41:27,061 - stpipe.Spec2Pipeline.photom - INFO - grating: G395M
2025-05-13 14:41:27,093 - stpipe.Spec2Pipeline.photom - INFO - Working on slit 72
2025-05-13 14:41:27,093 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1.98814e+12
2025-05-13 14:41:27,100 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 14:41:27,465 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_cal.fits>,).
2025-05-13 14:41:27,466 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 14:41:27,671 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_cal.fits>,).
2025-05-13 14:41:27,807 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_cal.fits
2025-05-13 14:41:28,134 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 14:41:28,143 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10694 arcsec.
2025-05-13 14:41:28,145 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.10693693569272517 arcsec.
2025-05-13 14:41:28,145 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 14:41:28,145 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 14:41:28,146 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 14:41:28,146 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: ivm
2025-05-13 14:41:28,147 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:41:28,201 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:41:28,207 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:41:28,214 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:41:28,221 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:41:28,324 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 110.843681192 -73.435396742 110.846105595 -73.435396742 110.846105595 -73.434834269 110.843681192 -73.434834269
2025-05-13 14:41:28,456 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_s2d.fits
2025-05-13 14:41:28,457 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 14:41:28,518 - stpipe.Spec2Pipeline - INFO - Extracting 1 MSA slitlets
2025-05-13 14:41:28,721 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs1_s2d.fits>,).
2025-05-13 14:41:28,806 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json
2025-05-13 14:41:28,816 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits
2025-05-13 14:41:28,857 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit 72
2025-05-13 14:41:28,858 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 14:41:28,858 - stpipe.Spec2Pipeline.extract_1d - INFO - Setting use_source_posn to False for exposure type NRS_MSASPEC, source type EXTENDED
2025-05-13 14:41:28,860 - stpipe.Spec2Pipeline.extract_1d - INFO - Aperture start/stop: 12.50 -> 17.50 (inclusive)
2025-05-13 14:41:28,913 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 14:41:28,975 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_x1d.fits
2025-05-13 14:41:28,976 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1
2025-05-13 14:41:28,977 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 14:41:28,978 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:41:29,173 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_cal.fits
2025-05-13 14:41:29,173 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 14:41:29,174 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 14:41:29,206 - 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 14:41:29,318 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:41:29,345 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:41:29,371 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 14:41:29,372 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 14:41:29,373 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 14:41:29,374 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 14:41:29,375 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 14:41:29,376 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 14:41:29,377 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 14:41:29,378 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 14:41:29,382 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 14:41:29,383 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:41:29,384 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:41:29,385 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:41:29,386 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 14:41:29,387 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:41:29,388 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:41:29,390 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:41:29,391 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 14:41:29,392 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:41:29,393 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 14:41:29,394 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 14:41:29,395 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 14:41:29,396 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 14:41:29,397 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:41:29,398 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:41:29,398 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 14:41:29,399 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 14:41:29,400 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:41:29,402 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:41:29,403 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 14:41:29,405 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:41:29,626 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_03103_00001_nrs2_l2asn.json',).
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits
2025-05-13 14:41:29,661 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names:
- '72'
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: none
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: ivm
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
2025-05-13 14:41:29,670 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:41:29,717 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00001_nrs2_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange', 'wfssbkg']
2025-05-13 14:41:29,724 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits 688.9 M bytes (1 / 2 files) (0 / 1.0 G bytes)
2025-05-13 14:41:36,106 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0207.fits 336.6 M bytes (2 / 2 files) (688.9 M / 1.0 G bytes)
2025-05-13 14:41:38,270 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits'.
2025-05-13 14:41:38,271 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits'.
2025-05-13 14:41:38,272 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits'.
2025-05-13 14:41:38,272 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 14:41:38,273 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 14:41:38,273 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 14:41:38,274 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits'.
2025-05-13 14:41:38,274 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf'.
2025-05-13 14:41:38,275 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 14:41:38,275 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json'.
2025-05-13 14:41:38,276 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits'.
2025-05-13 14:41:38,276 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 14:41:38,277 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 14:41:38,277 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf'.
2025-05-13 14:41:38,278 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 14:41:38,278 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 14:41:38,279 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 14:41:38,279 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 14:41:38,279 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 14:41:38,280 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 14:41:38,280 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 14:41:38,280 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json'.
2025-05-13 14:41:38,281 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 14:41:38,281 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 14:41:38,281 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits'.
2025-05-13 14:41:38,282 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits'.
2025-05-13 14:41:38,283 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 14:41:38,283 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 14:41:38,284 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0207.fits'.
2025-05-13 14:41:38,284 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 14:41:38,285 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 14:41:38,285 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 14:41:38,285 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf'.
2025-05-13 14:41:38,286 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 14:41:38,286 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 14:41:38,287 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 14:41:38,293 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:41:38,294 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2
2025-05-13 14:41:38,294 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits ...
2025-05-13 14:41:38,508 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:38,730 - stpipe.Spec2Pipeline.assign_wcs - INFO - Retrieving open MSA slitlets for msa_metadata_id = 76 and dither_index = 1
2025-05-13 14:41:38,737 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 2 contains virtual source, with source_id=-32
2025-05-13 14:41:38,739 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 3 contains virtual source, with source_id=-33
2025-05-13 14:41:38,742 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 4 contains virtual source, with source_id=-34
2025-05-13 14:41:38,744 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 5 contains virtual source, with source_id=-35
2025-05-13 14:41:38,747 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 6 contains virtual source, with source_id=-36
2025-05-13 14:41:38,749 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 7 contains virtual source, with source_id=-37
2025-05-13 14:41:38,754 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 9 contains virtual source, with source_id=-38
2025-05-13 14:41:38,767 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 15 contains virtual source, with source_id=-39
2025-05-13 14:41:38,776 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 19 contains virtual source, with source_id=-40
2025-05-13 14:41:38,781 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 21 contains virtual source, with source_id=-41
2025-05-13 14:41:38,790 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 25 contains virtual source, with source_id=-42
2025-05-13 14:41:38,797 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 28 contains virtual source, with source_id=-43
2025-05-13 14:41:38,800 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 29 contains virtual source, with source_id=-44
2025-05-13 14:41:38,806 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 31 contains virtual source, with source_id=-45
2025-05-13 14:41:38,808 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 32 contains virtual source, with source_id=-46
2025-05-13 14:41:38,820 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 37 contains virtual source, with source_id=-47
2025-05-13 14:41:38,827 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 40 contains virtual source, with source_id=-48
2025-05-13 14:41:38,829 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 41 contains virtual source, with source_id=-49
2025-05-13 14:41:38,843 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 47 contains virtual source, with source_id=-50
2025-05-13 14:41:38,850 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 50 contains virtual source, with source_id=-51
2025-05-13 14:41:38,855 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 52 contains virtual source, with source_id=-52
2025-05-13 14:41:38,865 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 56 contains virtual source, with source_id=-53
2025-05-13 14:41:38,872 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 59 contains virtual source, with source_id=-54
2025-05-13 14:41:38,875 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 60 contains virtual source, with source_id=-55
2025-05-13 14:41:38,882 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 63 contains virtual source, with source_id=-56
2025-05-13 14:41:38,888 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 66 contains virtual source, with source_id=-57
2025-05-13 14:41:38,891 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 67 contains virtual source, with source_id=-58
2025-05-13 14:41:38,900 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 71 contains virtual source, with source_id=-59
2025-05-13 14:41:38,905 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 73 contains virtual source, with source_id=-60
2025-05-13 14:41:38,908 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 74 contains virtual source, with source_id=-61
2025-05-13 14:41:38,911 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 75 contains virtual source, with source_id=-62
2025-05-13 14:41:38,938 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:41:38,939 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:41:38,939 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:41:38,940 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:41:40,228 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 74 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:40,490 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 75 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:40,491 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS2: [np.int16(2), np.int16(3), np.int16(4), np.int16(5), np.int16(6), np.int16(7), np.int16(8), np.int16(9), np.int16(10), np.int16(11), np.int16(12), np.int16(13), np.int16(14), np.int16(15), np.int16(16), np.int16(17), np.int16(18), np.int16(19), np.int16(20), np.int16(21), np.int16(22), np.int16(23), np.int16(24), np.int16(25), np.int16(26), np.int16(27), np.int16(28), np.int16(29), np.int16(30), np.int16(31), np.int16(32), np.int16(33), np.int16(34), np.int16(35), np.int16(36), np.int16(37), np.int16(38), np.int16(39), np.int16(40), np.int16(41), np.int16(42), np.int16(43), np.int16(44), np.int16(45), np.int16(46), np.int16(47), np.int16(48), np.int16(49), np.int16(50), np.int16(51), np.int16(52), np.int16(53), np.int16(54), np.int16(55), np.int16(56), np.int16(57), np.int16(58), np.int16(59), np.int16(60), np.int16(61), np.int16(62), np.int16(63), np.int16(64), np.int16(65), np.int16(66), np.int16(67), np.int16(68), np.int16(69), np.int16(70), np.int16(71), np.int16(72), np.int16(73)]
2025-05-13 14:41:40,492 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 72 open slitlets
2025-05-13 14:41:40,518 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:41:40,519 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:41:40,519 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:41:40,520 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:41:40,532 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:41:40,628 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999883916038974
2025-05-13 14:41:40,657 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 19 open slits in quadrant 1
2025-05-13 14:41:40,772 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 26 open slits in quadrant 2
2025-05-13 14:41:40,928 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 14 open slits in quadrant 3
2025-05-13 14:41:41,219 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 13 open slits in quadrant 4
2025-05-13 14:41:41,296 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:41:41,457 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf', 'camera': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf', 'collimator': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf', 'disperser': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf', 'fpa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf', 'msa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf', 'ote': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_01_msa.fits'}
2025-05-13 14:41:43,024 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 14:41:43,030 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 14:41:43,286 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs2_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits']).
2025-05-13 14:41:43,287 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 14:41:43,519 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:43,534 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json
2025-05-13 14:41:43,629 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:41:43,629 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:41:43,630 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:41:43,631 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:41:43,642 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:41:43,738 - stpipe.Spec2Pipeline.msa_flagging - INFO - Applied Barycentric velocity correction : 0.9999883916038974
2025-05-13 14:41:43,767 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 6 open slits in quadrant 1
2025-05-13 14:41:43,803 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2025-05-13 14:41:43,822 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 12 open slits in quadrant 3
2025-05-13 14:41:43,894 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2025-05-13 14:41:43,913 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:41:47,882 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2025-05-13 14:41:48,222 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:48,223 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 14:41:48,456 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs2_rate.fits>, []).
2025-05-13 14:41:48,457 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:41:48,696 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits', []).
2025-05-13 14:41:48,696 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:41:48,924 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits', []).
2025-05-13 14:41:48,924 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:41:49,165 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs2_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits']).
2025-05-13 14:41:49,318 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits
2025-05-13 14:41:49,402 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits
2025-05-13 14:41:49,479 - stpipe.Spec2Pipeline.bkg_subtract - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:327: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
2025-05-13 14:41:49,870 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw02736007001_03103_00001_nrs2_rate.fits
2025-05-13 14:41:51,015 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 14:41:51,315 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:51,330 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_MSASPEC
2025-05-13 14:41:51,330 - stpipe.Spec2Pipeline.extract_2d - INFO - Slits selected:
2025-05-13 14:41:51,331 - stpipe.Spec2Pipeline.extract_2d - INFO - Name: 72, source_id: 6355
2025-05-13 14:41:52,480 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 72
2025-05-13 14:41:52,481 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 0 181
2025-05-13 14:41:52,481 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1586 1619
2025-05-13 14:41:52,623 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 14:41:52,631 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 110.843614826 -73.434854652 110.845969148 -73.435400859 110.846091091 -73.435357606 110.843736796 -73.434811390
2025-05-13 14:41:52,632 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 110.843614826 -73.434854652 110.845969148 -73.435400859 110.846091091 -73.435357606 110.843736796 -73.434811390
2025-05-13 14:41:52,677 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 14:41:53,056 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:53,063 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_MSASPEC
2025-05-13 14:41:53,064 - stpipe.Spec2Pipeline.srctype - INFO - source_id=6355, stellarity=0.1000, type=EXTENDED
2025-05-13 14:41:53,065 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 14:41:53,479 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:53,480 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 14:41:53,480 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:41:53,776 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:53,792 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf
2025-05-13 14:41:53,902 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 72
2025-05-13 14:41:53,904 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 14:41:54,211 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:54,249 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 14:41:54,306 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits
2025-05-13 14:41:54,496 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0207.fits
2025-05-13 14:41:54,642 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits
2025-05-13 14:41:54,738 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 72
2025-05-13 14:41:54,929 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 14:41:55,239 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:55,254 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits
2025-05-13 14:41:55,280 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_MSASPEC
2025-05-13 14:41:55,384 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit 0
2025-05-13 14:41:55,384 - stpipe.Spec2Pipeline.pathloss - INFO - Shutter state = 1x111, using MOS1x3 entry in ref file
2025-05-13 14:41:55,398 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 14:41:55,704 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:55,719 - stpipe.Spec2Pipeline.barshadow - INFO - Using BARSHADOW reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits
2025-05-13 14:41:55,838 - stpipe.Spec2Pipeline.barshadow - INFO - Working on slitlet 72
2025-05-13 14:41:55,857 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow done
2025-05-13 14:41:56,170 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs2_rate.fits>,).
2025-05-13 14:41:56,193 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits
2025-05-13 14:41:56,193 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits
2025-05-13 14:41:56,268 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 14:41:56,268 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS2
2025-05-13 14:41:56,269 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_MSASPEC
2025-05-13 14:41:56,269 - stpipe.Spec2Pipeline.photom - INFO - filter: F290LP
2025-05-13 14:41:56,269 - stpipe.Spec2Pipeline.photom - INFO - grating: G395M
2025-05-13 14:41:56,297 - stpipe.Spec2Pipeline.photom - INFO - Working on slit 72
2025-05-13 14:41:56,298 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1.98814e+12
2025-05-13 14:41:56,303 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 14:41:56,727 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_cal.fits>,).
2025-05-13 14:41:56,728 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 14:41:56,975 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_cal.fits>,).
2025-05-13 14:41:57,109 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_cal.fits
2025-05-13 14:41:57,391 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 14:41:57,400 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10698 arcsec.
2025-05-13 14:41:57,401 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.10697869382026925 arcsec.
2025-05-13 14:41:57,401 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 14:41:57,402 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 14:41:57,403 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 14:41:57,403 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: ivm
2025-05-13 14:41:57,404 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:41:57,437 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:41:57,439 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:41:57,441 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:41:57,443 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:41:57,520 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 110.843716622 -73.435386426 110.846061126 -73.435386426 110.846061126 -73.434842490 110.843716622 -73.434842490
2025-05-13 14:41:57,624 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_s2d.fits
2025-05-13 14:41:57,625 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 14:41:57,676 - stpipe.Spec2Pipeline - INFO - Extracting 1 MSA slitlets
2025-05-13 14:41:57,947 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw02736007001_03103_00001_nrs2_s2d.fits>,).
2025-05-13 14:41:58,013 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json
2025-05-13 14:41:58,022 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits
2025-05-13 14:41:58,056 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit 72
2025-05-13 14:41:58,057 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 14:41:58,058 - stpipe.Spec2Pipeline.extract_1d - INFO - Setting use_source_posn to False for exposure type NRS_MSASPEC, source type EXTENDED
2025-05-13 14:41:58,059 - stpipe.Spec2Pipeline.extract_1d - INFO - Aperture start/stop: 12.00 -> 17.00 (inclusive)
2025-05-13 14:41:58,106 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 14:41:58,169 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_x1d.fits
2025-05-13 14:41:58,170 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2
2025-05-13 14:41:58,171 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 14:41:58,171 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:41:58,369 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_cal.fits
2025-05-13 14:41:58,369 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 14:41:58,370 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 14:41:58,402 - 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 14:41:58,488 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:41:58,516 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:41:58,542 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 14:41:58,543 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 14:41:58,544 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 14:41:58,545 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 14:41:58,546 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 14:41:58,547 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 14:41:58,548 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 14:41:58,549 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 14:41:58,554 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 14:41:58,555 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:41:58,556 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:41:58,557 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:41:58,558 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 14:41:58,559 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:41:58,560 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:41:58,562 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:41:58,563 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 14:41:58,563 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:41:58,564 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 14:41:58,566 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 14:41:58,567 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 14:41:58,568 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 14:41:58,569 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:41:58,570 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:41:58,571 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 14:41:58,571 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 14:41:58,572 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:41:58,573 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:41:58,575 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 14:41:58,577 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits
2025-05-13 14:41:58,864 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_03103_00002_nrs1_l2asn.json',).
2025-05-13 14:41:58,896 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names:
- '72'
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: none
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: ivm
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
2025-05-13 14:41:58,905 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:41:58,954 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00002_nrs1_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange', 'wfssbkg']
2025-05-13 14:41:58,960 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits'.
2025-05-13 14:41:58,961 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits'.
2025-05-13 14:41:58,961 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits'.
2025-05-13 14:41:58,962 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 14:41:58,962 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 14:41:58,963 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 14:41:58,963 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits'.
2025-05-13 14:41:58,964 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf'.
2025-05-13 14:41:58,964 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 14:41:58,965 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json'.
2025-05-13 14:41:58,965 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits'.
2025-05-13 14:41:58,966 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 14:41:58,966 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 14:41:58,967 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf'.
2025-05-13 14:41:58,968 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 14:41:58,968 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 14:41:58,969 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 14:41:58,969 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 14:41:58,969 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 14:41:58,970 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 14:41:58,970 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 14:41:58,971 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json'.
2025-05-13 14:41:58,972 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 14:41:58,972 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 14:41:58,972 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits'.
2025-05-13 14:41:58,973 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits'.
2025-05-13 14:41:58,973 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 14:41:58,973 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 14:41:58,974 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0177.fits'.
2025-05-13 14:41:58,975 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 14:41:58,975 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 14:41:58,975 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 14:41:58,976 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf'.
2025-05-13 14:41:58,976 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 14:41:58,977 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 14:41:58,978 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 14:41:58,984 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:41:58,984 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1
2025-05-13 14:41:58,985 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits ...
2025-05-13 14:41:59,201 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:41:59,420 - stpipe.Spec2Pipeline.assign_wcs - INFO - Retrieving open MSA slitlets for msa_metadata_id = 76 and dither_index = 2
2025-05-13 14:41:59,426 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 2 contains virtual source, with source_id=-32
2025-05-13 14:41:59,427 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 3 is background only; assigned source_id=3
2025-05-13 14:41:59,429 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 4 contains virtual source, with source_id=-34
2025-05-13 14:41:59,430 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 5 is background only; assigned source_id=5
2025-05-13 14:41:59,431 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 6 is background only; assigned source_id=6
2025-05-13 14:41:59,434 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 7 contains virtual source, with source_id=-37
2025-05-13 14:41:59,437 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 9 is background only; assigned source_id=9
2025-05-13 14:41:59,451 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 15 contains virtual source, with source_id=-39
2025-05-13 14:41:59,460 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 19 contains virtual source, with source_id=-40
2025-05-13 14:41:59,463 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 21 is background only; assigned source_id=21
2025-05-13 14:41:59,471 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 25 is background only; assigned source_id=25
2025-05-13 14:41:59,479 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 28 contains virtual source, with source_id=-43
2025-05-13 14:41:59,481 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 29 contains virtual source, with source_id=-44
2025-05-13 14:41:59,484 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 31 is background only; assigned source_id=31
2025-05-13 14:41:59,485 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 32 is background only; assigned source_id=32
2025-05-13 14:41:59,496 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 37 is background only; assigned source_id=37
2025-05-13 14:41:59,503 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 40 contains virtual source, with source_id=-48
2025-05-13 14:41:59,505 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 41 contains virtual source, with source_id=-49
2025-05-13 14:41:59,517 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 47 is background only; assigned source_id=47
2025-05-13 14:41:59,525 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 50 contains virtual source, with source_id=-51
2025-05-13 14:41:59,530 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 52 contains virtual source, with source_id=-52
2025-05-13 14:41:59,539 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 56 contains virtual source, with source_id=-53
2025-05-13 14:41:59,546 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 59 contains virtual source, with source_id=-54
2025-05-13 14:41:59,549 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 60 contains virtual source, with source_id=-55
2025-05-13 14:41:59,556 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 63 contains virtual source, with source_id=-56
2025-05-13 14:41:59,561 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 66 is background only; assigned source_id=66
2025-05-13 14:41:59,564 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 67 contains virtual source, with source_id=-58
2025-05-13 14:41:59,573 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 71 contains virtual source, with source_id=-59
2025-05-13 14:41:59,578 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 73 contains virtual source, with source_id=-60
2025-05-13 14:41:59,578 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 74 is background only; assigned source_id=74
2025-05-13 14:41:59,581 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 75 contains virtual source, with source_id=-62
2025-05-13 14:41:59,608 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:41:59,609 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:41:59,610 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:41:59,610 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:41:59,802 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,822 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,841 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,861 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,881 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 10 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,900 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 11 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,919 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 12 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,938 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 13 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,958 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 14 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:41:59,977 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 16 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:00,165 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:00,184 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:00,203 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 5 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:00,222 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 9 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:00,241 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 15 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:01,143 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS1: [np.int16(17), np.int16(18), np.int16(19), np.int16(20), np.int16(21), np.int16(22), np.int16(23), np.int16(24), np.int16(25), np.int16(26), np.int16(27), np.int16(28), np.int16(29), np.int16(30), np.int16(31), np.int16(32), np.int16(33), np.int16(34), np.int16(35), np.int16(36), np.int16(37), np.int16(38), np.int16(39), np.int16(40), np.int16(41), np.int16(42), np.int16(43), np.int16(44), np.int16(45), np.int16(46), np.int16(47), np.int16(48), np.int16(49), np.int16(50), np.int16(51), np.int16(52), np.int16(53), np.int16(54), np.int16(55), np.int16(56), np.int16(57), np.int16(58), np.int16(59), np.int16(60), np.int16(61), np.int16(62), np.int16(63), np.int16(64), np.int16(65), np.int16(66), np.int16(67), np.int16(68), np.int16(69), np.int16(70), np.int16(71), np.int16(72), np.int16(73), np.int16(74), np.int16(75)]
2025-05-13 14:42:01,144 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 59 open slitlets
2025-05-13 14:42:01,171 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:42:01,171 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:42:01,172 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:42:01,173 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:42:01,184 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:42:01,279 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999883840655238
2025-05-13 14:42:01,309 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 9 open slits in quadrant 1
2025-05-13 14:42:01,364 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 21 open slits in quadrant 2
2025-05-13 14:42:01,489 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 15 open slits in quadrant 3
2025-05-13 14:42:01,581 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 14 open slits in quadrant 4
2025-05-13 14:42:01,899 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:42:02,060 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf', 'camera': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf', 'collimator': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf', 'disperser': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf', 'fpa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf', 'msa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf', 'ote': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_01_msa.fits'}
2025-05-13 14:42:03,144 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 14:42:03,150 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 14:42:03,386 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits']).
2025-05-13 14:42:03,387 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 14:42:03,609 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:03,625 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json
2025-05-13 14:42:03,721 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:42:03,722 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:42:03,722 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:42:03,723 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:42:03,735 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:42:03,829 - stpipe.Spec2Pipeline.msa_flagging - INFO - Applied Barycentric velocity correction : 0.9999883840655238
2025-05-13 14:42:03,858 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 6 open slits in quadrant 1
2025-05-13 14:42:03,895 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2025-05-13 14:42:03,913 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 12 open slits in quadrant 3
2025-05-13 14:42:03,987 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2025-05-13 14:42:04,005 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:42:07,924 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2025-05-13 14:42:08,271 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:08,272 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 14:42:08,527 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs1_rate.fits>, []).
2025-05-13 14:42:08,528 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:08,759 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', []).
2025-05-13 14:42:08,759 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:08,986 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits', []).
2025-05-13 14:42:08,987 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:09,235 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits']).
2025-05-13 14:42:09,363 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits
2025-05-13 14:42:09,462 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits
2025-05-13 14:42:09,573 - stpipe.Spec2Pipeline.bkg_subtract - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:327: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
2025-05-13 14:42:09,971 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw02736007001_03103_00002_nrs1_rate.fits
2025-05-13 14:42:10,941 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 14:42:11,239 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:11,254 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_MSASPEC
2025-05-13 14:42:11,255 - stpipe.Spec2Pipeline.extract_2d - INFO - Slits selected:
2025-05-13 14:42:11,255 - stpipe.Spec2Pipeline.extract_2d - INFO - Name: 72, source_id: 6355
2025-05-13 14:42:12,216 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 72
2025-05-13 14:42:12,217 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1014 2048
2025-05-13 14:42:12,217 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1586 1624
2025-05-13 14:42:12,371 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 14:42:12,380 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 110.843213328 -73.434762058 110.845567620 -73.435308272 110.845689563 -73.435265019 110.843335298 -73.434718797
2025-05-13 14:42:12,381 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 110.843213328 -73.434762058 110.845567620 -73.435308272 110.845689563 -73.435265019 110.843335298 -73.434718797
2025-05-13 14:42:12,429 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 14:42:12,791 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:12,798 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_MSASPEC
2025-05-13 14:42:12,799 - stpipe.Spec2Pipeline.srctype - INFO - source_id=6355, stellarity=0.1000, type=EXTENDED
2025-05-13 14:42:12,800 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 14:42:13,198 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:13,199 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 14:42:13,200 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:42:13,492 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:13,507 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf
2025-05-13 14:42:13,617 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 72
2025-05-13 14:42:13,619 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 14:42:13,922 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:13,962 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 14:42:14,019 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits
2025-05-13 14:42:14,206 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0177.fits
2025-05-13 14:42:14,347 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits
2025-05-13 14:42:14,444 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 72
2025-05-13 14:42:14,710 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 14:42:15,015 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:15,030 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits
2025-05-13 14:42:15,057 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_MSASPEC
2025-05-13 14:42:15,155 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit 0
2025-05-13 14:42:15,156 - stpipe.Spec2Pipeline.pathloss - INFO - Shutter state = x1111, using MOS1x3 entry in ref file
2025-05-13 14:42:15,156 - stpipe.Spec2Pipeline.pathloss - INFO - Shutter below fiducial is closed, using lower region of pathloss array
2025-05-13 14:42:15,171 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 14:42:15,474 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:15,490 - stpipe.Spec2Pipeline.barshadow - INFO - Using BARSHADOW reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits
2025-05-13 14:42:15,604 - stpipe.Spec2Pipeline.barshadow - INFO - Working on slitlet 72
2025-05-13 14:42:15,630 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow done
2025-05-13 14:42:15,937 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs1_rate.fits>,).
2025-05-13 14:42:15,960 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits
2025-05-13 14:42:15,961 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits
2025-05-13 14:42:16,037 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 14:42:16,037 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS1
2025-05-13 14:42:16,038 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_MSASPEC
2025-05-13 14:42:16,038 - stpipe.Spec2Pipeline.photom - INFO - filter: F290LP
2025-05-13 14:42:16,039 - stpipe.Spec2Pipeline.photom - INFO - grating: G395M
2025-05-13 14:42:16,067 - stpipe.Spec2Pipeline.photom - INFO - Working on slit 72
2025-05-13 14:42:16,068 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1.9878e+12
2025-05-13 14:42:16,075 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 14:42:16,488 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_cal.fits>,).
2025-05-13 14:42:16,489 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 14:42:16,726 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_cal.fits>,).
2025-05-13 14:42:16,862 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_cal.fits
2025-05-13 14:42:17,182 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 14:42:17,191 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10694 arcsec.
2025-05-13 14:42:17,193 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.10693693487974193 arcsec.
2025-05-13 14:42:17,193 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 14:42:17,193 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 14:42:17,194 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 14:42:17,194 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: ivm
2025-05-13 14:42:17,195 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:42:17,249 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:42:17,256 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:42:17,263 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:42:17,269 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:42:17,372 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 110.843279690 -73.435304154 110.845704062 -73.435304154 110.845704062 -73.434741675 110.843279690 -73.434741675
2025-05-13 14:42:17,502 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_s2d.fits
2025-05-13 14:42:17,502 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 14:42:17,565 - stpipe.Spec2Pipeline - INFO - Extracting 1 MSA slitlets
2025-05-13 14:42:17,830 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs1_s2d.fits>,).
2025-05-13 14:42:17,902 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json
2025-05-13 14:42:17,911 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits
2025-05-13 14:42:17,945 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit 72
2025-05-13 14:42:17,946 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 14:42:17,946 - stpipe.Spec2Pipeline.extract_1d - INFO - Setting use_source_posn to False for exposure type NRS_MSASPEC, source type EXTENDED
2025-05-13 14:42:17,947 - stpipe.Spec2Pipeline.extract_1d - INFO - Aperture start/stop: 12.50 -> 17.50 (inclusive)
2025-05-13 14:42:17,997 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 14:42:18,058 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_x1d.fits
2025-05-13 14:42:18,059 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1
2025-05-13 14:42:18,060 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 14:42:18,060 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:42:18,256 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_cal.fits
2025-05-13 14:42:18,256 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 14:42:18,257 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 14:42:18,290 - 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 14:42:18,371 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:42:18,398 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:42:18,423 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 14:42:18,425 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 14:42:18,426 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 14:42:18,427 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 14:42:18,428 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 14:42:18,429 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 14:42:18,430 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 14:42:18,431 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 14:42:18,435 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 14:42:18,436 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:42:18,437 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:42:18,438 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:42:18,439 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 14:42:18,440 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:42:18,441 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:42:18,443 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:42:18,444 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 14:42:18,445 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:42:18,445 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 14:42:18,446 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 14:42:18,447 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 14:42:18,448 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 14:42:18,449 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:42:18,450 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:42:18,451 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 14:42:18,452 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 14:42:18,452 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:42:18,453 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:42:18,455 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 14:42:18,457 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:42:18,731 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_03103_00002_nrs2_l2asn.json',).
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits
2025-05-13 14:42:18,763 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names:
- '72'
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: none
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: ivm
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
2025-05-13 14:42:18,774 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:42:18,822 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00002_nrs2_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange', 'wfssbkg']
2025-05-13 14:42:18,828 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits'.
2025-05-13 14:42:18,829 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits'.
2025-05-13 14:42:18,829 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits'.
2025-05-13 14:42:18,830 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 14:42:18,830 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 14:42:18,831 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 14:42:18,832 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits'.
2025-05-13 14:42:18,833 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf'.
2025-05-13 14:42:18,833 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 14:42:18,834 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json'.
2025-05-13 14:42:18,834 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits'.
2025-05-13 14:42:18,834 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 14:42:18,835 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 14:42:18,835 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf'.
2025-05-13 14:42:18,836 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 14:42:18,836 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 14:42:18,836 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 14:42:18,837 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 14:42:18,837 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 14:42:18,837 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 14:42:18,838 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 14:42:18,839 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json'.
2025-05-13 14:42:18,839 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 14:42:18,840 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 14:42:18,840 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits'.
2025-05-13 14:42:18,840 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits'.
2025-05-13 14:42:18,841 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 14:42:18,841 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 14:42:18,842 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0207.fits'.
2025-05-13 14:42:18,842 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 14:42:18,842 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 14:42:18,843 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 14:42:18,843 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf'.
2025-05-13 14:42:18,843 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 14:42:18,845 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 14:42:18,846 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 14:42:18,852 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:42:18,853 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2
2025-05-13 14:42:18,853 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits ...
2025-05-13 14:42:19,078 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:19,304 - stpipe.Spec2Pipeline.assign_wcs - INFO - Retrieving open MSA slitlets for msa_metadata_id = 76 and dither_index = 2
2025-05-13 14:42:19,311 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 2 contains virtual source, with source_id=-32
2025-05-13 14:42:19,312 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 3 is background only; assigned source_id=3
2025-05-13 14:42:19,314 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 4 contains virtual source, with source_id=-34
2025-05-13 14:42:19,315 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 5 is background only; assigned source_id=5
2025-05-13 14:42:19,316 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 6 is background only; assigned source_id=6
2025-05-13 14:42:19,319 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 7 contains virtual source, with source_id=-37
2025-05-13 14:42:19,322 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 9 is background only; assigned source_id=9
2025-05-13 14:42:19,335 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 15 contains virtual source, with source_id=-39
2025-05-13 14:42:19,344 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 19 contains virtual source, with source_id=-40
2025-05-13 14:42:19,347 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 21 is background only; assigned source_id=21
2025-05-13 14:42:19,355 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 25 is background only; assigned source_id=25
2025-05-13 14:42:19,362 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 28 contains virtual source, with source_id=-43
2025-05-13 14:42:19,364 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 29 contains virtual source, with source_id=-44
2025-05-13 14:42:19,367 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 31 is background only; assigned source_id=31
2025-05-13 14:42:19,368 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 32 is background only; assigned source_id=32
2025-05-13 14:42:19,378 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 37 is background only; assigned source_id=37
2025-05-13 14:42:19,385 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 40 contains virtual source, with source_id=-48
2025-05-13 14:42:19,387 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 41 contains virtual source, with source_id=-49
2025-05-13 14:42:19,399 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 47 is background only; assigned source_id=47
2025-05-13 14:42:19,406 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 50 contains virtual source, with source_id=-51
2025-05-13 14:42:19,411 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 52 contains virtual source, with source_id=-52
2025-05-13 14:42:19,420 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 56 contains virtual source, with source_id=-53
2025-05-13 14:42:19,427 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 59 contains virtual source, with source_id=-54
2025-05-13 14:42:19,430 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 60 contains virtual source, with source_id=-55
2025-05-13 14:42:19,437 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 63 contains virtual source, with source_id=-56
2025-05-13 14:42:19,442 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 66 is background only; assigned source_id=66
2025-05-13 14:42:19,444 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 67 contains virtual source, with source_id=-58
2025-05-13 14:42:19,453 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 71 contains virtual source, with source_id=-59
2025-05-13 14:42:19,458 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 73 contains virtual source, with source_id=-60
2025-05-13 14:42:19,459 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 74 is background only; assigned source_id=74
2025-05-13 14:42:19,461 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 75 contains virtual source, with source_id=-62
2025-05-13 14:42:19,489 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:42:19,490 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:42:19,491 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:42:19,491 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:42:20,788 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 74 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:21,049 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 75 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:21,050 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS2: [np.int16(2), np.int16(3), np.int16(4), np.int16(5), np.int16(6), np.int16(7), np.int16(8), np.int16(9), np.int16(10), np.int16(11), np.int16(12), np.int16(13), np.int16(14), np.int16(15), np.int16(16), np.int16(17), np.int16(18), np.int16(19), np.int16(20), np.int16(21), np.int16(22), np.int16(23), np.int16(24), np.int16(25), np.int16(26), np.int16(27), np.int16(28), np.int16(29), np.int16(30), np.int16(31), np.int16(32), np.int16(33), np.int16(34), np.int16(35), np.int16(36), np.int16(37), np.int16(38), np.int16(39), np.int16(40), np.int16(41), np.int16(42), np.int16(43), np.int16(44), np.int16(45), np.int16(46), np.int16(47), np.int16(48), np.int16(49), np.int16(50), np.int16(51), np.int16(52), np.int16(53), np.int16(54), np.int16(55), np.int16(56), np.int16(57), np.int16(58), np.int16(59), np.int16(60), np.int16(61), np.int16(62), np.int16(63), np.int16(64), np.int16(65), np.int16(66), np.int16(67), np.int16(68), np.int16(69), np.int16(70), np.int16(71), np.int16(72), np.int16(73)]
2025-05-13 14:42:21,051 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 72 open slitlets
2025-05-13 14:42:21,077 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:42:21,078 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:42:21,078 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:42:21,079 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:42:21,091 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:42:21,187 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999883840655238
2025-05-13 14:42:21,215 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 19 open slits in quadrant 1
2025-05-13 14:42:21,331 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 26 open slits in quadrant 2
2025-05-13 14:42:21,488 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 14 open slits in quadrant 3
2025-05-13 14:42:21,796 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 13 open slits in quadrant 4
2025-05-13 14:42:21,876 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:42:22,041 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf', 'camera': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf', 'collimator': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf', 'disperser': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf', 'fpa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf', 'msa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf', 'ote': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_01_msa.fits'}
2025-05-13 14:42:23,664 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 14:42:23,671 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 14:42:23,926 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs2_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits']).
2025-05-13 14:42:23,927 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 14:42:24,177 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:24,193 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json
2025-05-13 14:42:24,289 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:42:24,290 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:42:24,291 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:42:24,292 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:42:24,303 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:42:24,398 - stpipe.Spec2Pipeline.msa_flagging - INFO - Applied Barycentric velocity correction : 0.9999883840655238
2025-05-13 14:42:24,427 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 6 open slits in quadrant 1
2025-05-13 14:42:24,467 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2025-05-13 14:42:24,486 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 12 open slits in quadrant 3
2025-05-13 14:42:24,561 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2025-05-13 14:42:24,579 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:42:28,614 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2025-05-13 14:42:28,975 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:28,976 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 14:42:29,217 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs2_rate.fits>, []).
2025-05-13 14:42:29,218 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:29,462 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', []).
2025-05-13 14:42:29,463 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:29,713 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits', []).
2025-05-13 14:42:29,713 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:29,961 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs2_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits']).
2025-05-13 14:42:30,083 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits
2025-05-13 14:42:30,165 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits
2025-05-13 14:42:30,244 - stpipe.Spec2Pipeline.bkg_subtract - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:327: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
2025-05-13 14:42:30,631 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw02736007001_03103_00002_nrs2_rate.fits
2025-05-13 14:42:31,770 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 14:42:32,106 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:32,121 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_MSASPEC
2025-05-13 14:42:32,122 - stpipe.Spec2Pipeline.extract_2d - INFO - Slits selected:
2025-05-13 14:42:32,123 - stpipe.Spec2Pipeline.extract_2d - INFO - Name: 72, source_id: 6355
2025-05-13 14:42:33,289 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 72
2025-05-13 14:42:33,290 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 0 181
2025-05-13 14:42:33,290 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1586 1619
2025-05-13 14:42:33,433 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 14:42:33,441 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 110.843213328 -73.434762058 110.845567620 -73.435308272 110.845689563 -73.435265019 110.843335298 -73.434718797
2025-05-13 14:42:33,441 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 110.843213328 -73.434762058 110.845567620 -73.435308272 110.845689563 -73.435265019 110.843335298 -73.434718797
2025-05-13 14:42:33,485 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 14:42:33,869 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:33,876 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_MSASPEC
2025-05-13 14:42:33,877 - stpipe.Spec2Pipeline.srctype - INFO - source_id=6355, stellarity=0.1000, type=EXTENDED
2025-05-13 14:42:33,878 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 14:42:34,347 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:34,347 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 14:42:34,348 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:42:34,680 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:34,695 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf
2025-05-13 14:42:34,802 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 72
2025-05-13 14:42:34,805 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 14:42:35,137 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:35,176 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 14:42:35,233 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits
2025-05-13 14:42:35,423 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0207.fits
2025-05-13 14:42:35,566 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits
2025-05-13 14:42:35,668 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 72
2025-05-13 14:42:35,859 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 14:42:36,198 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:36,213 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits
2025-05-13 14:42:36,240 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_MSASPEC
2025-05-13 14:42:36,339 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit 0
2025-05-13 14:42:36,340 - stpipe.Spec2Pipeline.pathloss - INFO - Shutter state = x1111, using MOS1x3 entry in ref file
2025-05-13 14:42:36,340 - stpipe.Spec2Pipeline.pathloss - INFO - Shutter below fiducial is closed, using lower region of pathloss array
2025-05-13 14:42:36,354 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 14:42:36,690 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:36,706 - stpipe.Spec2Pipeline.barshadow - INFO - Using BARSHADOW reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits
2025-05-13 14:42:36,820 - stpipe.Spec2Pipeline.barshadow - INFO - Working on slitlet 72
2025-05-13 14:42:36,839 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow done
2025-05-13 14:42:37,183 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs2_rate.fits>,).
2025-05-13 14:42:37,206 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits
2025-05-13 14:42:37,207 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits
2025-05-13 14:42:37,281 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 14:42:37,281 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS2
2025-05-13 14:42:37,282 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_MSASPEC
2025-05-13 14:42:37,282 - stpipe.Spec2Pipeline.photom - INFO - filter: F290LP
2025-05-13 14:42:37,283 - stpipe.Spec2Pipeline.photom - INFO - grating: G395M
2025-05-13 14:42:37,311 - stpipe.Spec2Pipeline.photom - INFO - Working on slit 72
2025-05-13 14:42:37,312 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1.9878e+12
2025-05-13 14:42:37,317 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 14:42:37,777 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_cal.fits>,).
2025-05-13 14:42:37,778 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 14:42:38,056 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_cal.fits>,).
2025-05-13 14:42:38,192 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_cal.fits
2025-05-13 14:42:38,478 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 14:42:38,486 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10698 arcsec.
2025-05-13 14:42:38,488 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.10697869293297786 arcsec.
2025-05-13 14:42:38,488 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 14:42:38,489 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 14:42:38,489 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 14:42:38,489 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: ivm
2025-05-13 14:42:38,490 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:42:38,526 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:42:38,528 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:42:38,530 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:42:38,532 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:42:38,607 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 110.843315263 -73.435293871 110.845659738 -73.435293871 110.845659738 -73.434749929 110.843315263 -73.434749929
2025-05-13 14:42:38,711 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_s2d.fits
2025-05-13 14:42:38,712 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 14:42:38,764 - stpipe.Spec2Pipeline - INFO - Extracting 1 MSA slitlets
2025-05-13 14:42:39,040 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw02736007001_03103_00002_nrs2_s2d.fits>,).
2025-05-13 14:42:39,105 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json
2025-05-13 14:42:39,113 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits
2025-05-13 14:42:39,147 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit 72
2025-05-13 14:42:39,148 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 14:42:39,149 - stpipe.Spec2Pipeline.extract_1d - INFO - Setting use_source_posn to False for exposure type NRS_MSASPEC, source type EXTENDED
2025-05-13 14:42:39,150 - stpipe.Spec2Pipeline.extract_1d - INFO - Aperture start/stop: 12.00 -> 17.00 (inclusive)
2025-05-13 14:42:39,197 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 14:42:39,258 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_x1d.fits
2025-05-13 14:42:39,259 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2
2025-05-13 14:42:39,260 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 14:42:39,261 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:42:39,457 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_cal.fits
2025-05-13 14:42:39,458 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 14:42:39,458 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 14:42:39,491 - 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 14:42:39,573 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:42:39,601 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:42:39,626 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 14:42:39,628 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 14:42:39,629 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 14:42:39,629 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 14:42:39,630 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 14:42:39,631 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 14:42:39,632 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 14:42:39,633 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 14:42:39,637 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 14:42:39,638 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:42:39,640 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:42:39,641 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:42:39,642 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 14:42:39,643 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:42:39,644 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:42:39,646 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:42:39,647 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 14:42:39,647 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:42:39,648 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 14:42:39,649 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 14:42:39,650 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 14:42:39,652 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 14:42:39,653 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:42:39,654 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:42:39,655 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 14:42:39,656 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 14:42:39,657 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:42:39,658 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:42:39,659 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 14:42:39,661 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits
2025-05-13 14:42:39,965 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_03103_00003_nrs1_l2asn.json',).
2025-05-13 14:42:39,998 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names:
- '72'
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: none
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: ivm
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
2025-05-13 14:42:40,007 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:42:40,055 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00003_nrs1_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange', 'wfssbkg']
2025-05-13 14:42:40,061 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits'.
2025-05-13 14:42:40,062 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits'.
2025-05-13 14:42:40,063 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits'.
2025-05-13 14:42:40,063 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 14:42:40,063 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 14:42:40,064 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 14:42:40,064 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits'.
2025-05-13 14:42:40,065 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf'.
2025-05-13 14:42:40,065 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 14:42:40,066 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json'.
2025-05-13 14:42:40,066 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits'.
2025-05-13 14:42:40,067 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 14:42:40,067 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 14:42:40,067 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf'.
2025-05-13 14:42:40,068 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 14:42:40,068 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 14:42:40,068 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 14:42:40,069 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 14:42:40,069 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 14:42:40,070 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 14:42:40,070 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 14:42:40,070 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json'.
2025-05-13 14:42:40,071 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 14:42:40,071 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 14:42:40,071 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits'.
2025-05-13 14:42:40,072 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits'.
2025-05-13 14:42:40,072 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 14:42:40,073 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 14:42:40,073 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0177.fits'.
2025-05-13 14:42:40,073 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 14:42:40,074 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 14:42:40,074 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 14:42:40,074 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf'.
2025-05-13 14:42:40,075 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 14:42:40,075 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 14:42:40,076 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 14:42:40,084 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:42:40,085 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1
2025-05-13 14:42:40,086 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits ...
2025-05-13 14:42:40,313 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:40,549 - stpipe.Spec2Pipeline.assign_wcs - INFO - Retrieving open MSA slitlets for msa_metadata_id = 76 and dither_index = 3
2025-05-13 14:42:40,554 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 2 is background only; assigned source_id=2
2025-05-13 14:42:40,554 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 3 is background only; assigned source_id=3
2025-05-13 14:42:40,555 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 4 is background only; assigned source_id=4
2025-05-13 14:42:40,556 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 5 is background only; assigned source_id=5
2025-05-13 14:42:40,557 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 6 is background only; assigned source_id=6
2025-05-13 14:42:40,558 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 7 is background only; assigned source_id=7
2025-05-13 14:42:40,562 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 9 is background only; assigned source_id=9
2025-05-13 14:42:40,573 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 15 is background only; assigned source_id=15
2025-05-13 14:42:40,582 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 19 contains virtual source, with source_id=-40
2025-05-13 14:42:40,585 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 21 is background only; assigned source_id=21
2025-05-13 14:42:40,592 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 25 is background only; assigned source_id=25
2025-05-13 14:42:40,601 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 28 contains virtual source, with source_id=-43
2025-05-13 14:42:40,602 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 29 is background only; assigned source_id=29
2025-05-13 14:42:40,605 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 31 is background only; assigned source_id=31
2025-05-13 14:42:40,606 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 32 is background only; assigned source_id=32
2025-05-13 14:42:40,615 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 37 is background only; assigned source_id=37
2025-05-13 14:42:40,622 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 40 contains virtual source, with source_id=-48
2025-05-13 14:42:40,625 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 41 contains virtual source, with source_id=-49
2025-05-13 14:42:40,637 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 47 is background only; assigned source_id=47
2025-05-13 14:42:40,645 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 50 contains virtual source, with source_id=-51
2025-05-13 14:42:40,650 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 52 contains virtual source, with source_id=-52
2025-05-13 14:42:40,660 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 56 contains virtual source, with source_id=-53
2025-05-13 14:42:40,665 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 59 is background only; assigned source_id=59
2025-05-13 14:42:40,668 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 60 contains virtual source, with source_id=-55
2025-05-13 14:42:40,674 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 63 is background only; assigned source_id=63
2025-05-13 14:42:40,678 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 66 is background only; assigned source_id=66
2025-05-13 14:42:40,679 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 67 is background only; assigned source_id=67
2025-05-13 14:42:40,687 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 71 is background only; assigned source_id=71
2025-05-13 14:42:40,690 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 73 is background only; assigned source_id=73
2025-05-13 14:42:40,691 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 74 is background only; assigned source_id=74
2025-05-13 14:42:40,691 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 75 is background only; assigned source_id=75
2025-05-13 14:42:40,719 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:42:40,719 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:42:40,720 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:42:40,721 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:42:40,918 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:40,938 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:40,958 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:40,977 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:40,997 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 10 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,017 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 11 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,036 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 12 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,056 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 13 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,075 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 14 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,094 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 16 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,280 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,299 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,318 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 5 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,337 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 9 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:41,356 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 15 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:42:42,265 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS1: [np.int16(17), np.int16(18), np.int16(19), np.int16(20), np.int16(21), np.int16(22), np.int16(23), np.int16(24), np.int16(25), np.int16(26), np.int16(27), np.int16(28), np.int16(29), np.int16(30), np.int16(31), np.int16(32), np.int16(33), np.int16(34), np.int16(35), np.int16(36), np.int16(37), np.int16(38), np.int16(39), np.int16(40), np.int16(41), np.int16(42), np.int16(43), np.int16(44), np.int16(45), np.int16(46), np.int16(47), np.int16(48), np.int16(49), np.int16(50), np.int16(51), np.int16(52), np.int16(53), np.int16(54), np.int16(55), np.int16(56), np.int16(57), np.int16(58), np.int16(59), np.int16(60), np.int16(61), np.int16(62), np.int16(63), np.int16(64), np.int16(65), np.int16(66), np.int16(67), np.int16(68), np.int16(69), np.int16(70), np.int16(71), np.int16(72), np.int16(73), np.int16(74), np.int16(75)]
2025-05-13 14:42:42,266 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 59 open slitlets
2025-05-13 14:42:42,293 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:42:42,293 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:42:42,294 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:42:42,295 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:42:42,306 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:42:42,401 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999883758933936
2025-05-13 14:42:42,431 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 9 open slits in quadrant 1
2025-05-13 14:42:42,487 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 21 open slits in quadrant 2
2025-05-13 14:42:42,615 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 15 open slits in quadrant 3
2025-05-13 14:42:42,708 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 14 open slits in quadrant 4
2025-05-13 14:42:43,052 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:42:43,210 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf', 'camera': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf', 'collimator': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf', 'disperser': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf', 'fpa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf', 'msa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf', 'ote': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_01_msa.fits'}
2025-05-13 14:42:44,307 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 14:42:44,313 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 14:42:44,575 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits']).
2025-05-13 14:42:44,576 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 14:42:44,809 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:44,825 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json
2025-05-13 14:42:44,922 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:42:44,923 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:42:44,924 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:42:44,924 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:42:44,936 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:42:45,031 - stpipe.Spec2Pipeline.msa_flagging - INFO - Applied Barycentric velocity correction : 0.9999883758933936
2025-05-13 14:42:45,060 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 6 open slits in quadrant 1
2025-05-13 14:42:45,098 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2025-05-13 14:42:45,116 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 12 open slits in quadrant 3
2025-05-13 14:42:45,190 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2025-05-13 14:42:45,209 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:42:49,200 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2025-05-13 14:42:49,523 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:49,524 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 14:42:49,762 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs1_rate.fits>, []).
2025-05-13 14:42:49,763 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:50,006 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', []).
2025-05-13 14:42:50,006 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:50,242 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits', []).
2025-05-13 14:42:50,242 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:42:50,500 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits']).
2025-05-13 14:42:50,623 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs1_rate.fits
2025-05-13 14:42:50,705 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs1_rate.fits
2025-05-13 14:42:50,783 - stpipe.Spec2Pipeline.bkg_subtract - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:327: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
2025-05-13 14:42:51,169 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw02736007001_03103_00003_nrs1_rate.fits
2025-05-13 14:42:52,145 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 14:42:52,462 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:52,478 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_MSASPEC
2025-05-13 14:42:52,479 - stpipe.Spec2Pipeline.extract_2d - INFO - Slits selected:
2025-05-13 14:42:52,479 - stpipe.Spec2Pipeline.extract_2d - INFO - Name: 72, source_id: 6355
2025-05-13 14:42:53,461 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 72
2025-05-13 14:42:53,462 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1014 2048
2025-05-13 14:42:53,462 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1586 1624
2025-05-13 14:42:53,617 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 14:42:53,625 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 110.844015385 -73.434946949 110.846369729 -73.435493153 110.846491672 -73.435449900 110.844137355 -73.434903687
2025-05-13 14:42:53,626 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 110.844015385 -73.434946949 110.846369729 -73.435493153 110.846491672 -73.435449900 110.844137355 -73.434903687
2025-05-13 14:42:53,671 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 14:42:54,049 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:54,055 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_MSASPEC
2025-05-13 14:42:54,056 - stpipe.Spec2Pipeline.srctype - INFO - source_id=6355, stellarity=0.1000, type=EXTENDED
2025-05-13 14:42:54,057 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 14:42:54,483 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:54,483 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 14:42:54,484 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:42:54,794 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:54,809 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf
2025-05-13 14:42:54,915 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 72
2025-05-13 14:42:54,918 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 14:42:55,234 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:55,273 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 14:42:55,332 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits
2025-05-13 14:42:55,519 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0177.fits
2025-05-13 14:42:55,661 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits
2025-05-13 14:42:55,757 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 72
2025-05-13 14:42:56,017 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 14:42:56,337 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:56,352 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits
2025-05-13 14:42:56,378 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_MSASPEC
2025-05-13 14:42:56,485 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit 0
2025-05-13 14:42:56,486 - stpipe.Spec2Pipeline.pathloss - INFO - Shutter state = 11x11, using MOS1x3 entry in ref file
2025-05-13 14:42:56,505 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 14:42:56,824 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:56,840 - stpipe.Spec2Pipeline.barshadow - INFO - Using BARSHADOW reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits
2025-05-13 14:42:56,956 - stpipe.Spec2Pipeline.barshadow - INFO - Working on slitlet 72
2025-05-13 14:42:56,982 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow done
2025-05-13 14:42:57,306 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs1_rate.fits>,).
2025-05-13 14:42:57,329 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits
2025-05-13 14:42:57,330 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits
2025-05-13 14:42:57,405 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 14:42:57,405 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS1
2025-05-13 14:42:57,405 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_MSASPEC
2025-05-13 14:42:57,406 - stpipe.Spec2Pipeline.photom - INFO - filter: F290LP
2025-05-13 14:42:57,406 - stpipe.Spec2Pipeline.photom - INFO - grating: G395M
2025-05-13 14:42:57,435 - stpipe.Spec2Pipeline.photom - INFO - Working on slit 72
2025-05-13 14:42:57,436 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1.98847e+12
2025-05-13 14:42:57,443 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 14:42:57,896 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_cal.fits>,).
2025-05-13 14:42:57,897 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 14:42:58,194 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_cal.fits>,).
2025-05-13 14:42:58,329 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_cal.fits
2025-05-13 14:42:58,650 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 14:42:58,659 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10694 arcsec.
2025-05-13 14:42:58,661 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.10693693406477042 arcsec.
2025-05-13 14:42:58,661 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 14:42:58,661 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 14:42:58,662 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 14:42:58,662 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: ivm
2025-05-13 14:42:58,663 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:42:58,718 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:42:58,725 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:42:58,732 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:42:58,738 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (31, 1034)
2025-05-13 14:42:58,843 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 110.844081772 -73.435489041 110.846506198 -73.435489041 110.846506198 -73.434926572 110.844081772 -73.434926572
2025-05-13 14:42:58,972 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_s2d.fits
2025-05-13 14:42:58,973 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 14:42:59,036 - stpipe.Spec2Pipeline - INFO - Extracting 1 MSA slitlets
2025-05-13 14:42:59,307 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs1_s2d.fits>,).
2025-05-13 14:42:59,379 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json
2025-05-13 14:42:59,388 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits
2025-05-13 14:42:59,422 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit 72
2025-05-13 14:42:59,423 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 14:42:59,424 - stpipe.Spec2Pipeline.extract_1d - INFO - Setting use_source_posn to False for exposure type NRS_MSASPEC, source type EXTENDED
2025-05-13 14:42:59,425 - stpipe.Spec2Pipeline.extract_1d - INFO - Aperture start/stop: 12.50 -> 17.50 (inclusive)
2025-05-13 14:42:59,476 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 14:42:59,540 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_x1d.fits
2025-05-13 14:42:59,541 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs1
2025-05-13 14:42:59,543 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 14:42:59,543 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:42:59,741 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_cal.fits
2025-05-13 14:42:59,742 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 14:42:59,742 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 14:42:59,775 - 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 14:42:59,857 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:42:59,884 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:42:59,910 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 14:42:59,911 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 14:42:59,912 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 14:42:59,913 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 14:42:59,914 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 14:42:59,915 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 14:42:59,916 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 14:42:59,917 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 14:42:59,921 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 14:42:59,923 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:42:59,924 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:42:59,925 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:42:59,926 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 14:42:59,927 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:42:59,928 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:42:59,930 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:42:59,931 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 14:42:59,932 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 14:42:59,932 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 14:42:59,934 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 14:42:59,934 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 14:42:59,935 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 14:42:59,936 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 14:42:59,937 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 14:42:59,938 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 14:42:59,939 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 14:42:59,940 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:42:59,941 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:42:59,943 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 14:42:59,945 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:43:00,243 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_03103_00003_nrs2_l2asn.json',).
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits
2025-05-13 14:43:00,278 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_bsub: False
fail_on_exception: True
save_wfss_esec: False
steps:
assign_wcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sip_approx: True
sip_max_pix_error: 0.01
sip_degree: None
sip_max_inv_pix_error: 0.01
sip_inv_degree: None
sip_npoints: 12
slit_y_low: -0.55
slit_y_high: 0.55
badpix_selfcal:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
flagfrac_lower: 0.001
flagfrac_upper: 0.001
kernel_size: 15
force_single: False
save_flagged_bkg: False
msa_flagging:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
nsclean:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
fit_method: fft
fit_by_channel: False
background_method: None
background_box_size: None
mask_spectral_regions: True
n_sigma: 5.0
fit_histogram: False
single_mask: False
user_mask: None
save_mask: False
save_background: False
save_noise: False
bkg_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_combined_background: False
sigma: 3.0
maxiters: None
wfss_mmag_extract: None
wfss_maxiter: 5
wfss_rms_stop: 0.0
wfss_outlier_percent: 1.0
imprint_subtract:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
extract_2d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
slit_names:
- '72'
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
wavecorr:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
srctype:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
source_type: None
straylight:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
clean_showers: False
shower_plane: 3
shower_x_stddev: 18.0
shower_y_stddev: 5.0
shower_low_reject: 0.1
shower_high_reject: 99.9
fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
residual_fringe:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: residual_fringe
search_output_file: False
input_dir: ''
save_intermediate_results: False
ignore_region_min: None
ignore_region_max: None
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
wfss_contam:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
save_simulated_image: False
save_contam_images: False
maximum_cores: none
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: ivm
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
2025-05-13 14:43:00,287 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:43:00,335 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00003_nrs2_rate.fits' reftypes = ['apcorr', 'area', 'barshadow', 'camera', 'collimator', 'cubepar', 'dflat', 'disperser', 'distortion', 'extract1d', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'pastasoss', 'pathloss', 'photom', 'psf', 'regions', 'sflat', 'speckernel', 'specprofile', 'specwcs', 'wavecorr', 'wavelengthrange', 'wfssbkg']
2025-05-13 14:43:00,341 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits'.
2025-05-13 14:43:00,342 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits'.
2025-05-13 14:43:00,343 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits'.
2025-05-13 14:43:00,343 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 14:43:00,344 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 14:43:00,344 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 14:43:00,344 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits'.
2025-05-13 14:43:00,345 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf'.
2025-05-13 14:43:00,345 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 14:43:00,345 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json'.
2025-05-13 14:43:00,346 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits'.
2025-05-13 14:43:00,346 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 14:43:00,347 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 14:43:00,347 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf'.
2025-05-13 14:43:00,347 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 14:43:00,348 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 14:43:00,348 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 14:43:00,348 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 14:43:00,349 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 14:43:00,349 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 14:43:00,349 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 14:43:00,350 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json'.
2025-05-13 14:43:00,351 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 14:43:00,352 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 14:43:00,352 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits'.
2025-05-13 14:43:00,353 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits'.
2025-05-13 14:43:00,353 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 14:43:00,354 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 14:43:00,354 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0207.fits'.
2025-05-13 14:43:00,354 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 14:43:00,355 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 14:43:00,355 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 14:43:00,355 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf'.
2025-05-13 14:43:00,356 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 14:43:00,356 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 14:43:00,357 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 14:43:00,364 - stpipe.Spec2Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:43:00,364 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2
2025-05-13 14:43:00,365 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits ...
2025-05-13 14:43:00,598 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:00,833 - stpipe.Spec2Pipeline.assign_wcs - INFO - Retrieving open MSA slitlets for msa_metadata_id = 76 and dither_index = 3
2025-05-13 14:43:00,837 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 2 is background only; assigned source_id=2
2025-05-13 14:43:00,838 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 3 is background only; assigned source_id=3
2025-05-13 14:43:00,839 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 4 is background only; assigned source_id=4
2025-05-13 14:43:00,840 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 5 is background only; assigned source_id=5
2025-05-13 14:43:00,840 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 6 is background only; assigned source_id=6
2025-05-13 14:43:00,841 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 7 is background only; assigned source_id=7
2025-05-13 14:43:00,845 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 9 is background only; assigned source_id=9
2025-05-13 14:43:00,857 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 15 is background only; assigned source_id=15
2025-05-13 14:43:00,866 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 19 contains virtual source, with source_id=-40
2025-05-13 14:43:00,869 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 21 is background only; assigned source_id=21
2025-05-13 14:43:00,876 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 25 is background only; assigned source_id=25
2025-05-13 14:43:00,884 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 28 contains virtual source, with source_id=-43
2025-05-13 14:43:00,885 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 29 is background only; assigned source_id=29
2025-05-13 14:43:00,888 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 31 is background only; assigned source_id=31
2025-05-13 14:43:00,889 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 32 is background only; assigned source_id=32
2025-05-13 14:43:00,898 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 37 is background only; assigned source_id=37
2025-05-13 14:43:00,905 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 40 contains virtual source, with source_id=-48
2025-05-13 14:43:00,908 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 41 contains virtual source, with source_id=-49
2025-05-13 14:43:00,919 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 47 is background only; assigned source_id=47
2025-05-13 14:43:00,927 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 50 contains virtual source, with source_id=-51
2025-05-13 14:43:00,932 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 52 contains virtual source, with source_id=-52
2025-05-13 14:43:00,942 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 56 contains virtual source, with source_id=-53
2025-05-13 14:43:00,947 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 59 is background only; assigned source_id=59
2025-05-13 14:43:00,949 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 60 contains virtual source, with source_id=-55
2025-05-13 14:43:00,954 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 63 is background only; assigned source_id=63
2025-05-13 14:43:00,959 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 66 is background only; assigned source_id=66
2025-05-13 14:43:00,960 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 67 is background only; assigned source_id=67
2025-05-13 14:43:00,967 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 71 is background only; assigned source_id=71
2025-05-13 14:43:00,970 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 73 is background only; assigned source_id=73
2025-05-13 14:43:00,971 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 74 is background only; assigned source_id=74
2025-05-13 14:43:00,973 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slitlet 75 is background only; assigned source_id=75
2025-05-13 14:43:01,000 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:43:01,001 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:43:01,001 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:43:01,002 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:43:02,297 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 74 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:43:02,565 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 75 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 14:43:02,566 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS2: [np.int16(2), np.int16(3), np.int16(4), np.int16(5), np.int16(6), np.int16(7), np.int16(8), np.int16(9), np.int16(10), np.int16(11), np.int16(12), np.int16(13), np.int16(14), np.int16(15), np.int16(16), np.int16(17), np.int16(18), np.int16(19), np.int16(20), np.int16(21), np.int16(22), np.int16(23), np.int16(24), np.int16(25), np.int16(26), np.int16(27), np.int16(28), np.int16(29), np.int16(30), np.int16(31), np.int16(32), np.int16(33), np.int16(34), np.int16(35), np.int16(36), np.int16(37), np.int16(38), np.int16(39), np.int16(40), np.int16(41), np.int16(42), np.int16(43), np.int16(44), np.int16(45), np.int16(46), np.int16(47), np.int16(48), np.int16(49), np.int16(50), np.int16(51), np.int16(52), np.int16(53), np.int16(54), np.int16(55), np.int16(56), np.int16(57), np.int16(58), np.int16(59), np.int16(60), np.int16(61), np.int16(62), np.int16(63), np.int16(64), np.int16(65), np.int16(66), np.int16(67), np.int16(68), np.int16(69), np.int16(70), np.int16(71), np.int16(72), np.int16(73)]
2025-05-13 14:43:02,567 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 72 open slitlets
2025-05-13 14:43:02,593 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:43:02,594 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:43:02,594 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:43:02,595 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:43:02,607 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:43:02,703 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999883758933936
2025-05-13 14:43:02,731 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 19 open slits in quadrant 1
2025-05-13 14:43:02,848 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 26 open slits in quadrant 2
2025-05-13 14:43:03,006 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 14 open slits in quadrant 3
2025-05-13 14:43:03,335 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 13 open slits in quadrant 4
2025-05-13 14:43:03,414 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:43:03,578 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf', 'camera': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf', 'collimator': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf', 'disperser': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0055.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0047.asdf', 'fpa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf', 'msa': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf', 'ote': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/jw02736007001_01_msa.fits'}
2025-05-13 14:43:05,192 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 14:43:05,198 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 14:43:05,484 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs2_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits']).
2025-05-13 14:43:05,485 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 14:43:05,734 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:05,750 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0004.json
2025-05-13 14:43:05,848 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.17768137199999573 deg
2025-05-13 14:43:05,849 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.28318609999999356 deg
2025-05-13 14:43:05,849 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: 0.00018879504418603372 deg
2025-05-13 14:43:05,850 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0003478343500772812 deg
2025-05-13 14:43:05,862 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= -1, wrange=[2.87e-06, 5.27e-06]
2025-05-13 14:43:05,957 - stpipe.Spec2Pipeline.msa_flagging - INFO - Applied Barycentric velocity correction : 0.9999883758933936
2025-05-13 14:43:05,986 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 6 open slits in quadrant 1
2025-05-13 14:43:06,024 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2025-05-13 14:43:06,043 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 12 open slits in quadrant 3
2025-05-13 14:43:06,117 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2025-05-13 14:43:06,136 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
2025-05-13 14:43:10,221 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2025-05-13 14:43:10,607 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:10,608 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 14:43:10,879 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs2_rate.fits>, []).
2025-05-13 14:43:10,879 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:43:11,149 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', []).
2025-05-13 14:43:11,150 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:43:11,402 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits', []).
2025-05-13 14:43:11,403 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 14:43:11,655 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs2_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits']).
2025-05-13 14:43:11,778 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00001_nrs2_rate.fits
2025-05-13 14:43:11,859 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00002_nrs2_rate.fits
2025-05-13 14:43:11,937 - stpipe.Spec2Pipeline.bkg_subtract - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:327: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
2025-05-13 14:43:12,320 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw02736007001_03103_00003_nrs2_rate.fits
2025-05-13 14:43:13,493 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 14:43:13,842 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(2048, 2048) from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:13,857 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_MSASPEC
2025-05-13 14:43:13,857 - stpipe.Spec2Pipeline.extract_2d - INFO - Slits selected:
2025-05-13 14:43:13,858 - stpipe.Spec2Pipeline.extract_2d - INFO - Name: 72, source_id: 6355
2025-05-13 14:43:15,023 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 72
2025-05-13 14:43:15,023 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 0 181
2025-05-13 14:43:15,024 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1586 1619
2025-05-13 14:43:15,165 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 14:43:15,173 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 110.844015385 -73.434946949 110.846369729 -73.435493153 110.846491672 -73.435449900 110.844137355 -73.434903687
2025-05-13 14:43:15,174 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 110.844015385 -73.434946949 110.846369729 -73.435493153 110.846491672 -73.435449900 110.844137355 -73.434903687
2025-05-13 14:43:15,217 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 14:43:15,620 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:15,626 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_MSASPEC
2025-05-13 14:43:15,627 - stpipe.Spec2Pipeline.srctype - INFO - source_id=6355, stellarity=0.1000, type=EXTENDED
2025-05-13 14:43:15,629 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 14:43:16,073 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:16,074 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 14:43:16,075 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:43:16,412 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:16,427 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0004.asdf
2025-05-13 14:43:16,541 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 72
2025-05-13 14:43:16,543 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 14:43:16,891 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:16,930 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 14:43:16,987 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0146.fits
2025-05-13 14:43:17,174 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0207.fits
2025-05-13 14:43:17,316 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits
2025-05-13 14:43:17,419 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 72
2025-05-13 14:43:17,613 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 14:43:17,986 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:18,001 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0005.fits
2025-05-13 14:43:18,028 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_MSASPEC
2025-05-13 14:43:18,131 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit 0
2025-05-13 14:43:18,131 - stpipe.Spec2Pipeline.pathloss - INFO - Shutter state = 11x11, using MOS1x3 entry in ref file
2025-05-13 14:43:18,145 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 14:43:18,513 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:18,528 - stpipe.Spec2Pipeline.barshadow - INFO - Using BARSHADOW reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_barshadow_0008.fits
2025-05-13 14:43:18,645 - stpipe.Spec2Pipeline.barshadow - INFO - Working on slitlet 72
2025-05-13 14:43:18,664 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow done
2025-05-13 14:43:19,023 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs2_rate.fits>,).
2025-05-13 14:43:19,047 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits
2025-05-13 14:43:19,047 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits
2025-05-13 14:43:19,124 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 14:43:19,124 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS2
2025-05-13 14:43:19,125 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_MSASPEC
2025-05-13 14:43:19,125 - stpipe.Spec2Pipeline.photom - INFO - filter: F290LP
2025-05-13 14:43:19,126 - stpipe.Spec2Pipeline.photom - INFO - grating: G395M
2025-05-13 14:43:19,154 - stpipe.Spec2Pipeline.photom - INFO - Working on slit 72
2025-05-13 14:43:19,155 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1.98847e+12
2025-05-13 14:43:19,161 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 14:43:19,631 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_cal.fits>,).
2025-05-13 14:43:19,632 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 14:43:19,919 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_cal.fits>,).
2025-05-13 14:43:20,054 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_cal.fits
2025-05-13 14:43:20,340 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 14:43:20,348 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10698 arcsec.
2025-05-13 14:43:20,349 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.1069786920854226 arcsec.
2025-05-13 14:43:20,350 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 14:43:20,350 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 14:43:20,351 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 14:43:20,351 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: ivm
2025-05-13 14:43:20,352 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:20,386 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:20,387 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:43:20,389 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:43:20,391 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (30, 181)
2025-05-13 14:43:20,468 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 110.844117040 -73.435478687 110.846461567 -73.435478687 110.846461567 -73.434934755 110.844117040 -73.434934755
2025-05-13 14:43:20,574 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_s2d.fits
2025-05-13 14:43:20,575 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 14:43:20,627 - stpipe.Spec2Pipeline - INFO - Extracting 1 MSA slitlets
2025-05-13 14:43:20,915 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw02736007001_03103_00003_nrs2_s2d.fits>,).
2025-05-13 14:43:20,980 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json
2025-05-13 14:43:20,989 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits
2025-05-13 14:43:21,022 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit 72
2025-05-13 14:43:21,023 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 14:43:21,024 - stpipe.Spec2Pipeline.extract_1d - INFO - Setting use_source_posn to False for exposure type NRS_MSASPEC, source type EXTENDED
2025-05-13 14:43:21,025 - stpipe.Spec2Pipeline.extract_1d - INFO - Aperture start/stop: 12.00 -> 17.00 (inclusive)
2025-05-13 14:43:21,072 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 14:43:21,134 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_x1d.fits
2025-05-13 14:43:21,135 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage1/jw02736007001_03103_00003_nrs2
2025-05-13 14:43:21,136 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 14:43:21,136 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:43:21,330 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_cal.fits
2025-05-13 14:43:21,331 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 14:43:21,331 - stpipe - INFO - Results used jwst version: 1.18.0
Stage 2 has been completed!
# List the Stage 2 products.
# -----------------------------Science files-----------------------------
sci_cal = sorted(glob.glob(spec2_dir + '*_cal.fits'))
sci_s2d = sorted(glob.glob(spec2_dir + '*_s2d.fits'))
sci_x1d = sorted(glob.glob(spec2_dir + '*_x1d.fits'))
print(f"SCIENCE | Stage 2 CAL Products:\n{'-' * 20}\n" + "\n".join(sci_cal))
print(f"SCIENCE | Stage 2 S2D Products:\n{'-' * 20}\n" + "\n".join(sci_s2d))
print(f"SCIENCE | Stage 2 X1D Products:\n{'-' * 20}\n" + "\n".join(sci_x1d))
SCIENCE | Stage 2 CAL Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_cal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_cal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_cal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_cal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_cal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_cal.fits
SCIENCE | Stage 2 S2D Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_s2d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_s2d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_s2d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_s2d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_s2d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_s2d.fits
SCIENCE | Stage 2 X1D Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs1_x1d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00001_nrs2_x1d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs1_x1d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00002_nrs2_x1d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs1_x1d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage2/jw02736007001_03103_00003_nrs2_x1d.fits
7. Stage 3: Spec3Pipeline (calwebb_spec3)#
In this section, we process our calibrated spectra from Stage 2 (calwebb_spec2) through the Spec3 (calwebb_spec3) pipeline to create Stage 3 data products.
Input: An ASN file that lists multiple calibrated exposures (
_cal.fits) in addition to any background exposures (_x1d.fits).Output: A single calibrated product (rectified and unrectified) and 1D spectrum. These data products have units of MJy/sr (or Jy for extracted point-source spectra).
_cal.fits: Calibrated 2D (unrectified) spectra (ncols x nrows).
_crf.fits: Calibrated 2D (unrectified) spectra whose DQ array has been updated to flag pixels detected as outliers (ncols x nrows).
_s2d.fits: Resampled (rectified) 2D spectra (ncols x nrows).
_x1d.fits: Extracted 1D spectroscopic data.
In Stage 3, single files are created for each source, one extension in the file.
The Spec3Pipeline performs additional corrections (e.g., outlier detection) and combines calibrated data from multiple exposures (e.g. a dither/nod pattern) into a single 2D spectral product, as well as a combined 1D spectrum.
7.1 Configure Spec3Pipeline#
The Spec3Pipeline has the following steps available for NIRSpec MOS:
assign_mtwcs: Modifies the WCS output frame in each exposure of a Moving Target (MT) observation association.
outlier_detection: Identification of bad pixels or cosmic-rays that remain in each of the input images.
pixel_replace: Interpolates and estimates flux values for pixels flagged as DO_NOT_USE in 2D extracted spectra.
resample_spec: Resamples each input 2D spectral image using WCS and distortion information.
extract_1d: Extracts a 1D signal from 2D or 3D datasets.
For more information about each step and a full list of step arguments, please refer to the official documentation: JDox and ReadtheDocs
Below, we set up a dictionary that defines how the Spec3Pipeline should be configured for MOS data.
To override specific steps and reference files, use the examples below.
# Set up a dictionary to define how the Spec3 pipeline should be configured.
# -------------------------Boilerplate dictionary setup-------------------------
spec3dict = {}
spec3dict['assign_mtwcs'], spec3dict['outlier_detection'] = {}, {}
spec3dict['pixel_replace'], spec3dict['resample_spec'] = {}, {}
spec3dict['extract_1d'] = {}
# ---------------------------Override reference files---------------------------
# Overrides for various reference files.
# Files should be in the base local directory or provide full path.
#spec3dict['extract_1d']['override_extract1d'] = 'myfile.json'
# -----------------------------Set step parameters------------------------------
# Overrides for whether or not certain steps should be skipped (example).
spec3dict['outlier_detection']['skip'] = False
# Run pixel replacement code to extrapolate values for otherwise bad pixels.
# This can help mitigate 5-10% negative dips in spectra of bright sources.
# Use the 'fit_profile' algorithm.
#spec3dict['pixel_replace']['skip'] = False
#spec3dict['pixel_replace']['n_adjacent_cols'] = 5
#spec3dict['pixel_replace']['algorithm'] = 'fit_profile'
# Resample weight_type.
spec3dict['resample_spec']['weight_type'] = 'ivm'
7.2 Create Spec3Pipeline Association Files#
Stage 3 ASN files for MOS data includes science exposure types. A Stage 3 ASN file requires at least one science file, although there is usually more than one. Note that the science exposures should be in the _cal.fits format.
In practice, Stage 3 ASN files can be downloaded directly from MAST, however, here we provide an example of manually creating Stage 3 ASN files. Below we create an ASN files for each GRATING/FILTER combination.
def writel3asn(scifiles):
"""
Create a Level 3 association file.
Parameters
----------
scifiles : list of str
List of all science exposure files.
Returns
-------
None.
"""
# Filter based on GRATING/FILTER.
from collections import defaultdict
grouped = defaultdict(lambda: {'sci': [], 'bg': []})
for f in scifiles:
k = (fits.getval(f, 'FILTER'), fits.getval(f, 'GRATING'))
grouped[k]['sci'].append(f)
# Make ASN for each FILTER/GRATING.
for (filt, grat), files in grouped.items():
name = f"{filt}_{grat}".lower()
asnfile = os.path.join(asn_dir, f"{name}_l3asn.json")
asn = afl.asn_from_list(files['sci'], rule=DMS_Level3_Base, product_name=name)
with open(asnfile, 'w') as f:
f.write(asn.dump()[1])
print("Level 3 ASN creation complete!")
if dospec3:
writel3asn(sci_cal)
2025-05-13 14:43:21,368 - 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)
Level 3 ASN creation complete!
Check that the association files for Stage 3
# Open an ASN file as an example.
# Check that file paths have been correctly updated.
if dospec3:
spec3_asn = glob.glob(asn_dir+'*l3asn.json')[0]
with open(spec3_asn, 'r') as f_obj:
asnfile_data = json.load(f_obj)
display(JSON(asnfile_data, expanded=True))
<IPython.core.display.JSON object>
7.3 Run Spec3Pipeline#
Run the science files through the calwebb_spec3 pipeline using the .call() method.
time_spec3 = time.perf_counter()
# Run Stage 3 pipeline using the custom spec3dict dictionary.
if dospec3:
for spec3_asn in glob.glob(asn_dir+'*l3asn.json'):
print(f"Applying Stage 3 Corrections & Calibrations to: "f"{os.path.basename(spec3_asn)}")
spec3_result = Spec3Pipeline.call(spec3_asn,
save_results=True,
steps=spec3dict,
output_dir=spec3_dir)
print("Stage 3 has been completed! \n")
else:
print("Skipping Stage 3. \n")
Applying Stage 3 Corrections & Calibrations to: f290lp_g395m_l3asn.json
2025-05-13 14:43:21,769 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-outlierdetectionstep_0006.asdf 1.6 K bytes (1 / 1 files) (0 / 1.6 K bytes)
2025-05-13 14:43:21,819 - stpipe - INFO - PARS-OUTLIERDETECTIONSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-outlierdetectionstep_0006.asdf
2025-05-13 14:43:21,833 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 14:43:21,865 - stpipe.Spec3Pipeline - INFO - Spec3Pipeline instance created.
2025-05-13 14:43:21,865 - stpipe.Spec3Pipeline.assign_mtwcs - INFO - AssignMTWcsStep instance created.
2025-05-13 14:43:21,867 - stpipe.Spec3Pipeline.master_background - INFO - MasterBackgroundStep instance created.
2025-05-13 14:43:21,868 - stpipe.Spec3Pipeline.mrs_imatch - INFO - MRSIMatchStep instance created.
2025-05-13 14:43:21,869 - stpipe.Spec3Pipeline.outlier_detection - INFO - OutlierDetectionStep instance created.
2025-05-13 14:43:21,870 - stpipe.Spec3Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 14:43:21,871 - stpipe.Spec3Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 14:43:21,872 - stpipe.Spec3Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 14:43:21,874 - stpipe.Spec3Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 14:43:21,876 - stpipe.Spec3Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 14:43:21,877 - stpipe.Spec3Pipeline.combine_1d - INFO - Combine1dStep instance created.
2025-05-13 14:43:21,877 - stpipe.Spec3Pipeline.spectral_leak - INFO - SpectralLeakStep instance created.
2025-05-13 14:43:22,205 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/asn/f290lp_g395m_l3asn.json',).
2025-05-13 14:43:22,221 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: True
skip: False
suffix: None
search_output_file: True
input_dir: ''
steps:
assign_mtwcs:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: assign_mtwcs
search_output_file: True
input_dir: ''
master_background:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
median_kernel: 1
user_background: None
save_background: False
force_subtract: False
mrs_imatch:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
bkg_degree: 1
subtract: False
outlier_detection:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: False
input_dir: ''
weight_type: ivm
pixfrac: 1.0
kernel: square
fillval: NaN
maskpt: 0.0
snr: 5.0 4.0
scale: 3.0 2.0
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
in_memory: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: ivm
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
combine_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
exptime_key: exposure_time
sigma_clip: None
spectral_leak:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 14:43:22,230 - stpipe.Spec3Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:43:22,434 - stpipe.Spec3Pipeline - INFO - Prefetching reference files for dataset: 'jw02736007001_03103_00001_nrs1_cal.fits' reftypes = ['apcorr', 'area', 'cubepar', 'extract1d', 'mrsptcorr', 'pastasoss', 'photom', 'psf', 'speckernel', 'specprofile']
2025-05-13 14:43:22,441 - stpipe.Spec3Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits'.
2025-05-13 14:43:22,441 - stpipe.Spec3Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0051.fits'.
2025-05-13 14:43:22,442 - stpipe.Spec3Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 14:43:22,442 - stpipe.Spec3Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json'.
2025-05-13 14:43:22,443 - stpipe.Spec3Pipeline - INFO - Prefetch for MRSPTCORR reference file is 'N/A'.
2025-05-13 14:43:22,443 - stpipe.Spec3Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 14:43:22,443 - stpipe.Spec3Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0015.fits'.
2025-05-13 14:43:22,444 - stpipe.Spec3Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 14:43:22,444 - stpipe.Spec3Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 14:43:22,445 - stpipe.Spec3Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 14:43:22,446 - stpipe.Spec3Pipeline - INFO - Starting calwebb_spec3 ...
2025-05-13 14:43:22,454 - stpipe.Spec3Pipeline - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 14:43:23,914 - stpipe.Spec3Pipeline - INFO - Convert from exposure-based to source-based data.
2025-05-13 14:43:23,914 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw02736007001_03103_00001_nrs1_cal.fits
2025-05-13 14:43:24,030 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw02736007001_03103_00001_nrs2_cal.fits
2025-05-13 14:43:24,079 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw02736007001_03103_00002_nrs1_cal.fits
2025-05-13 14:43:24,126 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw02736007001_03103_00002_nrs2_cal.fits
2025-05-13 14:43:24,173 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw02736007001_03103_00003_nrs1_cal.fits
2025-05-13 14:43:24,220 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw02736007001_03103_00003_nrs2_cal.fits
2025-05-13 14:43:25,414 - stpipe.Spec3Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_cal.fits
2025-05-13 14:43:25,636 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection running with args (<jwst.datamodels.source_container.SourceModelContainer object at 0x7f0590ca56a0>,).
2025-05-13 14:43:25,636 - stpipe.Spec3Pipeline.outlier_detection - INFO - Outlier Detection mode: spec
2025-05-13 14:43:25,637 - stpipe.Spec3Pipeline.outlier_detection - INFO - Outlier Detection asn_id: None
2025-05-13 14:43:26,080 - stpipe.Spec3Pipeline.outlier_detection - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 14:43:26,089 - stpipe.Spec3Pipeline.outlier_detection - INFO - Computed output pixel scale: 0.10694 arcsec.
2025-05-13 14:43:26,093 - stpipe.Spec3Pipeline.outlier_detection - INFO - Output pixel scale: 0.10693693568463916 arcsec.
2025-05-13 14:43:26,094 - stpipe.Spec3Pipeline.outlier_detection - INFO - Driz parameter kernel: square
2025-05-13 14:43:26,095 - stpipe.Spec3Pipeline.outlier_detection - INFO - Driz parameter pixfrac: 1.0
2025-05-13 14:43:26,095 - stpipe.Spec3Pipeline.outlier_detection - INFO - Driz parameter fillval: NaN
2025-05-13 14:43:26,096 - stpipe.Spec3Pipeline.outlier_detection - INFO - Driz parameter weight_type: ivm
2025-05-13 14:43:26,097 - stpipe.Spec3Pipeline.outlier_detection - INFO - 2 exposures to drizzle together
2025-05-13 14:43:26,149 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 14:43:26,238 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 14:43:26,280 - stpipe.Spec3Pipeline.outlier_detection - INFO - 2 exposures to drizzle together
2025-05-13 14:43:26,333 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 14:43:26,421 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 14:43:26,465 - stpipe.Spec3Pipeline.outlier_detection - INFO - 2 exposures to drizzle together
2025-05-13 14:43:26,518 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 14:43:26,610 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 14:43:26,747 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (38, 1034) <-- (41, 1215)
2025-05-13 14:43:26,802 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (38, 1034) <-- (41, 1215)
2025-05-13 14:43:26,805 - stpipe.Spec3Pipeline.outlier_detection - INFO - 97 pixels marked as outliers
2025-05-13 14:43:26,836 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (33, 181) <-- (41, 1215)
2025-05-13 14:43:26,866 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (33, 181) <-- (41, 1215)
2025-05-13 14:43:26,868 - stpipe.Spec3Pipeline.outlier_detection - INFO - 286 pixels marked as outliers
2025-05-13 14:43:26,922 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (38, 1034) <-- (41, 1215)
2025-05-13 14:43:26,973 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (38, 1034) <-- (41, 1215)
2025-05-13 14:43:26,975 - stpipe.Spec3Pipeline.outlier_detection - INFO - 116 pixels marked as outliers
2025-05-13 14:43:27,007 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (33, 181) <-- (41, 1215)
2025-05-13 14:43:27,041 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (33, 181) <-- (41, 1215)
2025-05-13 14:43:27,042 - stpipe.Spec3Pipeline.outlier_detection - INFO - 51 pixels marked as outliers
2025-05-13 14:43:27,093 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (38, 1034) <-- (41, 1215)
2025-05-13 14:43:27,144 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (38, 1034) <-- (41, 1215)
2025-05-13 14:43:27,146 - stpipe.Spec3Pipeline.outlier_detection - INFO - 163 pixels marked as outliers
2025-05-13 14:43:27,181 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (33, 181) <-- (41, 1215)
2025-05-13 14:43:27,211 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (33, 181) <-- (41, 1215)
2025-05-13 14:43:27,213 - stpipe.Spec3Pipeline.outlier_detection - INFO - 42 pixels marked as outliers
2025-05-13 14:43:28,096 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_crf.fits
2025-05-13 14:43:28,097 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection done
2025-05-13 14:43:28,343 - stpipe.Spec3Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<jwst.datamodels.source_container.SourceModelContainer object at 0x7f0590ca56a0>,).
2025-05-13 14:43:28,344 - stpipe.Spec3Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 14:43:28,578 - stpipe.Spec3Pipeline.resample_spec - INFO - Step resample_spec running with args (<jwst.datamodels.source_container.SourceModelContainer object at 0x7f0590ca56a0>,).
2025-05-13 14:43:29,705 - stpipe.Spec3Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 14:43:29,714 - stpipe.Spec3Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10694 arcsec.
2025-05-13 14:43:29,719 - stpipe.Spec3Pipeline.resample_spec - INFO - Output pixel scale: 0.10693693568463916 arcsec.
2025-05-13 14:43:29,720 - stpipe.Spec3Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 14:43:29,720 - stpipe.Spec3Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 14:43:29,720 - stpipe.Spec3Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 14:43:29,721 - stpipe.Spec3Pipeline.resample_spec - INFO - Driz parameter weight_type: ivm
2025-05-13 14:43:29,722 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:29,772 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:29,779 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:29,785 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:29,792 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:29,879 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:29,880 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:29,882 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:29,884 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:29,940 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:29,947 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:29,954 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:29,960 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:29,998 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:30,000 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:30,002 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:30,004 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:30,059 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:30,065 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:30,072 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:30,079 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (38, 1034) --> (41, 1215)
2025-05-13 14:43:30,121 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 14:43:30,123 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:30,125 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:30,127 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (33, 181) --> (41, 1215)
2025-05-13 14:43:30,416 - stpipe.Spec3Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 110.843276681 -73.435490341 110.846509218 -73.435490341 110.846509218 -73.434740378 110.843276681 -73.434740378
2025-05-13 14:43:30,655 - stpipe.Spec3Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_s2d.fits
2025-05-13 14:43:30,655 - stpipe.Spec3Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 14:43:30,894 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d running with args (<SlitModel(41, 1215) from f290lp_g395m_s000006355_s2d.fits>,).
2025-05-13 14:43:31,006 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0009.json
2025-05-13 14:43:31,058 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits
2025-05-13 14:43:31,136 - stpipe.Spec3Pipeline.extract_1d - INFO - Processing spectral order -1
2025-05-13 14:43:31,137 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for exposure type NRS_MSASPEC, source type EXTENDED
2025-05-13 14:43:31,139 - stpipe.Spec3Pipeline.extract_1d - INFO - Aperture start/stop: 17.50 -> 22.50 (inclusive)
2025-05-13 14:43:31,250 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_x1d.fits
2025-05-13 14:43:31,251 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 14:43:31,253 - stpipe.Spec3Pipeline - INFO - Ending calwebb_spec3
2025-05-13 14:43:31,257 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline done
2025-05-13 14:43:31,258 - stpipe - INFO - Results used jwst version: 1.18.0
Stage 3 has been completed!
# Print out the time benchmarks.
time4 = time.perf_counter()
print(f"Runtime so far: {round((time4 - time0) / 60.0, 1):0.4f} min")
print(f"Runtime for Spec3: {round((time4 - time_spec3) / 60.0, 1):0.4f} min")
Runtime so far: 53.8000 min
Runtime for Spec3: 0.2000 min
# List the Stage 3 products.
stage3_cal = sorted(glob.glob(spec3_dir + '*_cal.fits'))
stage3_s2d = sorted(glob.glob(spec3_dir + '*_s2d.fits'))
stage3_x1d = sorted(glob.glob(spec3_dir + '*_x1d.fits'))
print(f"Stage 3 CAL Products:\n{'-' * 20}\n" + "\n".join(stage3_cal))
print(f"Stage 3 S3D Products:\n{'-' * 20}\n" + "\n".join(stage3_s2d))
print(f"Stage 3 X1D Products:\n{'-' * 20}\n" + "\n".join(stage3_x1d))
Stage 3 CAL Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_cal.fits
Stage 3 S3D Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_s2d.fits
Stage 3 X1D Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_x1d.fits
8. Visualize the Data#
Define convenience funcitons for visualization. For some plots we utilize jdaviz, a package of astronomical data analysis visualization tools designed to work in Jupyter notebooks.
Define a function to display Stage 1 products.
def display_rate(rates,
slits_models=[],
integration=0,
extname='data',
cmap='viridis',
bad_color=(1, 0.7, 0.7),
vmin=None,
vmax=None,
scale='asinh',
aspect='auto',
title_prefix=None,
title_path=False,
save_plot=False):
"""
Display countrate images.
Parameters
----------
rates : list of str
A list of RATE[INTS] files to be displayed.
slits_models : list of str, optional
A list of CAL[INTS] or S2D files containing the slit models.
If provided, slit cutouts will be overlaid on the countrate images.
integration : {None, 'min', int}, optional
Specifies the integration to use for multi-integration data.
If 'min', the minimum value across all integrations is used.
If an integer, the specific integration index is used (default 0).
extname : str, optional
The name of the data extension to extract from ('data', 'dq', etc.).
cmap : str, optional
Colormap to use for displaying the image. Default is 'viridis'.
bad_color : tuple of float, optional
Color to use for NaN pixels. Default is light red (1, 0.7, 0.7).
vmin : float, optional
Minimum value for color scaling. If None, determined from the data.
vmax : float, optional
Maximum value for color scaling. If None, determined from the data.
scale : {'linear', 'log', 'asinh'}, optional
Scale to use for the image normalization. Default is 'asinh'.
aspect : str, optional
Aspect ratio of the plot. Default is 'auto'.
title_prefix : str, optional
Optional prefix for the plot title.
title_path : bool, optional
If True, uses the full file path for the title;
otherwise, uses the basename. Default is False.
save_plot : bool, optional
If True, saves the plot as a PNG file. Default is False.
Returns
-------
None.
"""
# -------------------------------Check Inputs-------------------------------
rates = [rates] if isinstance(rates, str) else rates
slits_models = [slits_models] if isinstance(slits_models, str) else slits_models
nrates = len(rates)
# ------------------------------Set up figures------------------------------
fig, axes = plt.subplots(nrates, 1, figsize=(12, 12 * nrates),
sharex=True, height_ratios=[1] * nrates)
fig.subplots_adjust(hspace=0.2, wspace=0.2)
axes = [axes] if nrates == 1 else axes
cmap = plt.get_cmap(cmap) # Set up colormap and bad pixel color.
cmap.set_bad(bad_color, 1.0)
# ---------------------------Plot countrate image---------------------------
for i, (rate, cal) in enumerate(itertools.zip_longest(rates,
slits_models,
fillvalue=None)):
# -------------------Open files as JWST datamodels-------------------
model = datamodels.open(rate)
slits_model = datamodels.open(cal) if cal else None
# -----------------------Extract the 2D/3D data----------------------
data_2d = getattr(model, extname)
if data_2d.ndim == 3: # Handle multi-integration data.
if integration == 'min':
data_2d = np.nanmin(data_2d, axis=0)
elif isinstance(integration, int) and 0 <= integration < data_2d.shape[0]:
data_2d = data_2d[integration]
else:
raise ValueError(f"Invalid integration '{integration}' for 3D data.")
# ---------------------------Scale the data-------------------------
sigma_clipped_data = sigma_clip(data_2d, sigma=5, maxiters=3)
vmin = np.nanmin(sigma_clipped_data) if vmin is None else vmin
vmax = np.nanmax(sigma_clipped_data) if vmax is None else vmax
stretch_map = {'log': LogStretch(), 'linear': LinearStretch(),
'asinh': AsinhStretch()}
if scale in stretch_map:
norm = ImageNormalize(sigma_clipped_data,
interval=ManualInterval(vmin=vmin, vmax=vmax),
stretch=stretch_map[scale])
else:
norm = simple_norm(sigma_clipped_data, vmin=vmin, vmax=vmax)
# -----------------Draw slits and label source ids------------------
# slits_model can be s2d/cal from spec2 - contains slit models for all sources.
if slits_model:
slit_patches = []
for slit in slits_model.slits:
slit_patch = Rectangle((slit.xstart, slit.ystart),
slit.xsize, slit.ysize)
slit_patches.append(slit_patch)
y = slit.ystart + slit.ysize / 2
ha = 'right' if 'nrs1' in rate else 'left'
plt.text(slit.xstart, y, slit.source_id, color='w', ha=ha, va='center',
fontsize=7, path_effects=[], weight='bold')
axes[i].add_collection(PatchCollection(slit_patches, ec='r', fc='None'))
# ----------------Plot the countrate image & colorbar---------------
plt.subplots_adjust(left=0.05, right=0.85)
im = axes[i].imshow(data_2d, origin='lower', cmap=cmap,
norm=norm, aspect=aspect, interpolation='nearest')
units = model.meta.bunit_data
cbar_ax = fig.add_axes([axes[i].get_position().x1 + 0.02,
axes[i].get_position().y0, 0.02,
axes[i].get_position().height])
cbar = fig.colorbar(im, cax=cbar_ax)
cbar.set_label(units, fontsize=12)
# -----------------Construct title and axis labels------------------
filename = model.meta.filename
title = (f"{title_prefix + ' ' if title_prefix else ''}"
f"{filename if title_path else os.path.basename(filename)}")
if integration is not None:
title = title.replace('rateints', f'rateints[{integration}]')
axes[i].set_title(title, fontsize=14)
axes[i].set_xlabel("Pixel Column", fontsize=12)
axes[i].set_ylabel("Pixel Row", fontsize=12)
# -------------------------Save the figure?-------------------------
if save_plot:
save_plot = rate.replace('fits', 'png')
if integration:
save_plot = save_plot.replace('.png', '%s.png' % integration)
fig.savefig(save_plot, dpi=200)
fig.show()
Function to create plots of the Stage 2/3 spectra.
def display_spectra(spectra,
compare_x1d=None,
compare_mast=None,
integration=None,
extname='data',
source_id=None,
source_type=None,
expand_wavelength_gap=True,
plot_resample=True,
plot_errors=False,
cmap='viridis',
bad_color=(1, 0.7, 0.7),
aspect='auto',
vmin=None,
vmax=None,
scale='asinh',
title_prefix=None,
title_path=False,
y_limits=None,
is_stage3=False):
"""
Display 2D and 1D spectra (Stage 2/3).
Parameters
----------
spectra : list of str
A list of data products (e.g., CAL, S2D, X1D files).
compare_x1d : list of str, optional
A list of 1D spectra for comparison (X1D files).
compare_mast : list of str, optional
A list of 1D spectra from MAST for comparison (X1D files).
integration : {None, 'min', int}, optional
Specifies the integration to use for multi-integration data.
If 'min', the minimum value across all integrations is used.
If an integer, the specific integration index is used (default 0).
extname : str, optional
The name of the data extension to extract ('data', 'dq', etc.).
source_id : int or none, optional
Identifier for the source/slit to be displayed. Default is None.
source_type : str, optional
Override data source type ('POINT' or 'EXTENDED').
expand_wavelength_gap : bool, optional
If True, expands gaps in the wavelength data for better visualization.
plot_resample : bool, optional
If True, plots resampled (S2D) data products;
otherwise, plots calibrated (CAL) data. Default is True.
plot_errors : bool, optional
If True, plots the error bands for the 1D spectra. Default is False.
cmap : str, optional
Colormap to use for displaying the images. Default is 'viridis'.
bad_color : tuple of float, optional
Color to use for bad pixels. Default is light red (1, 0.7, 0.7).
aspect : str, optional
Aspect ratio of the plot. Default is 'auto'.
vmin : float, optional
Minimum value for color scaling. If None, determined from the data.
vmax : float, optional
Maximum value for color scaling. If None, determined from the data.
scale : {'linear', 'log', 'asinh'}, optional
Scale to use for the image normalization. Default is 'asinh'.
title_prefix : str, optional
Optional prefix for the plot title.
title_path : bool, optional
If True, uses the full file path for the title;
otherwise, uses the basename. Default is False.
y_limits : tuple of float, optional
Limits for the y-axis of the 1D spectrum plot.
If None, limits are determined from the data.
is_stage3 : bool, optional
Plot stage 3 products? Default is False.
Returns
-------
None.
"""
# ---------------------------------Check Inputs---------------------------------
spectra = [spectra] if isinstance(spectra, str) else spectra
compare_x1d = [compare_x1d] if isinstance(compare_x1d, str) else compare_x1d
compare_mast = [compare_mast] if isinstance(compare_mast, str) else compare_mast
# Assign a default source_id if one was not supplied.
if source_id is None:
ftype = "cal"
if plot_resample:
ftype = "s2d"
for file in spectra:
if ftype in file:
source_id = datamodels.open(file)[0].slits[0].source_id
break
src_str = str(source_id)
# Plot stage 3 products?
if is_stage3:
# Stage 3 products should include the source_id in the filename.
# Sort based on filename rather than open all.
def filter_prod(products, source_id):
"""Filter products based on the source_id."""
return [
f for f in products
if src_str.lower() in f and ('FXD_SLIT' not in fits.getheader(f, ext=0) or fits.getheader(f, ext=0)['FXD_SLIT'].lower() == src_str.lower())]
spectra = filter_prod(spectra, source_id)
compare_x1d = filter_prod(compare_x1d, source_id) if compare_x1d else None
compare_mast = filter_prod(compare_mast, source_id) if compare_mast else None
ftypes = {ftype: [f for f in spectra
if ftype in f] for ftype in ["cal", "s2d", "x1d"]}
products = sorted(ftypes['s2d']) if plot_resample else sorted(ftypes['cal'])
if not products:
raise ValueError("No valid data products found for plotting.")
# --------------------------------Set up figures-------------------------------
total_plots = len(products) + bool(ftypes['x1d'])
height_ratios = [1] * len(products) + ([3] if bool(ftypes['x1d']) else [])
fig, axes = plt.subplots(total_plots, 1, figsize=(15, 5 * total_plots),
sharex=False, height_ratios=height_ratios)
fig.subplots_adjust(hspace=0.2, wspace=0.2)
ax2d, ax1d = (axes[:-1], axes[-1]) if bool(ftypes['x1d']) else (axes, None)
cmap = plt.get_cmap(cmap) # Set up colormap and bad pixel color.
cmap.set_bad(bad_color, 1.0)
colors = plt.get_cmap('tab10').colors
color_cycle = itertools.cycle(colors)
# ---------------------------------Plot spectra--------------------------------
for i, product in enumerate(products):
model = datamodels.open(product) # Open files as JWST datamodels.
# Extract the correct 2D source spectrum if there are multiple.
slit_m = model
if 'slits' in model:
slits = model.slits
slit_m = next((s for s in slits
if getattr(s, 'name', None) == source_id), None)
slit_m = slit_m or next((s for s in model.slits
if s.source_id == source_id), None)
if not slit_m:
print(f"'{source_id}' not found/invalid.")
print(f"Available source_ids: {[s.source_id for s in slits][:5]}")
break
# Check if 'fixed_slit' exists, otherwise fall back to 'slitlet_id'
slit_name = (f"SLIT: {getattr(slit_m, 'name', None) or slit_m.slitlet_id}, "
f"SOURCE: {getattr(slit_m, 'source_id', '')}")
# -----------------------Extract the 2D/3D data----------------------
data_2d = getattr(slit_m, extname)
if data_2d.ndim == 3: # Handle multi-integration data.
if integration == 'min':
data_2d = np.nanmin(data_2d, axis=0)
elif isinstance(integration, int) and 0 <= integration < data_2d.shape[0]:
data_2d = data_2d[integration]
else:
raise ValueError(f"Invalid integration '{integration}' for 3D data.")
# -----------Convert from pixels to wavelength (x-axis)--------------
wcsobj = slit_m.meta.wcs # Obtaining the WCS object from the meta data.
y, x = np.mgrid[:slit_m.data.shape[0], :slit_m.data.shape[1]]
# Coordinate transform from detector space (pixels) to sky (RA, DEC).
det2sky = wcsobj.get_transform('detector', 'world')
ra, dec, s2dwave = det2sky(x, y) # RA/Dec, wavelength (microns) for each pixel.
s2dwaves = s2dwave[0, :] # Single row since this is the rectified spectrum.
x_arr = np.arange(0, slit_m.data.shape[1], int(len(slit_m.data[1]) / 4))
wav = np.round(s2dwaves[x_arr], 2) # Populating the wavelength array.
ax2d[i].set_xticks(x_arr, wav)
# xticks = np.arange(np.ceil(wave_1d[0]), wave_1d[-1], 0.2)
# xtick_pos = np.interp(xticks, wave_1d, np.arange(num_waves))
# ax1d.set_xticks(xtick_pos)
# ax1d.set_xticklabels([f'{xtick:.1f}' for xtick in xticks])
# ---------------------------Scale the data-------------------------
sigma_clipped_data = sigma_clip(data_2d, sigma=5, maxiters=3)
vmin = np.nanmin(sigma_clipped_data) if vmin is None else vmin
vmax = np.nanmax(sigma_clipped_data) if vmax is None else vmax
stretch_map = {'log': LogStretch(), 'linear': LinearStretch(),
'asinh': AsinhStretch()}
if scale in stretch_map:
norm = ImageNormalize(sigma_clipped_data,
interval=ManualInterval(vmin=vmin, vmax=vmax),
stretch=stretch_map[scale])
else:
norm = simple_norm(sigma_clipped_data, vmin=vmin, vmax=vmax)
# -------------------------Plot 1D Spectra-------------------------
for k, (prods_1d, prefix) in enumerate([(sorted(ftypes['x1d']),
f'{title_prefix} '),
(compare_x1d, 'RE-EXTRACTION '),
(compare_mast, 'MAST ')]):
if prods_1d:
model_1d = datamodels.open(prods_1d[i])
specs = model_1d.spec
spec = next((s for s in specs if
getattr(s, 'name', None) == source_id), None)
spec = spec or next((s for s in specs
if s.source_id == source_id), None)
if spec:
tab = spec.spec_table
source_type = source_type if source_type else slit_m.source_type
wave = tab.WAVELENGTH
flux = tab.FLUX if source_type == 'POINT' else tab.SURF_BRIGHT
errs = tab.FLUX_ERROR if source_type == 'POINT' else tab.SB_ERROR
# Expand the array to visualize the wavelength gap.
if expand_wavelength_gap:
dx1d_wave = wave[1:] - wave[:-1]
igap = np.argmax(dx1d_wave)
dx_replace = (dx1d_wave[igap - 1] + dx1d_wave[igap + 1]) / 2.
nfill = int(np.round(np.nanmax(dx1d_wave) / dx_replace))
if nfill > 1:
print(nfill)
print(f"Expanding wavelength gap {wave[igap]:.2f} "
f"-- {wave[igap + 1]:.2f} μm")
wave_fill = np.mgrid[wave[igap]:wave[igap + 1]:(nfill + 1) * 1j]
wave = np.concatenate([wave[:igap + 1],
wave_fill[1:-1],
wave[igap + 1:]])
if prefix != 'RE-EXTRACTION ':
num_rows, num_waves = data_2d.shape
fill_2d = np.zeros(shape=(num_rows, nfill - 1)) * np.nan
data_2d = np.concatenate([data_2d[:, :igap + 1],
fill_2d, data_2d[:, igap + 1:]],
axis=1)
fill = np.zeros(shape=(nfill - 1)) * np.nan
flux = np.concatenate([flux[:igap + 1], fill, flux[igap + 1:]])
errs = np.concatenate([errs[:igap + 1], fill, errs[igap + 1:]])
else:
nfill = 0
# ----------------Construct legends and annotations-----------------
detector = slit_m.meta.instrument.detector
ffilter = slit_m.meta.instrument.filter
grating = slit_m.meta.instrument.grating
dither = model.meta.dither.position_number
label_2d = f'{grating}/{ffilter}'
label_1d = f'{detector} ({grating}/{ffilter})'
if not is_stage3:
label_2d = f'Dither/Nod {dither} ({label_2d})'
label_1d = (f'{prefix} Dither/Nod {dither} {label_1d}')
else:
label_1d = f'{prefix}{label_1d}'
ax2d[i].annotate(label_2d, xy=(1, 1), xycoords='axes fraction',
xytext=(-10, -10), textcoords='offset points',
bbox=dict(boxstyle="round,pad=0.3",
edgecolor='white',
facecolor='white', alpha=0.8),
fontsize=12, ha='right', va='top')
title_2d = (f"{title_prefix + ' ' if title_prefix else ''}"
f"{model.meta.filename} | {slit_name}")
if integration:
title_2d = title_2d.replace('.fits', f'[{integration}].fits')
ax2d[i].set_title(title_2d, fontsize=14)
if not bool(ftypes['x1d']):
ax2d[i].set_xlabel("Wavelength (μm)", fontsize=12)
ax2d[i].set_ylabel("Pixel Row", fontsize=12)
ax2d[i].legend(fontsize=12)
# ------------------------------------------------------------------
num_waves = len(wave)
color = next(color_cycle)
ax1d.step(wave, flux, lw=1, label=label_1d, color=color)
if plot_errors:
ax1d.fill_between(np.arange(num_waves), flux - errs,
flux + errs, color='grey', alpha=0.3)
ax1d.legend(fontsize=12)
ax1d.set_title(f"{title_prefix + ' ' if title_prefix else ''}"
f"Extracted 1D Spectra | {slit_name}", fontsize=14)
ax1d.set_ylabel("Flux (Jy)" if source_type == 'POINT'
else "Surface Brightness (MJy/sr)", fontsize=12)
ax1d.set_xlabel("Wavelength (μm)", fontsize=12)
ax1d.set_ylim(y_limits or (np.nanpercentile(flux, 1),
np.nanpercentile(flux, 99.5)))
# --------------------Plot the 2D spectra & colorbar---------------
plt.subplots_adjust(left=0.05, right=0.85)
if k == 0:
im = ax2d[i].imshow(data_2d, origin='lower',
cmap=cmap, norm=norm,
aspect=aspect, interpolation='nearest')
units = slit_m.meta.bunit_data
cbar_ax = fig.add_axes([ax2d[i].get_position().x1 + 0.02,
ax2d[i].get_position().y0, 0.02,
ax2d[i].get_position().height])
cbar = fig.colorbar(im, cax=cbar_ax)
cbar.set_label(units, fontsize=12)
# ----------------------Add extraction region---------------------
ystart, ystop, xstart, xstop = (spec.extraction_ystart - 1,
spec.extraction_ystop - 1,
spec.extraction_xstart - 1,
spec.extraction_xstop - 1)
extract_width = ystop - ystart + 1
box = Rectangle((xstart, ystart), xstop - xstart + nfill,
extract_width, fc='None', ec=color,
lw=2, label=prefix)
ax2d[i].add_patch(box)
ax2d[i].legend()
8.1 Display Detector1Pipeline Products#
Inspect the Stage 1 slope products.
if doviz:
rate_file = rate_sci[-1] # Show the last rate file, as an example.
display_rate(rate_file, vmin=-0.003, vmax=0.022, scale='linear',
title_prefix='REPROCESSED') # , extname='dq')
2025-05-13 14:43:31,370 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:407: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
8.2 Display Spec2Pipeline Products#
Use Jdaviz Mosviz to visualize and analyze the Stage 2 2D and 1D calibrated spectra. For more information on these visualization tools and plotting capabilities, refer to the official documentation linked.
# Plot the Stage 3 MOS spectra with Mosviz.
if doviz:
mosviz = Mosviz()
spectra_1d = glob.glob(spec2_dir+'*x1d.fits')
spectra_2d = glob.glob(spec2_dir+'*s2d.fits')
image = None # If you have 'mymosaic.fits'
mosviz.load_data(spectra_1d=spectra_1d, spectra_2d=spectra_2d, images=image)
mosviz.show()
Draw boxes around the extraction regions for each source in a _rate.fits file using the slit information from the corresponding Stage 2 calibrated products (_cal.fits or _s2d.fits). These boxes should be large enough to accommodate the curved spectral traces. While neighboring boxes may overlap, the spectra themselves do not.
if doviz:
rate_file = rate_sci[-1] # Show the last rate file, as an example.
display_rate(rate_file, slits_models=sci_cal[0], vmin=-0.003, vmax=0.022, scale='linear',
title_prefix='REPROCESSED') # , extname='dq')
2025-05-13 14:43:35,619 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:407: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
Please note that the demo source data is technically defined and processed as an extended source, even though the plots above are presented in units of Jy (for point sources). For extended sources, the extraction box for the 1D spectra defaults to the center of the slitlet. In these cases, you may need to manually adjust the position of the extraction box.
Additionally, with point source data, you may sometimes observe that the extraction region is not always perfectly centered on the source. Recent improvements in resampling might exacerbate some off-centered cases, and in certain situations, the source may be completely missed. The workaround for this issue is found in Section 9.
8.3 Display Spec3Pipeline Products#
Inspect the Stage 3 combined calibrated spectra with Mosviz.
if doviz:
mosviz = Mosviz()
spectra_1d = glob.glob(spec3_dir+'*x1d.fits')
spectra_2d = glob.glob(spec3_dir+'*s2d.fits')
image = None # If you have 'mymosaic.fits'
mosviz.load_data(spectra_1d=spectra_1d, spectra_2d=spectra_2d, images=image)
mosviz.show()
Note in the demo data, the default extraction region misses the positive signal for this 5-shutter slitlet target and instead extracts negative signal from one of the nod subtractions. A workaround in Section 9 is provided.
9. Modifying the EXTRACT1D Reference File (as needed)#
extract_1d • Editing JSON reference file
The extract_1d step’s use_source_pos parameter in Stage 2 generally centers the 1D extraction box on the actual source location effectively and thus doesn’t usually require manual adjustment. However, in some cases, adjusting the position of the extraction box by modifying the EXTRACT1D reference file may be useful. The following section demonstrates how to modify which rows in the 2D spectrum (S2D) are used for extracting the 1D spectrum (X1D).
The EXTRACT1D reference file, along with several other parameter files, can be found in the CRDS_PATH directory. While some files, like .json files, can be manually edited, we modify them using Python.
Warning: Currently, there is no aperture correction in place for NIRSpec, so the extract_width parameter MUST remain unchanged (6 pixels wide) to ensure proper flux calibration! The extraction box limits (ystart and ystop) can be modified; however, if ystart and ystop do not match the extract_width, the extract_width takes precedence and is applied symmetrically around the midpoint between ystart and ystop.
# Modify the EXTRACT1D reference file.
# If you don't know the reference file name this should work.
# extract_1d_ref = Spec3Pipeline().get_reference_file(stage3_s2d, 'extract1d')
refs = api.dump_references(crds_client.get_context_used('jwst'),
['jwst_nirspec_extract1d_0009.json'])
extract_1d_ref = refs['jwst_nirspec_extract1d_0009.json']
# Open EXTRACT1D reference file in read-mode.
with open(extract_1d_ref, "r") as ref_file:
params = json.load(ref_file)
# All of these values are zero-indexed integers.
# The start and stop limits are inclusive.
# ANY MOS SLITLET
params["apertures"][0]["extract_width"] = 6
params["apertures"][0]["ystart"] = 22
params["apertures"][0]["ystop"] = 27
# Write changes to a new file.
newData = json.dumps(params, indent=4)
# Add the suffix '_fs' to distinguish the file from the default version.
basename = os.path.basename(extract_1d_ref)[:-5]
extract_1d_ref_mod = os.path.join(spec3_dir, basename + "_mos.json")
with open(extract_1d_ref_mod, "w") as file:
file.write(newData)
# Inspect the EXTRACT1D reference file.
with open(extract_1d_ref_mod, 'r') as f_obj:
extract_1d_ref_mod_data = json.load(f_obj)
JSON(extract_1d_ref_mod_data, expanded=True)
<IPython.core.display.JSON object>
Rerun Extract1d step using the new EXTRACT1D reference file.
for s2d in stage3_s2d:
Extract1dStep.call(s2d,
save_results=True,
output_dir=spec3_dir,
output_use_model=True,
suffix='x1d_mod', # Default suffix is `_extract1dstep.fits`
use_source_posn=False,
override_extract1d=extract_1d_ref_mod)
2025-05-13 14:43:38,440 - stpipe.Extract1dStep - INFO - Extract1dStep instance created.
2025-05-13 14:43:38,694 - stpipe.Extract1dStep - INFO - Step Extract1dStep running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_s2d.fits',).
2025-05-13 14:43:38,697 - stpipe.Extract1dStep - INFO - Step Extract1dStep parameters are:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: True
skip: False
suffix: x1d_mod
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: False
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: False
bkg_sigma_clip: 3.0
ifu_rfcorr: True
ifu_set_srctype: None
ifu_rscale: None
ifu_covar_scale: 1.0
soss_atoca: True
soss_threshold: 0.01
soss_n_os: 2
soss_wave_grid_in: None
soss_wave_grid_out: None
soss_estimate: None
soss_rtol: 0.0001
soss_max_grid_size: 20000
soss_tikfac: None
soss_width: 40.0
soss_bad_pix: masking
soss_modelname: None
2025-05-13 14:43:38,879 - stpipe.Extract1dStep - INFO - Using EXTRACT1D reference file /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/jwst_nirspec_extract1d_0009_mos.json
2025-05-13 14:43:38,934 - stpipe.Extract1dStep - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0004.fits
2025-05-13 14:43:39,013 - stpipe.Extract1dStep - INFO - Processing spectral order -1
2025-05-13 14:43:39,014 - stpipe.Extract1dStep - INFO - Aperture start/stop: 22.00 -> 27.00 (inclusive)
2025-05-13 14:43:39,066 - stpipe.Extract1dStep - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 14:43:39,130 - stpipe.Extract1dStep - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/MOS/mos_data_02736/Obs007/stage3/f290lp_g395m_s000006355_x1d_mod.fits
2025-05-13 14:43:39,130 - stpipe.Extract1dStep - INFO - Step Extract1dStep done
2025-05-13 14:43:39,130 - stpipe - INFO - Results used jwst version: 1.18.0
mosviz = Mosviz()
spectra_1d = glob.glob(spec3_dir+'*x1d_mod.fits')
spectra_2d = glob.glob(spec3_dir+'*s2d.fits')
image = None # If you have 'mymosaic.fits'
mosviz.load_data(spectra_1d=spectra_1d, spectra_2d=spectra_2d, images=image)
mosviz.show()
To overlay the spectra for comparison run the cell below.
if doviz:
stage3_x1ds_mod = sorted(glob.glob(spec3_dir + '*_x1d_mod.fits'))
display_spectra(stage3_s2d + stage3_x1d, compare_x1d=stage3_x1ds_mod,
source_id=source_ids[0] or None, source_type='POINT', scale='log',
vmin=0, vmax=3, y_limits=(-1e-6, 0.3e-5),
title_prefix='REPROCESSED', is_stage3=True)
2025-05-13 14:43:40,410 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/astropy/stats/sigma_clipping.py:407: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically clipped.
warnings.warn(
2025-05-13 14:43:40,469 - stpipe - WARNING - /tmp/ipykernel_2429/3154024895.py:267: UserWarning: No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
ax2d[i].legend(fontsize=12)
147
Expanding wavelength gap 4.70 -- 4.96 μm
147
Expanding wavelength gap 4.70 -- 4.96 μm
Related Notebooks#
Notebooks running pipeline on simulated NIRSpec MOS data: JWebbinar7 (Oct 2021) • JDAT (2021) • JADES (June 2022)
Notebook processing ERO SMACS0723 NIRSpec MOS data using the JWST pipeline and msaexp
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