NIRSpec FS Pipeline Notebook#
Authors: Elena Manjavacas (emanjavacas@stsci.edu), building on the work of Peter Zeidler (zeidler@stsci.edu), Kayli Glidic (kglidic@stsci.edu), and James Muzerolle (muzerol@stsci.edu); NIRSpec branch Last Updated: April 16, 2025 Pipeline Version: 1.18.0 (Build 11.3, Context jwst_1364.pmap)
Purpose:
This notebook provides a framework for processing generic Near-Infrared Spectrograph (NIRSpec) fixed slit (FS) data through the three stages of the JWST pipeline. It includes how to use associations for multi-exposure observations and how to interact and work with JWST datamodels. Data is assumed to be organized into two folders: science and background, as specified in the paths set up below. 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 HD1808347 A3V standard star (point source) with the G235M grism obtained by Proposal ID (PID) 1128, Observation 6. The demo data will be automatically downloaded in the demo_mode unless disabled (i.e., to use local files instead).
JWST pipeline version and CRDS context:
This notebook was written for the calibration pipeline version given above and uses the context associated with this version of the JWST Calibration Pipeline. Information about this an other contexts can be found in the JWST Calibration Reference Data System (CRDS)
server. If you use different pipeline versions, please refer to the table here to determine what context to use. To learn more about the differences for the pipeline, read the relevant documentation
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 (kglidic@stsci.edu).
November 4, 2024: Notebook updated to JWST pipeline version 1.16.0 (Build 11.1).
January 6, 2025: Updated formatting and added examples for creating association files.
January 27, 2025: Notebook updated to JWST pipeline version 1.17.1 (Build 11.2) and added more association file information.
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
Detector1Pipeline5.2.1 Calibrating Science Files
5.2.2 Calibrating Background Files
6. Stage 2:
Spec2Pipeline(calwebb_spec2)6.1 Configure
Spec2Pipeline6.2 Create
Spec2PipelineAssociation Files6.3 Run
Spec2Pipeline6.3.1 Calibrating Science Files
6.3.2 Calibrating Background Files
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_fs_pipeline python=3.12
conda activate nirspec_fs_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.bg_dir: Directory where dedicated background observation data is stored.
Backgroud subtraction methods:
master_bg=True: Apply master-background subtraction incalwebb_spec3. For dedicated background observations.pixel_bg=True: Apply pixel-to-pixel background subtraction incalwebb_spec2. This is the default pipeline setting. Typically uses noded 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, 'fs_data_01128/Obs006', '')
# Directory to background observation data; expects uncalibrated data in
# bg_dir/uncal/ and results in stage1, stage2, and stage3 directories.
#bg_dir = os.path.join(basedir, 'fs_data_02288/Obs002', '')
bg_dir = '' # If no background observation, use an empty string.
# ---------------------------Set Processing Steps----------------------------
# Individual pipeline stages can be turned on/off here. Note that a later
# stage won't be able to run unless data products have already been
# produced from the prior stage.
# Science processing.
dodet1 = True # calwebb_detector1
dospec2 = True # calwebb_spec2
dospec3 = True # calwebb_spec3
doviz = True # Visualize calwebb outputs
# Background Processing.
dodet1bg = False # calwebb_detector1
dospec2bg = False # calwebb_spec2 (needed for Master Background subtraction)
# How should background subtraction be done?
# Set one or None of the flags below.
# If none are selected, data will not be background subtracted.
# If background subtraction is done in Spec2 it will be skipped in Spec3.
# Note: Master-background subtraction is for dedicated background observations.
# Dedicated backgrounds must be processed through spec2 first.
master_bg = False # Master-background subtraction in spec3.
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.
# ------------------------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 Import----------------------
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 Specviz2d
Installation instructions for the JWST pipeline found in JWST User Documentation and 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 datamodels.
from jwst.associations import asn_from_list as afl # Tools for creating ASN files.
from jwst.associations.lib.rules_level2_base import DMSLevel2bBase # Lvl2 ASN file.
from jwst.associations.lib.rules_level3_base import DMS_Level3_Base # Lvl3 ASN file.
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 Convenience Functions#
Define a function that filters a list of files based on a specific FITS header key-value condition.
def filter_list(files, key, value):
"""
Filter a list of files based on a specific FITS header key-value condition.
Parameters
----------
files : list
List of file paths to FITS files.
key : str
The FITS header key to check.
value : Any
The value to match for the specified header key.
Returns
-------
list : A list of file paths that satisfy the key-value condition.
"""
return [file for file in files if fits.getheader(file).get(key) == value]
Define a function that filters files based on detector, filter, and grating.
def get_matching(files, detector, filt, grating, fxd_slit, 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.
fxd_slit : str
Fixed slit name.
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
detector_match = fits.getval(file, 'DETECTOR') == detector
filter_match = fits.getval(file, 'FILTER') == filt
grating_match = fits.getval(file, 'GRATING') == grating
slit_match = fits.getval(file, 'FXD_SLIT') == fxd_slit
if detector_match and filter_match and grating_match and slit_match:
# Only IFU and MOS observations have imprint exposures.
try:
is_imprt = fits.getval(file, 'IS_IMPRT')
except KeyError:
is_imprt = None
(files_imprint if is_imprt else files_regular).append(file)
return files_regular, files_imprint
Define a function that checks the grating wheel tilt value between two files.
def match_gwa(file1, file2):
"""
Check if GWA tilt values match closely enough to be associated.
Parameters
----------
file1, file2 : str
Input exposures FITS file paths.
Returns
-------
True if both GWA tilt values match within tolerance, else False.
"""
hdr1, hdr2 = fits.getheader(file1), fits.getheader(file2)
return np.allclose(
(hdr1['GWA_XTIL'], hdr1['GWA_YTIL']),
(hdr2['GWA_XTIL'], hdr2['GWA_YTIL']),
atol=1e-8, rtol=0
)
# 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 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 FS demo data in this notebook is from the NIRSpec calibration program 1128 and features observations of HD1808347 (point source) using the G235M grism. The program setup is briefly summarized in the table below.
Demo Target: HD1808347 A3V Standard Star |
||
|---|---|---|
PROGRAM |
01128 |
Program number |
OBSERVTN |
006 |
Observation number |
G235M/F170LP |
λ: 1.66–3.17 μm (a medium resolution, R ~ 1000) |
|
SUBARRAY |
SUBS200A1 |
Subarray used |
NINTS |
2 |
Number of integrations in exposure |
NGROUPS |
30 |
Number of groups in integration |
DURATION |
96.637 [s] |
Total duration of one exposure |
READPATT |
NRSRAPID |
Readout pattern |
PATTTYPE |
3-POINT-NOD |
Primary dither pattern type |
NUMDTHPT |
3 |
Total number of points in pattern |
SRCTYAPT |
POINT |
Source type selected in APT |
Note: The presence of a physical gap between detectors affects high-resolution FS observations because the spectra are 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!')
# 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 = "01128"
sci_observtn = "006"
bg_observtn = None
filters = ["F170LP;G235M"]
# ----------Define the base and observation directories----------
basedir = os.path.abspath(os.path.join(os.getcwd(), ''))
sci_dir = os.path.join(basedir, f'fs_data_{program}')
sci_dir = os.path.join(sci_dir, f'Obs{sci_observtn}')
uncal_dir = os.path.join(sci_dir, 'uncal/')
# If no background observation, leave blank.
bg_dir = os.path.join(basedir, f'fs_data_{program}')
bg_dir = os.path.join(bg_dir, f'Obs{bg_observtn}') if bg_observtn else ''
uncal_bgdir = os.path.join(bg_dir, 'uncal/') if bg_observtn else ''
# ------Ensure directories for downloading MAST data exists------
os.makedirs(uncal_dir, exist_ok=True)
# Makes directory only when a background observation is provided.
if bg_observtn:
os.makedirs(uncal_bgdir, exist_ok=True)
else:
print('Running with user provided data.')
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 tables of files from MAST associated with the science (SCI) and, if applicable, background (BG) observations. Note that the demo data does not have BG observations.
# 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/SLIT'],
provenance_name=["CALJWST"],
obs_id=[f'*{program}*{sci_observtn}*'])
if bg_dir:
# ------------------BACKGROUND Observation-------------------
bg_obs_id_table = Observations.query_criteria(instrument_name=['NIRSPEC/SLIT'],
provenance_name=["CALJWST"],
obs_id=[f'*{program}*{bg_observtn}*'])
The demo dataset consists of six _uncal.fits files, each approximately 15 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 background files.
sci_downloads, bg_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 = sci_products[sci_products['size'] > avg_sci_size]
sci_downloads.extend(pfilter(sci_products, **file_criteria)['dataURI'])
# --------Identify uncalibrated BACKGROUND files associated with each visit---------
if bg_dir:
for exposure in bg_obs_id_table:
bg_products = Observations.get_product_list(exposure)
# Filter for full-size background files (exclude smaller confirmation images).
avg_bg_size = np.nanmean(bg_products['size'])
bg_products = sci_products[bg_products['size'] > avg_bg_size]
bg_downloads.extend(pfilter(bg_products, **file_criteria)['dataURI'])
# Filter out other observations and remove duplicates.
sci_downloads = {f for f in sci_downloads if f"jw{program}{sci_observtn}" in f}
print(f"Science files selected for downloading: {len(sci_downloads)}")
if bg_dir:
bg_downloads = {f for f in bg_downloads if f"jw{program}{bg_observtn}" in f}
print(f"Background files selected for downloading: {len(bg_downloads)}")
else:
print("Background files selected for downloading: 0")
Science files selected for downloading: 6
Background files selected for downloading: 0
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 bg_downloads:
bg_manifest = Observations.download_file(file, local_path=uncal_bgdir)
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01128006001_0310c_00003_nrs1_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00003_nrs1_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01128006001_0310c_00001_nrs2_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00001_nrs2_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01128006001_0310c_00002_nrs2_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00002_nrs2_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01128006001_0310c_00002_nrs1_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00002_nrs1_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01128006001_0310c_00003_nrs2_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00003_nrs2_uncal.fits ...
[Done]
Downloading URL https://mast.stsci.edu/api/v0.1/Download/file?uri=mast:JWST/product/jw01128006001_0310c_00001_nrs1_uncal.fits to /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00001_nrs1_uncal.fits ...
[Done]
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.
asn_dir = os.path.join(sci_dir, 'asn/') # Association files.
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.
# Creates the directories if target directory does not exist.
os.makedirs(det1_dir, exist_ok=True)
os.makedirs(asn_dir, exist_ok=True)
os.makedirs(spec2_dir, exist_ok=True)
os.makedirs(spec3_dir, exist_ok=True)
# ---------------------------Background Directories-----------------------------
if bg_dir:
uncal_bgdir = os.path.join(bg_dir, 'uncal/') # Uncalibrated pipeline inputs.
asn_bgdir = os.path.join(bg_dir, 'asn/') # Association files.
det1_bgdir = os.path.join(bg_dir, 'stage1/') # calwebb_detector1 pipeline outputs.
spec2_bgdir = os.path.join(bg_dir, 'stage2/') # calwebb_spec2 pipeline outputs.
# Creates directories if background observations are provided and do not already exist.
os.makedirs(det1_bgdir, exist_ok=True)
os.makedirs(asn_bgdir, exist_ok=True)
os.makedirs(spec2_bgdir, 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: 4.1000 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 FS:
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 FS data.
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'] = True # This is the default.
# Suppress computations for saturated ramps with
# only one good (unsaturated) sample (default True).
# The demo data has some saturation.
det1dict['ramp_fit']['suppress_one_group'] = False
# Turn on multi-core processing (off by default).
# Choose what fraction of cores to use (quarter, half, or all).
det1dict['jump']['maximum_cores'] = 'half'
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 detection of cosmic ray snowballs (on by default).
det1dict['jump']['expand_large_events'] = True
det1dict['jump']['expand_factor'] = 3 # (default 2)
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.
# Turn on 1/f noise correction in Stage 1? (off by default).
#det1dict['clean_flicker_noise']['skip'] = False
#det1dict['clean_flicker_noise']['fit_method'] = 'fft'
#det1dict['clean_flicker_noise']['background_method'] = None
#det1dict['clean_flicker_noise']['mask_science_regions'] = False
#det1dict['clean_flicker_noise']['n_sigma'] = False
5.2 Run Detector1Pipeline#
Run the science files, nods, and, if available, any dedicated background files through the calwebb_detector1 pipeline using the .call() method.
We use .call() instead of .run() to ensure that the latest default parameters defined via reference files in CRDS, are applied (ReadtheDocs).
This stage takes approximately 2 minutes to process six _uncal.fits files from the demo data.
# 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))
if bg_dir:
uncal_bg = sorted(glob.glob(uncal_bgdir + '*uncal.fits'))
print(f"Background UNCAL Files:\n{'-'*20}\n" + "\n".join(uncal_bg))
Science UNCAL Files:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00001_nrs1_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00001_nrs2_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00002_nrs1_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00002_nrs2_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00003_nrs1_uncal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00003_nrs2_uncal.fits
time_det1 = time.perf_counter() # Tracks runtime for Stage 1.
5.2.1 Calibrating Science Files#
Identify the input science files and execute the calwebb_detector1 pipeline using the call method.
# Run Stage 1 pipeline on the science 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("Detector1 has been completed for SCI data! \n")
else:
print('Skipping Detector1 processing for SCI data.')
Applying Stage 1 Corrections & Calibrations to: jw01128006001_0310c_00001_nrs1_uncal.fits
2025-05-13 13:52:50,229 - CRDS - INFO - Calibration SW Found: jwst 1.18.0 (/usr/share/miniconda/lib/python3.13/site-packages/jwst-1.18.0.dist-info)
2025-05-13 13:52:50,536 - 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 13:52:50,619 - 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 13:52:50,699 - 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 13:52:50,823 - 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 13:52:50,903 - 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 13:52:50,985 - 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 13:52:51,115 - 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 13:52:51,197 - 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 13:52:51,322 - 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 13:52:51,447 - 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 13:52:51,528 - 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 13:52:51,611 - 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 13:52:51,725 - 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 13:52:51,829 - 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 13:52:51,930 - 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 13:52:52,013 - 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 13:52:52,119 - 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 13:52:52,222 - 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 13:52:52,304 - 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 13:52:52,386 - 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 13:52:52,471 - 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 13:52:52,551 - 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 13:52:52,657 - 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 13:52:52,738 - 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 13:52:52,842 - 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 13:52:52,947 - 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 13:52:53,029 - 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 13:52:53,134 - 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 13:52:53,217 - 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 13:52:53,309 - 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 13:52:53,393 - 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 13:52:53,475 - 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 13:52:53,578 - 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 13:52:53,662 - 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 13:52:53,766 - 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 13:52:53,851 - 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 13:52:53,932 - 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 13:52:54,036 - 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 13:52:54,118 - 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 13:52:54,198 - 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 13:52:54,278 - 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 13:52:54,381 - 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 13:52:54,463 - 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 13:52:54,572 - 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 13:52:54,683 - 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)
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2025-05-13 13:52:55,719 - 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)
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2025-05-13 13:52:55,985 - 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)
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2025-05-13 13:52:56,642 - 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 13:52:56,725 - 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 13:52:56,806 - 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 13:52:56,912 - 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 13:52:57,021 - 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 13:52:57,125 - 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 13:52:57,230 - 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 13:52:57,312 - 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 13:52:57,393 - 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 13:52:57,473 - 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 13:52:57,580 - 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 13:52:57,684 - 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 13:52:57,787 - 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 13:52:57,869 - 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 13:52:57,951 - 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 13:52:58,032 - 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 13:52:58,113 - 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 13:52:58,196 - 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 13:52:58,281 - 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 13:52:58,367 - 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 13:52:58,471 - 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 13:52:58,551 - 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 13:52:58,655 - 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 13:52:58,759 - 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 13:52:58,840 - 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 13:52:58,922 - 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 13:52:59,000 - 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 13:52:59,080 - 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 13:52:59,162 - 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 13:52:59,256 - 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 13:52:59,337 - 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 13:52:59,433 - 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 13:52:59,513 - 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 13:52:59,618 - 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 13:52:59,702 - 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 13:52:59,806 - 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 13:52:59,890 - 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 13:52:59,992 - 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 13:53:00,117 - 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 13:53:00,223 - 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 13:53:00,330 - 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 13:53:00,411 - 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 13:53:00,494 - 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 13:53:00,582 - 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 13:53:00,684 - 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 13:53:00,771 - 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 13:53:00,854 - 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 13:53:00,935 - 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 13:53:01,017 - 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 13:53:01,100 - 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 13:53:01,205 - 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 13:53:01,284 - 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 13:53:01,363 - 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 13:53:01,449 - 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 13:53:01,563 - 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 13:53:01,666 - 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 13:53:01,785 - 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 13:53:01,867 - 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 13:53:01,954 - 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 13:53:02,037 - 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 13:53:02,160 - 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 13:53:02,287 - 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 13:53:02,417 - 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 13:53:02,495 - 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 13:53:02,578 - 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 13:53:02,663 - 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 13:53:02,743 - 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 13:53:02,824 - 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 13:53:02,907 - 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 13:53:02,995 - 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 13:53:03,100 - 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 13:53:03,206 - 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 13:53:03,284 - 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 13:53:03,400 - 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 13:53:03,510 - 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 13:53:03,593 - 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 13:53:03,676 - 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 13:53:03,779 - 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 13:53:03,858 - 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 13:53:03,974 - 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 13:53:04,057 - 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 13:53:04,138 - 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 13:53:04,240 - 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 13:53:04,329 - 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 13:53:04,410 - 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 13:53:04,490 - 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 13:53:04,573 - 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 13:53:04,655 - 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 13:53:04,738 - 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 13:53:04,824 - 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 13:53:04,926 - 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 13:53:05,034 - 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 13:53:05,114 - 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 13:53:05,195 - 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 13:53:05,282 - 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 13:53:05,364 - 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 13:53:05,445 - 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 13:53:05,524 - 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 13:53:05,609 - 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 13:53:05,718 - 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 13:53:05,801 - 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 13:53:05,905 - 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 13:53:05,987 - 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 13:53:06,086 - 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 13:53:06,167 - 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 13:53:06,249 - 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 13:53:06,327 - 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 13:53:06,410 - 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 13:53:06,515 - 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 13:53:06,599 - 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 13:53:06,705 - 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 13:53:06,784 - 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 13:53:06,867 - 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 13:53:06,952 - 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 13:53:07,055 - 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 13:53:07,133 - 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 13:53:07,220 - 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 13:53:07,302 - 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 13:53:07,400 - 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 13:53:07,507 - 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 13:53:07,591 - 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 13:53:07,694 - 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 13:53:07,774 - 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 13:53:07,856 - 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 13:53:07,935 - 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 13:53:08,016 - 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 13:53:08,094 - 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 13:53:08,175 - 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 13:53:08,256 - 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 13:53:08,339 - 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 13:53:08,425 - 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 13:53:08,507 - 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 13:53:08,610 - 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 13:53:08,691 - 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 13:53:08,773 - 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 13:53:08,855 - 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 13:53:08,957 - 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 13:53:09,039 - 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 13:53:09,120 - 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 13:53:09,535 - 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 13:53:09,623 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 13:53:09,636 - 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 13:53:09,716 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 13:53:09,733 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:53:09,733 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:53:09,734 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:53:09,735 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:53:09,736 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:53:09,737 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:53:09,738 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:53:09,739 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:53:09,740 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:53:09,740 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:53:09,741 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:53:09,742 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:53:09,743 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:53:09,744 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:53:09,744 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:53:09,747 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:53:09,748 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:53:09,750 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:53:09,751 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:53:09,751 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:53:09,879 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00001_nrs1_uncal.fits',).
2025-05-13 13:53:09,901 - 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/FSlit/fs_data_01128/Obs006/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: None
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: 1
min_jump_area: 5
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: False
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:53:09,956 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_00001_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:53:09,959 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0379.fits 192.5 M bytes (1 / 7 files) (0 / 238.5 M bytes)
2025-05-13 13:53:29,506 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits 2.1 M bytes (2 / 7 files) (192.5 M / 238.5 M bytes)
2025-05-13 13:53:29,747 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0024.fits 14.9 M bytes (3 / 7 files) (194.6 M / 238.5 M bytes)
2025-05-13 13:53:30,490 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0051.fits 16.8 M bytes (4 / 7 files) (209.5 M / 238.5 M bytes)
2025-05-13 13:53:30,854 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits 4.2 M bytes (5 / 7 files) (226.3 M / 238.5 M bytes)
2025-05-13 13:53:31,148 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0028.fits 6.4 M bytes (6 / 7 files) (230.5 M / 238.5 M bytes)
2025-05-13 13:53:31,560 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0330.fits 1.6 M bytes (7 / 7 files) (236.9 M / 238.5 M bytes)
2025-05-13 13:53:31,912 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0379.fits'.
2025-05-13 13:53:31,913 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits'.
2025-05-13 13:53:31,913 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0024.fits'.
2025-05-13 13:53:31,914 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0051.fits'.
2025-05-13 13:53:31,914 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:53:31,915 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits'.
2025-05-13 13:53:31,915 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2025-05-13 13:53:31,916 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 13:53:31,916 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 13:53:31,916 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0028.fits'.
2025-05-13 13:53:31,917 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 13:53:31,917 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0330.fits'.
2025-05-13 13:53:31,917 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:53:31,918 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:53:31,920 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:53:32,162 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:32,169 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:53:32,169 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:53:32,171 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:53:32,298 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:32,315 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0051.fits
2025-05-13 13:53:32,389 - stpipe.Detector1Pipeline.dq_init - INFO - Extracting mask subarray to match science data
2025-05-13 13:53:32,406 - CRDS - INFO - Calibration SW Found: jwst 1.18.0 (/usr/share/miniconda/lib/python3.13/site-packages/jwst-1.18.0.dist-info)
2025-05-13 13:53:32,516 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:53:32,650 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:32,668 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0028.fits
2025-05-13 13:53:32,710 - stpipe.Detector1Pipeline.saturation - INFO - Extracting reference file subarray to match science data
2025-05-13 13:53:32,717 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:53:32,765 - stpipe.Detector1Pipeline.saturation - INFO - Detected 9 saturated pixels
2025-05-13 13:53:32,767 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2025-05-13 13:53:32,771 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:53:32,907 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:32,907 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:53:33,044 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:33,065 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0330.fits
2025-05-13 13:53:33,134 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 13:53:33,275 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:33,294 - stpipe.Detector1Pipeline.refpix - INFO - NIR subarray data
2025-05-13 13:53:33,298 - stpipe.Detector1Pipeline.refpix - INFO - Single readout amplifier used
2025-05-13 13:53:33,298 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is valid for this mode:
2025-05-13 13:53:33,299 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2025-05-13 13:53:33,299 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are not applicable and are ignored:
2025-05-13 13:53:33,300 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2025-05-13 13:53:33,300 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2025-05-13 13:53:33,300 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2025-05-13 13:53:33,301 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2025-05-13 13:53:33,455 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 13:53:33,595 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:33,627 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0024.fits
2025-05-13 13:53:33,648 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:53:33,728 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:53:33,873 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:33,891 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0379.fits
2025-05-13 13:53:33,960 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=30, nframes=1, groupgap=0
2025-05-13 13:53:33,960 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=180, nframes=1, groupgap=0
2025-05-13 13:53:34,005 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:53:34,153 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:34,153 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:53:34,300 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:34,307 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:53:34,308 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:53:34,331 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits
2025-05-13 13:53:34,340 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits
2025-05-13 13:53:34,365 - stpipe.Detector1Pipeline.jump - INFO - Extracting gain subarray to match science data
2025-05-13 13:53:34,370 - stpipe.Detector1Pipeline.jump - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:53:34,388 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:53:34,389 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:53:35,351 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 13:53:35,396 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 98
2025-05-13 13:53:35,397 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 1.00774 sec
2025-05-13 13:53:35,407 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 1.099352
2025-05-13 13:53:35,409 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:53:35,554 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:35,554 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:53:35,697 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:35,755 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits
2025-05-13 13:53:35,755 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits
2025-05-13 13:53:35,780 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting gain subarray to match science data
2025-05-13 13:53:35,785 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:53:35,790 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:53:35,791 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:53:35,861 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:53:36,516 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.6539833545684814
2025-05-13 13:53:36,562 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:53:36,710 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:36,724 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.429
2025-05-13 13:53:36,728 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:36,873 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 64, 2048) from jw01128006001_0310c_00001_nrs1_uncal.fits>,).
2025-05-13 13:53:36,889 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.429
2025-05-13 13:53:36,892 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:53:36,950 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rateints.fits
2025-05-13 13:53:36,950 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:53:36,951 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:53:37,001 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits
2025-05-13 13:53:37,002 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:53:37,002 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:53:37,066 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 13:53:37,077 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 13:53:37,092 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:53:37,093 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:53:37,094 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:53:37,094 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:53:37,095 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:53:37,096 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:53:37,097 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:53:37,098 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:53:37,099 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:53:37,100 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:53:37,101 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:53:37,102 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:53:37,103 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:53:37,104 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:53:37,105 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:53:37,106 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:53:37,107 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:53:37,109 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:53:37,110 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:53:37,111 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:53:37,252 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00001_nrs2_uncal.fits',).
Applying Stage 1 Corrections & Calibrations to: jw01128006001_0310c_00001_nrs2_uncal.fits
2025-05-13 13:53:37,274 - 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/FSlit/fs_data_01128/Obs006/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: None
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: 1
min_jump_area: 5
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: False
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:53:37,324 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_00001_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:53:37,328 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0367.fits 192.5 M bytes (1 / 7 files) (0 / 238.5 M bytes)
2025-05-13 13:53:57,245 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits 2.1 M bytes (2 / 7 files) (192.5 M / 238.5 M bytes)
2025-05-13 13:53:57,523 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0023.fits 14.9 M bytes (3 / 7 files) (194.6 M / 238.5 M bytes)
2025-05-13 13:53:58,436 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0049.fits 16.8 M bytes (4 / 7 files) (209.5 M / 238.5 M bytes)
2025-05-13 13:53:58,799 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits 4.2 M bytes (5 / 7 files) (226.3 M / 238.5 M bytes)
2025-05-13 13:53:59,065 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0029.fits 6.4 M bytes (6 / 7 files) (230.5 M / 238.5 M bytes)
2025-05-13 13:53:59,589 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0415.fits 1.6 M bytes (7 / 7 files) (236.9 M / 238.5 M bytes)
2025-05-13 13:53:59,967 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0367.fits'.
2025-05-13 13:53:59,968 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits'.
2025-05-13 13:53:59,969 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0023.fits'.
2025-05-13 13:53:59,969 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0049.fits'.
2025-05-13 13:53:59,970 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:53:59,970 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits'.
2025-05-13 13:53:59,970 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2025-05-13 13:53:59,971 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 13:53:59,971 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 13:53:59,972 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0029.fits'.
2025-05-13 13:53:59,972 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 13:53:59,973 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0415.fits'.
2025-05-13 13:53:59,974 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:53:59,974 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:53:59,975 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:54:00,210 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:00,218 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:54:00,218 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:54:00,220 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:54:00,352 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:00,368 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0049.fits
2025-05-13 13:54:00,445 - stpipe.Detector1Pipeline.dq_init - INFO - Extracting mask subarray to match science data
2025-05-13 13:54:00,460 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:54:00,607 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:00,622 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0029.fits
2025-05-13 13:54:00,658 - stpipe.Detector1Pipeline.saturation - INFO - Extracting reference file subarray to match science data
2025-05-13 13:54:00,665 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:54:00,717 - stpipe.Detector1Pipeline.saturation - INFO - Detected 489 saturated pixels
2025-05-13 13:54:00,719 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2025-05-13 13:54:00,723 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:54:00,862 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:00,863 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:54:01,000 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:01,015 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0415.fits
2025-05-13 13:54:01,074 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 13:54:01,213 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:01,232 - stpipe.Detector1Pipeline.refpix - INFO - NIR subarray data
2025-05-13 13:54:01,234 - stpipe.Detector1Pipeline.refpix - INFO - Single readout amplifier used
2025-05-13 13:54:01,234 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is valid for this mode:
2025-05-13 13:54:01,235 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2025-05-13 13:54:01,235 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are not applicable and are ignored:
2025-05-13 13:54:01,235 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2025-05-13 13:54:01,236 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2025-05-13 13:54:01,237 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2025-05-13 13:54:01,237 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2025-05-13 13:54:01,390 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 13:54:01,535 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:01,550 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0023.fits
2025-05-13 13:54:01,570 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:54:01,652 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:54:01,787 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:01,803 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0367.fits
2025-05-13 13:54:01,870 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=30, nframes=1, groupgap=0
2025-05-13 13:54:01,871 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=180, nframes=1, groupgap=0
2025-05-13 13:54:01,914 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:54:02,055 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:02,056 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:54:02,194 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:02,201 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:54:02,202 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:54:02,222 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits
2025-05-13 13:54:02,230 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits
2025-05-13 13:54:02,253 - stpipe.Detector1Pipeline.jump - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:02,259 - stpipe.Detector1Pipeline.jump - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:02,277 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:54:02,278 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:54:03,153 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 13:54:03,177 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 85
2025-05-13 13:54:03,177 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.899633 sec
2025-05-13 13:54:03,187 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 0.985380
2025-05-13 13:54:03,190 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:54:03,334 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:03,335 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:54:03,467 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:03,515 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits
2025-05-13 13:54:03,515 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits
2025-05-13 13:54:03,541 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:03,547 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:03,552 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:54:03,552 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:54:03,621 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:54:04,263 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.6415235996246338
2025-05-13 13:54:04,302 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:54:04,449 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:04,463 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.428
2025-05-13 13:54:04,466 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:04,616 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 64, 2048) from jw01128006001_0310c_00001_nrs2_uncal.fits>,).
2025-05-13 13:54:04,632 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.428
2025-05-13 13:54:04,635 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:04,689 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs2_rateints.fits
2025-05-13 13:54:04,689 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:54:04,690 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:54:04,738 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs2_rate.fits
2025-05-13 13:54:04,739 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:54:04,739 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:54:04,805 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 13:54:04,816 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 13:54:04,832 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:54:04,833 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:54:04,833 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:54:04,835 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:54:04,836 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:54:04,837 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:54:04,838 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:54:04,839 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:54:04,840 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:54:04,841 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:54:04,841 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:54:04,842 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:54:04,844 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:54:04,845 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:54:04,846 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:54:04,846 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:54:04,848 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:54:04,849 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:54:04,850 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:54:04,851 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
Applying Stage 1 Corrections & Calibrations to: jw01128006001_0310c_00002_nrs1_uncal.fits
2025-05-13 13:54:05,006 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00002_nrs1_uncal.fits',).
2025-05-13 13:54:05,025 - 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/FSlit/fs_data_01128/Obs006/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: None
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: 1
min_jump_area: 5
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: False
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:54:05,075 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_00002_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:54:05,079 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0379.fits'.
2025-05-13 13:54:05,079 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits'.
2025-05-13 13:54:05,079 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0024.fits'.
2025-05-13 13:54:05,080 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0051.fits'.
2025-05-13 13:54:05,081 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:54:05,081 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits'.
2025-05-13 13:54:05,082 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2025-05-13 13:54:05,082 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 13:54:05,083 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 13:54:05,083 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0028.fits'.
2025-05-13 13:54:05,084 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 13:54:05,084 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0330.fits'.
2025-05-13 13:54:05,084 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:54:05,085 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:54:05,086 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:54:05,325 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:05,333 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:54:05,333 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:54:05,335 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:54:05,472 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:05,487 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0051.fits
2025-05-13 13:54:05,574 - stpipe.Detector1Pipeline.dq_init - INFO - Extracting mask subarray to match science data
2025-05-13 13:54:05,590 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:54:05,744 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:05,760 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0028.fits
2025-05-13 13:54:05,793 - stpipe.Detector1Pipeline.saturation - INFO - Extracting reference file subarray to match science data
2025-05-13 13:54:05,801 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:54:05,853 - stpipe.Detector1Pipeline.saturation - INFO - Detected 36 saturated pixels
2025-05-13 13:54:05,855 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2025-05-13 13:54:05,859 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:54:06,016 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:06,017 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:54:06,168 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:06,184 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0330.fits
2025-05-13 13:54:06,243 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 13:54:06,391 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:06,410 - stpipe.Detector1Pipeline.refpix - INFO - NIR subarray data
2025-05-13 13:54:06,412 - stpipe.Detector1Pipeline.refpix - INFO - Single readout amplifier used
2025-05-13 13:54:06,413 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is valid for this mode:
2025-05-13 13:54:06,413 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2025-05-13 13:54:06,414 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are not applicable and are ignored:
2025-05-13 13:54:06,414 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2025-05-13 13:54:06,415 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2025-05-13 13:54:06,416 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2025-05-13 13:54:06,416 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2025-05-13 13:54:06,569 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 13:54:06,720 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:06,735 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0024.fits
2025-05-13 13:54:06,757 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:54:06,841 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:54:06,984 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:07,000 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0379.fits
2025-05-13 13:54:07,067 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=30, nframes=1, groupgap=0
2025-05-13 13:54:07,067 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=180, nframes=1, groupgap=0
2025-05-13 13:54:07,112 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:54:07,252 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:07,252 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:54:07,395 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:07,403 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:54:07,403 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:54:07,422 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits
2025-05-13 13:54:07,430 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits
2025-05-13 13:54:07,455 - stpipe.Detector1Pipeline.jump - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:07,460 - stpipe.Detector1Pipeline.jump - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:07,477 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:54:07,478 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:54:08,289 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 13:54:08,314 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 104
2025-05-13 13:54:08,315 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.83723 sec
2025-05-13 13:54:08,325 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 0.922224
2025-05-13 13:54:08,328 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:54:08,487 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:08,488 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:54:08,645 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:08,694 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits
2025-05-13 13:54:08,695 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits
2025-05-13 13:54:08,722 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:08,728 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:08,733 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:54:08,733 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:54:08,803 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:54:09,444 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.6397714614868164
2025-05-13 13:54:09,486 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:54:09,643 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:09,657 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.429
2025-05-13 13:54:09,661 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:09,813 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 64, 2048) from jw01128006001_0310c_00002_nrs1_uncal.fits>,).
2025-05-13 13:54:09,829 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.429
2025-05-13 13:54:09,832 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:09,886 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rateints.fits
2025-05-13 13:54:09,886 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:54:09,887 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:54:09,936 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits
2025-05-13 13:54:09,937 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:54:09,937 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:54:10,002 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 13:54:10,013 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 13:54:10,029 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:54:10,029 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:54:10,030 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:54:10,031 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:54:10,032 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:54:10,034 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:54:10,035 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:54:10,036 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:54:10,037 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:54:10,038 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:54:10,038 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:54:10,041 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:54:10,042 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:54:10,042 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:54:10,043 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:54:10,044 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:54:10,046 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:54:10,047 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:54:10,048 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:54:10,049 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:54:10,202 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00002_nrs2_uncal.fits',).
Applying Stage 1 Corrections & Calibrations to: jw01128006001_0310c_00002_nrs2_uncal.fits
2025-05-13 13:54:10,223 - 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/FSlit/fs_data_01128/Obs006/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: None
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: 1
min_jump_area: 5
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: False
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:54:10,274 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_00002_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:54:10,278 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0367.fits'.
2025-05-13 13:54:10,278 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits'.
2025-05-13 13:54:10,279 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0023.fits'.
2025-05-13 13:54:10,279 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0049.fits'.
2025-05-13 13:54:10,280 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:54:10,280 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits'.
2025-05-13 13:54:10,281 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2025-05-13 13:54:10,281 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 13:54:10,282 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 13:54:10,282 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0029.fits'.
2025-05-13 13:54:10,282 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 13:54:10,283 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0415.fits'.
2025-05-13 13:54:10,283 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:54:10,283 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:54:10,284 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:54:10,534 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:10,541 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:54:10,541 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:54:10,543 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:54:10,692 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:10,707 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0049.fits
2025-05-13 13:54:10,786 - stpipe.Detector1Pipeline.dq_init - INFO - Extracting mask subarray to match science data
2025-05-13 13:54:10,802 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:54:10,961 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:10,976 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0029.fits
2025-05-13 13:54:11,008 - stpipe.Detector1Pipeline.saturation - INFO - Extracting reference file subarray to match science data
2025-05-13 13:54:11,015 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:54:11,066 - stpipe.Detector1Pipeline.saturation - INFO - Detected 459 saturated pixels
2025-05-13 13:54:11,069 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2025-05-13 13:54:11,072 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:54:11,220 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:11,221 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:54:11,365 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:11,381 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0415.fits
2025-05-13 13:54:11,440 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 13:54:11,591 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:11,610 - stpipe.Detector1Pipeline.refpix - INFO - NIR subarray data
2025-05-13 13:54:11,612 - stpipe.Detector1Pipeline.refpix - INFO - Single readout amplifier used
2025-05-13 13:54:11,612 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is valid for this mode:
2025-05-13 13:54:11,613 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2025-05-13 13:54:11,614 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are not applicable and are ignored:
2025-05-13 13:54:11,614 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2025-05-13 13:54:11,615 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2025-05-13 13:54:11,615 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2025-05-13 13:54:11,616 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2025-05-13 13:54:11,777 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 13:54:11,926 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:11,943 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0023.fits
2025-05-13 13:54:11,964 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:54:12,049 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:54:12,202 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:12,218 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0367.fits
2025-05-13 13:54:12,286 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=30, nframes=1, groupgap=0
2025-05-13 13:54:12,287 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=180, nframes=1, groupgap=0
2025-05-13 13:54:12,332 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:54:12,490 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:12,491 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:54:12,642 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:12,649 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:54:12,650 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:54:12,670 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits
2025-05-13 13:54:12,678 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits
2025-05-13 13:54:12,702 - stpipe.Detector1Pipeline.jump - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:12,707 - stpipe.Detector1Pipeline.jump - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:12,725 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:54:12,726 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:54:13,563 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 13:54:13,587 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 79
2025-05-13 13:54:13,587 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.861799 sec
2025-05-13 13:54:13,597 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 0.948045
2025-05-13 13:54:13,600 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:54:13,755 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:13,756 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:54:13,905 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:13,954 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits
2025-05-13 13:54:13,954 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits
2025-05-13 13:54:13,981 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:13,987 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:13,992 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:54:13,992 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:54:14,062 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:54:14,712 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.6486372947692871
2025-05-13 13:54:14,752 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:54:14,907 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:14,921 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.428
2025-05-13 13:54:14,924 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:15,065 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 64, 2048) from jw01128006001_0310c_00002_nrs2_uncal.fits>,).
2025-05-13 13:54:15,081 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.428
2025-05-13 13:54:15,084 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:15,139 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs2_rateints.fits
2025-05-13 13:54:15,139 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:54:15,140 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:54:15,188 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs2_rate.fits
2025-05-13 13:54:15,188 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:54:15,189 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:54:15,253 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 13:54:15,263 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 13:54:15,279 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:54:15,279 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:54:15,280 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:54:15,282 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:54:15,282 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:54:15,283 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:54:15,285 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:54:15,286 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:54:15,287 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:54:15,287 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:54:15,288 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:54:15,289 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:54:15,290 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:54:15,291 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:54:15,292 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:54:15,293 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:54:15,295 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:54:15,296 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:54:15,297 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:54:15,298 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
Applying Stage 1 Corrections & Calibrations to: jw01128006001_0310c_00003_nrs1_uncal.fits
2025-05-13 13:54:15,446 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00003_nrs1_uncal.fits',).
2025-05-13 13:54:15,467 - 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/FSlit/fs_data_01128/Obs006/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: None
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: 1
min_jump_area: 5
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: False
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:54:15,519 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_00003_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:54:15,522 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0379.fits'.
2025-05-13 13:54:15,523 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits'.
2025-05-13 13:54:15,523 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0024.fits'.
2025-05-13 13:54:15,524 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0051.fits'.
2025-05-13 13:54:15,524 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:54:15,525 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits'.
2025-05-13 13:54:15,525 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2025-05-13 13:54:15,526 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 13:54:15,526 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 13:54:15,526 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0028.fits'.
2025-05-13 13:54:15,527 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 13:54:15,527 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0330.fits'.
2025-05-13 13:54:15,528 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:54:15,528 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:54:15,529 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:54:15,778 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:15,785 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:54:15,785 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:54:15,787 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:54:15,936 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:15,951 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0051.fits
2025-05-13 13:54:16,032 - stpipe.Detector1Pipeline.dq_init - INFO - Extracting mask subarray to match science data
2025-05-13 13:54:16,048 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:54:16,201 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:16,215 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0028.fits
2025-05-13 13:54:16,247 - stpipe.Detector1Pipeline.saturation - INFO - Extracting reference file subarray to match science data
2025-05-13 13:54:16,254 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:54:16,304 - stpipe.Detector1Pipeline.saturation - INFO - Detected 55 saturated pixels
2025-05-13 13:54:16,306 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2025-05-13 13:54:16,310 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:54:16,455 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:16,455 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:54:16,600 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:16,615 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0330.fits
2025-05-13 13:54:16,675 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 13:54:16,820 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:16,840 - stpipe.Detector1Pipeline.refpix - INFO - NIR subarray data
2025-05-13 13:54:16,842 - stpipe.Detector1Pipeline.refpix - INFO - Single readout amplifier used
2025-05-13 13:54:16,842 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is valid for this mode:
2025-05-13 13:54:16,843 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2025-05-13 13:54:16,843 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are not applicable and are ignored:
2025-05-13 13:54:16,844 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2025-05-13 13:54:16,844 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2025-05-13 13:54:16,845 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2025-05-13 13:54:16,845 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2025-05-13 13:54:16,996 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 13:54:17,137 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:17,152 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0024.fits
2025-05-13 13:54:17,175 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:54:17,259 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:54:17,402 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:17,418 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0379.fits
2025-05-13 13:54:17,485 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=30, nframes=1, groupgap=0
2025-05-13 13:54:17,486 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=180, nframes=1, groupgap=0
2025-05-13 13:54:17,531 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:54:17,673 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:17,674 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:54:17,810 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:17,817 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:54:17,818 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:54:17,837 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits
2025-05-13 13:54:17,845 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits
2025-05-13 13:54:17,868 - stpipe.Detector1Pipeline.jump - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:17,874 - stpipe.Detector1Pipeline.jump - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:17,890 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:54:17,891 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:54:18,738 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 13:54:18,761 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 103
2025-05-13 13:54:18,762 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.870758 sec
2025-05-13 13:54:18,772 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 0.954307
2025-05-13 13:54:18,774 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:54:18,914 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:18,915 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:54:19,048 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:19,096 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0043.fits
2025-05-13 13:54:19,096 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0025.fits
2025-05-13 13:54:19,121 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:19,126 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:19,131 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:54:19,132 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:54:19,201 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:54:19,848 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.645399808883667
2025-05-13 13:54:19,886 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:54:20,026 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:20,040 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.429
2025-05-13 13:54:20,043 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:20,185 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 64, 2048) from jw01128006001_0310c_00003_nrs1_uncal.fits>,).
2025-05-13 13:54:20,201 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.429
2025-05-13 13:54:20,205 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:20,259 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rateints.fits
2025-05-13 13:54:20,259 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:54:20,260 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:54:20,308 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits
2025-05-13 13:54:20,308 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:54:20,309 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:54:20,373 - stpipe - INFO - PARS-JUMPSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-jumpstep_0003.asdf
2025-05-13 13:54:20,383 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-detector1pipeline_0004.asdf
2025-05-13 13:54:20,398 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2025-05-13 13:54:20,399 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2025-05-13 13:54:20,400 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2025-05-13 13:54:20,401 - stpipe.Detector1Pipeline.emicorr - INFO - EmiCorrStep instance created.
2025-05-13 13:54:20,402 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2025-05-13 13:54:20,403 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2025-05-13 13:54:20,404 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2025-05-13 13:54:20,405 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2025-05-13 13:54:20,406 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2025-05-13 13:54:20,407 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2025-05-13 13:54:20,408 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2025-05-13 13:54:20,409 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2025-05-13 13:54:20,410 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2025-05-13 13:54:20,410 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2025-05-13 13:54:20,411 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2025-05-13 13:54:20,412 - stpipe.Detector1Pipeline.charge_migration - INFO - ChargeMigrationStep instance created.
2025-05-13 13:54:20,414 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2025-05-13 13:54:20,415 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - CleanFlickerNoiseStep instance created.
2025-05-13 13:54:20,416 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2025-05-13 13:54:20,417 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2025-05-13 13:54:20,559 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/uncal/jw01128006001_0310c_00003_nrs2_uncal.fits',).
Applying Stage 1 Corrections & Calibrations to: jw01128006001_0310c_00003_nrs2_uncal.fits
2025-05-13 13:54:20,581 - 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/FSlit/fs_data_01128/Obs006/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: None
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: 1
min_jump_area: 5
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: False
firstgroup: None
lastgroup: None
maximum_cores: '1'
gain_scale:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
2025-05-13 13:54:20,631 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_00003_nrs2_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'sirskernel', 'superbias', 'trapdensity', 'trappars']
2025-05-13 13:54:20,635 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0367.fits'.
2025-05-13 13:54:20,635 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits'.
2025-05-13 13:54:20,636 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0023.fits'.
2025-05-13 13:54:20,636 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0049.fits'.
2025-05-13 13:54:20,637 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2025-05-13 13:54:20,637 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits'.
2025-05-13 13:54:20,638 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2025-05-13 13:54:20,638 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2025-05-13 13:54:20,639 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2025-05-13 13:54:20,639 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0029.fits'.
2025-05-13 13:54:20,639 - stpipe.Detector1Pipeline - INFO - Prefetch for SIRSKERNEL reference file is 'N/A'.
2025-05-13 13:54:20,640 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0415.fits'.
2025-05-13 13:54:20,640 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2025-05-13 13:54:20,641 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2025-05-13 13:54:20,642 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2025-05-13 13:54:20,879 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:20,887 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2025-05-13 13:54:20,887 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2025-05-13 13:54:20,889 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2025-05-13 13:54:21,028 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:21,043 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_mask_0049.fits
2025-05-13 13:54:21,121 - stpipe.Detector1Pipeline.dq_init - INFO - Extracting mask subarray to match science data
2025-05-13 13:54:21,136 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2025-05-13 13:54:21,281 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:21,296 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_saturation_0029.fits
2025-05-13 13:54:21,327 - stpipe.Detector1Pipeline.saturation - INFO - Extracting reference file subarray to match science data
2025-05-13 13:54:21,334 - stpipe.Detector1Pipeline.saturation - INFO - Using read_pattern with nframes 1
2025-05-13 13:54:21,388 - stpipe.Detector1Pipeline.saturation - INFO - Detected 450 saturated pixels
2025-05-13 13:54:21,390 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2025-05-13 13:54:21,394 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2025-05-13 13:54:21,542 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:21,543 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2025-05-13 13:54:21,681 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:21,697 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_superbias_0415.fits
2025-05-13 13:54:21,757 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2025-05-13 13:54:21,908 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:21,929 - stpipe.Detector1Pipeline.refpix - INFO - NIR subarray data
2025-05-13 13:54:21,931 - stpipe.Detector1Pipeline.refpix - INFO - Single readout amplifier used
2025-05-13 13:54:21,931 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is valid for this mode:
2025-05-13 13:54:21,932 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2025-05-13 13:54:21,932 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are not applicable and are ignored:
2025-05-13 13:54:21,932 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2025-05-13 13:54:21,933 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2025-05-13 13:54:21,933 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2025-05-13 13:54:21,934 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2025-05-13 13:54:22,089 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2025-05-13 13:54:22,243 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:22,259 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_linearity_0023.fits
2025-05-13 13:54:22,280 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2025-05-13 13:54:22,366 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2025-05-13 13:54:22,507 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:22,523 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dark_0367.fits
2025-05-13 13:54:22,595 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=2, ngroups=30, nframes=1, groupgap=0
2025-05-13 13:54:22,596 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=180, nframes=1, groupgap=0
2025-05-13 13:54:22,641 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2025-05-13 13:54:22,787 - stpipe.Detector1Pipeline.charge_migration - INFO - Step charge_migration running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:22,788 - stpipe.Detector1Pipeline.charge_migration - INFO - Step skipped.
2025-05-13 13:54:22,932 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:22,939 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2025-05-13 13:54:22,940 - stpipe.Detector1Pipeline.jump - INFO - Maximum cores to use = half
2025-05-13 13:54:22,967 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits
2025-05-13 13:54:22,975 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits
2025-05-13 13:54:22,998 - stpipe.Detector1Pipeline.jump - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:23,004 - stpipe.Detector1Pipeline.jump - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:23,021 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2025-05-13 13:54:23,021 - stpipe.Detector1Pipeline.jump - INFO - Creating 2 processes for jump detection
2025-05-13 13:54:23,854 - stpipe.Detector1Pipeline.jump - INFO - Flagging Snowballs
2025-05-13 13:54:23,876 - stpipe.Detector1Pipeline.jump - INFO - Total snowballs = 76
2025-05-13 13:54:23,877 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 0.855208 sec
2025-05-13 13:54:23,887 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 0.947220
2025-05-13 13:54:23,889 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2025-05-13 13:54:24,035 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step clean_flicker_noise running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:24,036 - stpipe.Detector1Pipeline.clean_flicker_noise - INFO - Step skipped.
2025-05-13 13:54:24,184 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(2, 30, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:24,218 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_readnoise_0048.fits
2025-05-13 13:54:24,218 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_gain_0027.fits
2025-05-13 13:54:24,243 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting gain subarray to match science data
2025-05-13 13:54:24,248 - stpipe.Detector1Pipeline.ramp_fit - INFO - Extracting readnoise subarray to match science data
2025-05-13 13:54:24,253 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = OLS_C
2025-05-13 13:54:24,254 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
2025-05-13 13:54:24,308 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of multiprocessing slices: 1
2025-05-13 13:54:24,923 - stpipe.Detector1Pipeline.ramp_fit - INFO - Ramp Fitting C Time: 0.6140749454498291
2025-05-13 13:54:24,962 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2025-05-13 13:54:25,105 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:25,119 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.428
2025-05-13 13:54:25,123 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:25,263 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(2, 64, 2048) from jw01128006001_0310c_00003_nrs2_uncal.fits>,).
2025-05-13 13:54:25,279 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.428
2025-05-13 13:54:25,282 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2025-05-13 13:54:25,333 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs2_rateints.fits
2025-05-13 13:54:25,334 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2025-05-13 13:54:25,335 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:54:25,382 - stpipe.Detector1Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs2_rate.fits
2025-05-13 13:54:25,383 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2025-05-13 13:54:25,383 - stpipe - INFO - Results used jwst version: 1.18.0
Detector1 has been completed for SCI data!
5.2.2 Calibrating Background Files#
Identify the input background files and execute the calwebb_detector1 pipeline using the call method.
# Run Stage 1 pipeline on any background using the custom det1dict dictionary.
if dodet1bg:
#------------------------Background UNCAL files-------------------------
for uncal_file in sorted(glob.glob(uncal_bgdir + '*uncal.fits')):
print(f"Applying Stage 1 Corrections & Calibrations to: "
f"{os.path.basename(uncal_file)}")
det1bg_result = Detector1Pipeline.call(uncal_file,
save_results=True,
steps=det1dict,
output_dir=det1_bgdir)
print("Detector1 has been completed for BKG data! \n")
else:
print('Skipping Detector1 processing for BKG data.')
Skipping Detector1 processing for BKG data.
# 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: 5.7000 min
Runtime for Stage 1: 1.6000 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))
if bg_dir:
rate_bg = sorted(glob.glob(det1_bgdir + '*_rate.fits'))
rateints_bg = sorted(glob.glob(det1_bgdir + '*_rateints.fits'))
print(f"BACKGROUND | RATE[INTS] Files:\n{'-' * 20}\n" + "\n".join(rate_bg + rateints_bg))
SCIENCE | RATE[INTS] Files:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs2_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs2_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs2_rate.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs2_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs2_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rateints.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_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).
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 FS:
assign_wcs: Assigns wavelength solution for spectra.badpix_selfcal: Flags bad pixels in the input data using a self-calibration technique based on median filtering along the spectral axis.nsclean: Cleans 1/f noise.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.wavecorr: Updates wavelengths 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.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 FS data.
If pixel-to-pixel background subtraction was chosen above, it will be applied during this stage. To override specific steps and reference files, use the examples below.
# 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['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.
# 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'
# 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.
Resampling 2D spectra can sometimes introduce artificial noise and reduce the signal-to-noise ratio (SNR) in the resulting 1D spectra when using weight_type='ivm' (see known issues). The default is now set to set weight type to ‘exptime’. Consider the following when selecting a weight_type parameter:
‘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.
# Resample weight_type.
#spec2dict['resample_spec']['weight_type'] = 'exptime'
To correct for 1/f noise with nsclean in Stage 2, see the FS_NSClean_example demo notebook for FS data here.
# Run nsclean for 1/f noise.
#spec2dict['nsclean']['skip'] = False
#spec2dict['nsclean']['n_sigma'] = 2
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 FS 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.
Here, we provide an example of manually creating Stage 2 ASN files.
Background subtraction may not be correctly applied in Stage 2 if more than one science file is included in the association.
Additionally, pixel-to-pixel background subtraction will only be performed if the grating wheel has not moved between the target and off-scene associated background exposures. If the grating wheel moved between the target and background exposures (as would be the case if they were in different visits), pipeline processing will require a more involved “master background” subtraction done in Stage 3.
Association for nodded observations
def asn_nod(asn, onescifile, sci, sci_imprint, nod_num):
"""
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.
nod_num : int
Position in dither pattern.
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') - 1) // (fits.getval(file, 'SUBPXPTS'))) != nod_num:
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 associates background and selfcal exposures for dithered observations.
def asn_dither(asn, onescifile, sci, sci_imprint, bg, bg_imprint):
"""
Associate background, imprint, and selfcal exposures for dithered 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.
bg : list of str
List of background exposure file paths.
bg_imprint : list of str
List of background imprint exposure file paths.
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 bg:
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'})
for file in bg_imprint:
# Only IFU and MOS observations have imprint exposures.
if fits.getval(file, 'EXP_TYPE') == 'NRS_IFU' or 'NRS_MSASPEC':
if match_gwa(bg[0], file):
members.append({'expname': file, 'exptype': 'imprint'})
# Assign selfcal exposures.
for file in sci + sci_imprint + bg + bg_imprint:
members.append({'expname': file, 'exptype': 'selfcal'})
return asn
Function to write the association file
def writel2asn(onescifile, allscifiles, bgfiles, 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.
bgfiles : list of str
List of background 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')
fxd_slit = fits.getval(onescifile, 'FXD_SLIT')
patttype = fits.getval(onescifile, 'PATTTYPE') # Dither pattern type.
pattnum = fits.getval(onescifile, 'PATT_NUM') # Dither pattern number.
# primary_dithpts = fits.getval(onescifile, 'PRIDTPTS') # Points in primary dither pattern.
subpxpts = fits.getval(onescifile, 'SUBPXPTS') # Points in subpixel dither pattern.
# Position number within primary dither pattern.
nod_num = (pattnum - 1) // (subpxpts)
# 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, _ = get_matching(allscifiles, detector, filt, grating, fxd_slit, exp_type)
use_bg, _ = get_matching(bgfiles, detector, filt, grating, fxd_slit, exp_type) if bgfiles else ([], [])
# If this uses nodded exposures set up pixel-based background subtraction accordingly.
is_nod = 'NOD' in patttype.split('-')
if is_nod:
asn = asn_nod(asn, onescifile, use_sci, [], nod_num)
else: # Otherwise handle as dithered exposures.
asn = asn_dither(asn, onescifile, use_sci, [], use_bg, [])
# Write the association to a json file.
_, serialized = asn.dump()
with open(asnfile, 'w') as outfile:
outfile.write(serialized)
return True
# ---------------------Sort science and background files---------------------
# 'rate_sci' includes files marked as science targets.
# 'rate_bg' includes files marked as backgrounds in the science observation
# or dedicated background observations.
rate_sci = filter_list(rate_sci, 'BKGDTARG', False) or []
rate_bg = filter_list(rate_sci, 'BKGDTARG', True) or (rate_bg if bg_dir else [])
# Special case for FS S1600A1 with a 5-POINT-NOD.
# Exclude the top and bottom dithers [1, 5] that are close to slit edges.
excluded_files = [
file for file in rate_sci + rate_bg
# Considering number of points in primary dither pattern and
# Position number within primary dither pattern.
if (
(header := fits.getheader(file)).get('FXD_SLIT') == 'S1600A1' and header.get('PRIDTPTS') == 5 and (header.get('PATT_NUM') - 1) // header.get('SUBPXPTS') in [1, 5]
)
]
# Filter excluded files from both lists.
rate_sci = [file for file in rate_sci if file not in excluded_files]
rate_bg = [file for file in rate_bg if file not in excluded_files]
6.3 Run Spec2Pipeline#
Run the science files, associated nods and, if available, any background files through the calwebb_spec2 pipeline using the .call() method.
Perform pixel-to-pixel background subtraction (if desired) here in Stage 2. Otherwise, reduce the backgrounds individually for master background subtraction in Stage 3 (if desired).
time_spec2 = time.perf_counter()
6.3.1 Calibrating Science Files#
Identify the Stage 2 ASN files and execute the calwebb_spec2 pipeline using the call method.
# To save on runtime turns off creation of quicklook 2d/1d spectra for science data.
# Any master background subtraction in spec3 will require the 1d spectra from spec2.
#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:
# --------------------------Science 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, rate_bg, asnfile, 'Level2', 'NRS_FIXEDSLIT'):
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 NRS2.
print(f"Skipped processing {os.path.basename(asnfile)}: {e}")
print("Spec2 has been completed for SCI data! \n")
else:
print('Skipping Spec2 processing for SCI data.')
2025-05-13 13:54:25,506 - 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/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits
2025-05-13 13:54:25,631 - 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 13:54:25,716 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:54:25,739 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:54:25,763 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 13:54:25,765 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:54:25,766 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 13:54:25,767 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 13:54:25,768 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 13:54:25,769 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:54:25,770 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 13:54:25,771 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 13:54:25,775 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 13:54:25,776 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:54:25,777 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:54:25,778 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:54:25,779 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 13:54:25,780 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:54:25,782 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:54:25,784 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:54:25,784 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 13:54:25,786 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:54:25,786 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 13:54:25,788 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 13:54:25,788 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 13:54:25,789 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 13:54:25,790 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:54:25,791 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:54:25,792 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 13:54:25,793 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:54:25,794 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:54:25,795 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:54:25,797 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 13:54:25,799 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:54:25,947 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/asn/jw01128006001_0310c_00001_nrs1_l2asn.json',).
2025-05-13 13:54:25,980 - 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/FSlit/fs_data_01128/Obs006/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: None
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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 13:54:25,989 - 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 13:54:26,022 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_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 13:54:26,028 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits 8.1 M bytes (1 / 18 files) (0 / 781.9 M bytes)
2025-05-13 13:54:26,326 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits 11.5 K bytes (2 / 18 files) (8.1 M / 781.9 M bytes)
2025-05-13 13:54:26,415 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf 5.8 K bytes (3 / 18 files) (8.1 M / 781.9 M bytes)
2025-05-13 13:54:26,503 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf 5.9 K bytes (4 / 18 files) (8.1 M / 781.9 M bytes)
2025-05-13 13:54:26,585 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits 688.9 M bytes (5 / 18 files) (8.1 M / 781.9 M bytes)
2025-05-13 13:54:32,536 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0058.asdf 2.4 K bytes (6 / 18 files) (697.0 M / 781.9 M bytes)
2025-05-13 13:54:32,626 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json 1.3 K bytes (7 / 18 files) (697.0 M / 781.9 M bytes)
2025-05-13 13:54:32,715 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits 109.4 K bytes (8 / 18 files) (697.0 M / 781.9 M bytes)
2025-05-13 13:54:32,865 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.asdf 12.8 K bytes (9 / 18 files) (697.1 M / 781.9 M bytes)
2025-05-13 13:54:32,965 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf 4.3 K bytes (10 / 18 files) (697.2 M / 781.9 M bytes)
2025-05-13 13:54:33,052 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf 5.0 M bytes (11 / 18 files) (697.2 M / 781.9 M bytes)
2025-05-13 13:54:33,336 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0001.json 6.4 M bytes (12 / 18 files) (702.2 M / 781.9 M bytes)
2025-05-13 13:54:33,631 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf 7.6 K bytes (13 / 18 files) (708.6 M / 781.9 M bytes)
2025-05-13 13:54:33,714 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits 838.1 K bytes (14 / 18 files) (708.6 M / 781.9 M bytes)
2025-05-13 13:54:33,919 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits 95.0 K bytes (15 / 18 files) (709.4 M / 781.9 M bytes)
2025-05-13 13:54:34,044 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0149.fits 72.3 M bytes (16 / 18 files) (709.5 M / 781.9 M bytes)
2025-05-13 13:54:34,931 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf 76.9 K bytes (17 / 18 files) (781.9 M / 781.9 M bytes)
2025-05-13 13:54:35,061 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf 3.4 K bytes (18 / 18 files) (781.9 M / 781.9 M bytes)
2025-05-13 13:54:35,148 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits'.
2025-05-13 13:54:35,149 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits'.
2025-05-13 13:54:35,149 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-05-13 13:54:35,149 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 13:54:35,150 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 13:54:35,150 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 13:54:35,151 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits'.
2025-05-13 13:54:35,151 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0058.asdf'.
2025-05-13 13:54:35,151 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 13:54:35,152 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json'.
2025-05-13 13:54:35,152 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits'.
2025-05-13 13:54:35,153 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 13:54:35,153 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 13:54:35,153 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.asdf'.
2025-05-13 13:54:35,154 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 13:54:35,154 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 13:54:35,155 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:54:35,155 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:54:35,155 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:54:35,156 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 13:54:35,156 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 13:54:35,156 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0001.json'.
2025-05-13 13:54:35,157 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 13:54:35,158 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 13:54:35,158 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits'.
2025-05-13 13:54:35,158 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits'.
2025-05-13 13:54:35,159 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 13:54:35,159 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:54:35,160 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0149.fits'.
2025-05-13 13:54:35,161 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 13:54:35,161 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 13:54:35,161 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:54:35,162 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf'.
2025-05-13 13:54:35,162 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 13:54:35,162 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:54:35,163 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 13:54:35,170 - 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 13:54:35,170 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1
2025-05-13 13:54:35,171 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits ...
2025-05-13 13:54:35,361 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:35,496 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.1383225170000002 deg
2025-05-13 13:54:35,497 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:54:35,497 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:54:35,498 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125293189e-05 deg
2025-05-13 13:54:35,660 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS1: ['S200A1']
2025-05-13 13:54:35,661 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 1 open slitlets
2025-05-13 13:54:35,688 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.1383225170000002 deg
2025-05-13 13:54:35,689 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:54:35,689 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:54:35,690 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125293189e-05 deg
2025-05-13 13:54:35,703 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[1.66e-06, 3.17e-06]
2025-05-13 13:54:35,799 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999998742797083
2025-05-13 13:54:35,830 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 1
2025-05-13 13:54:35,831 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 2
2025-05-13 13:54:35,831 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 3
2025-05-13 13:54:35,832 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 4
2025-05-13 13:54:35,832 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 1 open slits in quadrant 5
2025-05-13 13:54:35,977 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_fixedslit 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_0058.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.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}
2025-05-13 13:54:36,091 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 13:54:36,096 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 13:54:36,256 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits']).
2025-05-13 13:54:36,257 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 13:54:36,416 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:36,417 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-05-13 13:54:36,576 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:36,577 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 13:54:36,741 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs1_rate.fits>, []).
2025-05-13 13:54:36,742 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:54:36,911 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits', []).
2025-05-13 13:54:36,913 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:54:37,068 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits', []).
2025-05-13 13:54:37,068 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:54:37,225 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits']).
2025-05-13 13:54:37,303 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits
2025-05-13 13:54:37,335 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits
2025-05-13 13:54:37,367 - 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 13:54:37,379 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw01128006001_0310c_00001_nrs1_rate.fits
2025-05-13 13:54:37,477 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 13:54:37,642 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:37,672 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_FIXEDSLIT
2025-05-13 13:54:37,672 - stpipe.Spec2Pipeline.extract_2d - INFO - All slits selected
2025-05-13 13:54:37,865 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: S200A1
2025-05-13 13:54:37,866 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 714 2048
2025-05-13 13:54:37,866 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 2 48
2025-05-13 13:54:38,040 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 13:54:38,041 - stpipe.Spec2Pipeline.extract_2d - INFO - xoffset, yoffset, 1.17337682969953e-06, 0.8734010234802524
2025-05-13 13:54:38,051 - stpipe.Spec2Pipeline.extract_2d - INFO - Source X/Y position in the slit: -0.0605792131226249, -0.31144336815102946
2025-05-13 13:54:38,060 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 272.144451799 69.458234418 272.145805401 69.457351681 272.145939176 69.457377429 272.144585608 69.458260174
2025-05-13 13:54:38,061 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 272.144451799 69.458234418 272.145805401 69.457351681 272.145939176 69.457377429 272.144585608 69.458260174
2025-05-13 13:54:38,109 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 13:54:38,266 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:38,272 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_FIXEDSLIT
2025-05-13 13:54:38,272 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-05-13 13:54:38,273 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-05-13 13:54:38,275 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 13:54:38,428 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:38,429 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 13:54:38,430 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:54:38,582 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:38,711 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf
2025-05-13 13:54:38,817 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a POINT source type in slit S200A1
2025-05-13 13:54:38,817 - stpipe.Spec2Pipeline.wavecorr - INFO - slit name S200A1
2025-05-13 13:54:38,929 - stpipe.Spec2Pipeline.wavecorr - INFO - Using wavelength zero-point correction for aperture S200A1
2025-05-13 13:54:38,975 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 13:54:39,151 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:39,192 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 13:54:39,219 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits
2025-05-13 13:54:39,281 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0149.fits
2025-05-13 13:54:39,433 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits
2025-05-13 13:54:39,546 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit S200A1
2025-05-13 13:54:40,072 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 13:54:40,235 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:40,257 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits
2025-05-13 13:54:40,310 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_FIXEDSLIT
2025-05-13 13:54:40,423 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit S200A1
2025-05-13 13:54:40,424 - stpipe.Spec2Pipeline.pathloss - INFO - Using aperture S200A1
2025-05-13 13:54:40,474 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 13:54:40,660 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:40,661 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-05-13 13:54:40,839 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw01128006001_0310c_00001_nrs1_rate.fits>,).
2025-05-13 13:54:40,867 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits
2025-05-13 13:54:40,868 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits
2025-05-13 13:54:40,973 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 13:54:40,973 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS1
2025-05-13 13:54:40,974 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_FIXEDSLIT
2025-05-13 13:54:40,974 - stpipe.Spec2Pipeline.photom - INFO - filter: F170LP
2025-05-13 13:54:40,975 - stpipe.Spec2Pipeline.photom - INFO - grating: G235M
2025-05-13 13:54:41,004 - stpipe.Spec2Pipeline.photom - INFO - Working on slit S200A1
2025-05-13 13:54:41,005 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1
2025-05-13 13:54:41,049 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 13:54:41,320 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_cal.fits>,).
2025-05-13 13:54:41,320 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 13:54:41,494 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_cal.fits>,).
2025-05-13 13:54:41,629 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_cal.fits
2025-05-13 13:54:41,991 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 13:54:42,001 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10551 arcsec.
2025-05-13 13:54:42,002 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.1055106506414472 arcsec.
2025-05-13 13:54:42,003 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 13:54:42,003 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:54:42,004 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 13:54:42,004 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: exptime
2025-05-13 13:54:42,005 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:54:42,072 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:54:42,082 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:54:42,091 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:54:42,101 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:54:42,217 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 272.144522681 69.457341365 272.145907846 69.457341365 272.145907846 69.458244702 272.144522681 69.458244702
2025-05-13 13:54:42,357 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_s2d.fits
2025-05-13 13:54:42,358 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 13:54:42,548 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw01128006001_0310c_00001_nrs1_s2d.fits>,).
2025-05-13 13:54:42,647 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json
2025-05-13 13:54:42,656 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits
2025-05-13 13:54:42,699 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit S200A1
2025-05-13 13:54:42,700 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 13:54:42,701 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = NRS_FIXEDSLIT
2025-05-13 13:54:42,704 - stpipe.Spec2Pipeline.extract_1d - INFO - Using source_xpos and source_ypos to center extraction.
2025-05-13 13:54:42,709 - stpipe.Spec2Pipeline.extract_1d - INFO - Computed source location is 27.68, at pixel 666, wavelength 2.36
2025-05-13 13:54:42,710 - stpipe.Spec2Pipeline.extract_1d - INFO - Nominal aperture start/stop: 26.50 -> 31.50 (inclusive)
2025-05-13 13:54:42,711 - stpipe.Spec2Pipeline.extract_1d - INFO - Nominal location is 29.00, so offset is -1.32 pixels
2025-05-13 13:54:42,712 - stpipe.Spec2Pipeline.extract_1d - INFO - Mean aperture start/stop from trace: 25.18 -> 30.18 (inclusive)
2025-05-13 13:54:42,716 - stpipe.Spec2Pipeline.extract_1d - INFO - Creating aperture correction.
2025-05-13 13:54:43,850 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_x1d.fits
2025-05-13 13:54:43,851 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 13:54:43,851 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1
2025-05-13 13:54:43,853 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 13:54:43,853 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:54:44,046 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_cal.fits
2025-05-13 13:54:44,047 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 13:54:44,047 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:54:44,093 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 13:54:44,154 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:54:44,175 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:54:44,199 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 13:54:44,200 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:54:44,201 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 13:54:44,202 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 13:54:44,203 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 13:54:44,205 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:54:44,206 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 13:54:44,207 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 13:54:44,211 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 13:54:44,212 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:54:44,213 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:54:44,214 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:54:44,215 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 13:54:44,216 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:54:44,217 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:54:44,219 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:54:44,220 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 13:54:44,221 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:54:44,222 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 13:54:44,223 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 13:54:44,224 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 13:54:44,225 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 13:54:44,226 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:54:44,227 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:54:44,228 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 13:54:44,228 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:54:44,229 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:54:44,230 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:54:44,232 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 13:54:44,234 - 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/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs2_rate.fits
2025-05-13 13:54:44,409 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/asn/jw01128006001_0310c_00001_nrs2_l2asn.json',).
2025-05-13 13:54:44,442 - 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/FSlit/fs_data_01128/Obs006/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: None
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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 13:54:44,450 - 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 13:54:44,483 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_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 13:54:44,489 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits 688.9 M bytes (1 / 2 files) (0 / 761.2 M bytes)
2025-05-13 13:54:55,991 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0159.fits 72.3 M bytes (2 / 2 files) (688.9 M / 761.2 M bytes)
2025-05-13 13:54:57,149 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits'.
2025-05-13 13:54:57,150 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits'.
2025-05-13 13:54:57,150 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-05-13 13:54:57,151 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 13:54:57,151 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 13:54:57,152 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 13:54:57,153 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits'.
2025-05-13 13:54:57,153 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0058.asdf'.
2025-05-13 13:54:57,153 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 13:54:57,154 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json'.
2025-05-13 13:54:57,155 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits'.
2025-05-13 13:54:57,155 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 13:54:57,156 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 13:54:57,156 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.asdf'.
2025-05-13 13:54:57,157 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 13:54:57,157 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 13:54:57,158 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:54:57,158 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:54:57,158 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:54:57,159 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 13:54:57,159 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 13:54:57,160 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0001.json'.
2025-05-13 13:54:57,160 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 13:54:57,161 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 13:54:57,161 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits'.
2025-05-13 13:54:57,162 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits'.
2025-05-13 13:54:57,162 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 13:54:57,163 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:54:57,163 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0159.fits'.
2025-05-13 13:54:57,164 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 13:54:57,164 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 13:54:57,165 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:54:57,165 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf'.
2025-05-13 13:54:57,166 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 13:54:57,166 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:54:57,167 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 13:54:57,173 - 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 13:54:57,174 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs2
2025-05-13 13:54:57,175 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs2_rate.fits ...
2025-05-13 13:54:57,373 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00001_nrs2_rate.fits>,).
2025-05-13 13:54:57,507 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.1383225170000002 deg
2025-05-13 13:54:57,507 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:54:57,508 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:54:57,509 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125293189e-05 deg
2025-05-13 13:54:57,665 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit S200A1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 13:54:57,666 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS2: []
2025-05-13 13:54:57,666 - stpipe.Spec2Pipeline.assign_wcs - CRITICAL - No open slits fall on detector NRS2.
2025-05-13 13:54:57,667 - stpipe.Spec2Pipeline - ERROR - Assign_wcs processing was skipped.
2025-05-13 13:54:57,668 - stpipe.Spec2Pipeline - ERROR - Aborting remaining processing for this exposure.
2025-05-13 13:54:57,668 - stpipe.Spec2Pipeline - ERROR - No output product will be created.
2025-05-13 13:54:57,714 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 13:54:57,776 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:54:57,798 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:54:57,822 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 13:54:57,823 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:54:57,824 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 13:54:57,825 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 13:54:57,826 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 13:54:57,827 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:54:57,828 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 13:54:57,829 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 13:54:57,834 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 13:54:57,835 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:54:57,836 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:54:57,837 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:54:57,838 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 13:54:57,839 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:54:57,840 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:54:57,841 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:54:57,842 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 13:54:57,844 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:54:57,845 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 13:54:57,846 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 13:54:57,847 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 13:54:57,848 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 13:54:57,849 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:54:57,850 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:54:57,851 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 13:54:57,852 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:54:57,852 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:54:57,854 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:54:57,855 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 13:54:57,857 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:54:58,024 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/asn/jw01128006001_0310c_00002_nrs1_l2asn.json',).
Skipped processing jw01128006001_0310c_00001_nrs2_l2asn.json: (64, 'No open slits fall on detector NRS2.')
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits
2025-05-13 13:54:58,059 - 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/FSlit/fs_data_01128/Obs006/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: None
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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 13:54:58,068 - 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 13:54:58,100 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_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 13:54:58,106 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits'.
2025-05-13 13:54:58,106 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits'.
2025-05-13 13:54:58,107 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-05-13 13:54:58,107 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 13:54:58,107 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 13:54:58,108 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 13:54:58,109 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits'.
2025-05-13 13:54:58,109 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0058.asdf'.
2025-05-13 13:54:58,110 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 13:54:58,110 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json'.
2025-05-13 13:54:58,110 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits'.
2025-05-13 13:54:58,111 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 13:54:58,111 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 13:54:58,111 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.asdf'.
2025-05-13 13:54:58,112 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 13:54:58,113 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 13:54:58,113 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:54:58,113 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:54:58,114 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:54:58,114 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 13:54:58,114 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 13:54:58,115 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0001.json'.
2025-05-13 13:54:58,116 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 13:54:58,116 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 13:54:58,117 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits'.
2025-05-13 13:54:58,118 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits'.
2025-05-13 13:54:58,118 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 13:54:58,118 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:54:58,119 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0149.fits'.
2025-05-13 13:54:58,119 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 13:54:58,119 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 13:54:58,120 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:54:58,120 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf'.
2025-05-13 13:54:58,121 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 13:54:58,121 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:54:58,122 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 13:54:58,129 - 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 13:54:58,130 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1
2025-05-13 13:54:58,130 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits ...
2025-05-13 13:54:58,327 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:54:58,458 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.1383225170000002 deg
2025-05-13 13:54:58,459 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:54:58,459 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:54:58,460 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125293189e-05 deg
2025-05-13 13:54:58,615 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS1: ['S200A1']
2025-05-13 13:54:58,616 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 1 open slitlets
2025-05-13 13:54:58,642 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.1383225170000002 deg
2025-05-13 13:54:58,642 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:54:58,643 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:54:58,644 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125293189e-05 deg
2025-05-13 13:54:58,656 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[1.66e-06, 3.17e-06]
2025-05-13 13:54:58,757 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999998749134799
2025-05-13 13:54:58,788 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 1
2025-05-13 13:54:58,789 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 2
2025-05-13 13:54:58,789 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 3
2025-05-13 13:54:58,790 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 4
2025-05-13 13:54:58,790 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 1 open slits in quadrant 5
2025-05-13 13:54:58,931 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_fixedslit 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_0058.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.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}
2025-05-13 13:54:59,043 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 13:54:59,047 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 13:54:59,224 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits']).
2025-05-13 13:54:59,225 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 13:54:59,391 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:54:59,392 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-05-13 13:54:59,565 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:54:59,566 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 13:54:59,739 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs1_rate.fits>, []).
2025-05-13 13:54:59,740 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:54:59,912 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', []).
2025-05-13 13:54:59,912 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:55:00,080 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits', []).
2025-05-13 13:55:00,080 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:55:00,252 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits']).
2025-05-13 13:55:00,331 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits
2025-05-13 13:55:00,364 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits
2025-05-13 13:55:00,396 - 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 13:55:00,408 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw01128006001_0310c_00002_nrs1_rate.fits
2025-05-13 13:55:00,506 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 13:55:00,687 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:55:00,701 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_FIXEDSLIT
2025-05-13 13:55:00,701 - stpipe.Spec2Pipeline.extract_2d - INFO - All slits selected
2025-05-13 13:55:00,876 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: S200A1
2025-05-13 13:55:00,877 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 714 2048
2025-05-13 13:55:00,877 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 2 48
2025-05-13 13:55:01,074 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 13:55:01,075 - stpipe.Spec2Pipeline.extract_2d - INFO - xoffset, yoffset, -2.432095523451e-11, 2.78147850004307e-11
2025-05-13 13:55:01,088 - stpipe.Spec2Pipeline.extract_2d - INFO - Source X/Y position in the slit: -0.06117519607309579, -0.04523893301215574
2025-05-13 13:55:01,094 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 272.144124041 69.458448048 272.145477669 69.457565313 272.145611445 69.457591061 272.144257851 69.458473804
2025-05-13 13:55:01,095 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 272.144124041 69.458448048 272.145477669 69.457565313 272.145611445 69.457591061 272.144257851 69.458473804
2025-05-13 13:55:01,144 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 13:55:01,322 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:55:01,329 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_FIXEDSLIT
2025-05-13 13:55:01,330 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-05-13 13:55:01,330 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-05-13 13:55:01,332 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 13:55:01,515 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:55:01,516 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 13:55:01,517 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:55:01,699 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:55:01,715 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf
2025-05-13 13:55:01,822 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a POINT source type in slit S200A1
2025-05-13 13:55:01,823 - stpipe.Spec2Pipeline.wavecorr - INFO - slit name S200A1
2025-05-13 13:55:01,934 - stpipe.Spec2Pipeline.wavecorr - INFO - Using wavelength zero-point correction for aperture S200A1
2025-05-13 13:55:01,980 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 13:55:02,169 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:55:02,208 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 13:55:02,231 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits
2025-05-13 13:55:02,289 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0149.fits
2025-05-13 13:55:02,439 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits
2025-05-13 13:55:02,550 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit S200A1
2025-05-13 13:55:03,081 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 13:55:03,268 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:55:03,283 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits
2025-05-13 13:55:03,336 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_FIXEDSLIT
2025-05-13 13:55:03,449 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit S200A1
2025-05-13 13:55:03,450 - stpipe.Spec2Pipeline.pathloss - INFO - Using aperture S200A1
2025-05-13 13:55:03,500 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 13:55:03,690 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:55:03,691 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-05-13 13:55:03,879 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw01128006001_0310c_00002_nrs1_rate.fits>,).
2025-05-13 13:55:03,902 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits
2025-05-13 13:55:03,903 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits
2025-05-13 13:55:04,015 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 13:55:04,015 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS1
2025-05-13 13:55:04,016 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_FIXEDSLIT
2025-05-13 13:55:04,016 - stpipe.Spec2Pipeline.photom - INFO - filter: F170LP
2025-05-13 13:55:04,017 - stpipe.Spec2Pipeline.photom - INFO - grating: G235M
2025-05-13 13:55:04,044 - stpipe.Spec2Pipeline.photom - INFO - Working on slit S200A1
2025-05-13 13:55:04,045 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1
2025-05-13 13:55:04,087 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 13:55:04,371 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_cal.fits>,).
2025-05-13 13:55:04,372 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 13:55:04,557 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_cal.fits>,).
2025-05-13 13:55:04,695 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_cal.fits
2025-05-13 13:55:05,062 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 13:55:05,071 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10551 arcsec.
2025-05-13 13:55:05,073 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.10551065052319546 arcsec.
2025-05-13 13:55:05,074 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 13:55:05,074 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:55:05,075 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 13:55:05,075 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: exptime
2025-05-13 13:55:05,076 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:55:05,144 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:55:05,153 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:55:05,163 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:55:05,173 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:55:05,289 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 272.144194924 69.457554997 272.145580115 69.457554997 272.145580115 69.458458331 272.144194924 69.458458331
2025-05-13 13:55:05,431 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_s2d.fits
2025-05-13 13:55:05,432 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 13:55:05,637 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw01128006001_0310c_00002_nrs1_s2d.fits>,).
2025-05-13 13:55:05,712 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json
2025-05-13 13:55:05,721 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits
2025-05-13 13:55:05,758 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit S200A1
2025-05-13 13:55:05,759 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 13:55:05,760 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = NRS_FIXEDSLIT
2025-05-13 13:55:05,763 - stpipe.Spec2Pipeline.extract_1d - INFO - Using source_xpos and source_ypos to center extraction.
2025-05-13 13:55:05,768 - stpipe.Spec2Pipeline.extract_1d - INFO - Computed source location is 19.40, at pixel 666, wavelength 2.36
2025-05-13 13:55:05,769 - stpipe.Spec2Pipeline.extract_1d - INFO - Nominal aperture start/stop: 26.50 -> 31.50 (inclusive)
2025-05-13 13:55:05,770 - stpipe.Spec2Pipeline.extract_1d - INFO - Nominal location is 29.00, so offset is -9.60 pixels
2025-05-13 13:55:05,771 - stpipe.Spec2Pipeline.extract_1d - INFO - Mean aperture start/stop from trace: 16.90 -> 21.90 (inclusive)
2025-05-13 13:55:05,775 - stpipe.Spec2Pipeline.extract_1d - INFO - Creating aperture correction.
2025-05-13 13:55:06,902 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_x1d.fits
2025-05-13 13:55:06,902 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 13:55:06,903 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1
2025-05-13 13:55:06,905 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 13:55:06,905 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:55:07,101 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_cal.fits
2025-05-13 13:55:07,101 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 13:55:07,102 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:55:07,147 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 13:55:07,210 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:55:07,232 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:55:07,257 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 13:55:07,259 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:55:07,260 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 13:55:07,260 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 13:55:07,262 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 13:55:07,263 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:55:07,264 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 13:55:07,265 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 13:55:07,269 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 13:55:07,270 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:55:07,271 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:55:07,271 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:55:07,273 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 13:55:07,273 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:55:07,275 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:55:07,276 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:55:07,277 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 13:55:07,278 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:55:07,279 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 13:55:07,281 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 13:55:07,282 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 13:55:07,283 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 13:55:07,284 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:55:07,285 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:55:07,286 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 13:55:07,286 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:55:07,287 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:55:07,289 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:55:07,290 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 13:55:07,292 - 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/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs2_rate.fits
2025-05-13 13:55:07,481 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/asn/jw01128006001_0310c_00002_nrs2_l2asn.json',).
2025-05-13 13:55:07,513 - 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/FSlit/fs_data_01128/Obs006/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: None
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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 13:55:07,522 - 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 13:55:07,554 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_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 13:55:07,559 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits'.
2025-05-13 13:55:07,560 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits'.
2025-05-13 13:55:07,560 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-05-13 13:55:07,560 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 13:55:07,561 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 13:55:07,562 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 13:55:07,562 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits'.
2025-05-13 13:55:07,562 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0058.asdf'.
2025-05-13 13:55:07,563 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 13:55:07,563 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json'.
2025-05-13 13:55:07,564 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits'.
2025-05-13 13:55:07,564 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 13:55:07,565 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 13:55:07,565 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.asdf'.
2025-05-13 13:55:07,566 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 13:55:07,566 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 13:55:07,567 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:55:07,567 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:55:07,567 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:55:07,568 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 13:55:07,568 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 13:55:07,569 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0001.json'.
2025-05-13 13:55:07,570 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 13:55:07,570 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 13:55:07,570 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits'.
2025-05-13 13:55:07,571 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits'.
2025-05-13 13:55:07,571 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 13:55:07,572 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:55:07,572 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0159.fits'.
2025-05-13 13:55:07,573 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 13:55:07,573 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 13:55:07,573 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:55:07,574 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf'.
2025-05-13 13:55:07,574 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 13:55:07,575 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:55:07,575 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 13:55:07,581 - 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 13:55:07,582 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs2
2025-05-13 13:55:07,582 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs2_rate.fits ...
2025-05-13 13:55:07,788 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00002_nrs2_rate.fits>,).
2025-05-13 13:55:07,918 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.13832251700000023 deg
2025-05-13 13:55:07,919 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:55:07,919 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:55:07,920 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125290031e-05 deg
2025-05-13 13:55:08,076 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit S200A1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 13:55:08,077 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS2: []
2025-05-13 13:55:08,077 - stpipe.Spec2Pipeline.assign_wcs - CRITICAL - No open slits fall on detector NRS2.
2025-05-13 13:55:08,078 - stpipe.Spec2Pipeline - ERROR - Assign_wcs processing was skipped.
2025-05-13 13:55:08,078 - stpipe.Spec2Pipeline - ERROR - Aborting remaining processing for this exposure.
2025-05-13 13:55:08,078 - stpipe.Spec2Pipeline - ERROR - No output product will be created.
2025-05-13 13:55:08,125 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 13:55:08,187 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:55:08,209 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:55:08,234 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 13:55:08,236 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:55:08,237 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 13:55:08,237 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 13:55:08,239 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 13:55:08,240 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:55:08,240 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 13:55:08,241 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 13:55:08,246 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 13:55:08,247 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:55:08,247 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:55:08,249 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:55:08,250 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 13:55:08,251 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:55:08,252 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:55:08,253 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:55:08,254 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 13:55:08,255 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:55:08,256 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 13:55:08,257 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 13:55:08,258 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 13:55:08,260 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 13:55:08,260 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:55:08,261 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:55:08,262 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 13:55:08,263 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:55:08,265 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:55:08,266 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:55:08,268 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 13:55:08,270 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:55:08,449 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/asn/jw01128006001_0310c_00003_nrs1_l2asn.json',).
Skipped processing jw01128006001_0310c_00002_nrs2_l2asn.json: (64, 'No open slits fall on detector NRS2.')
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits
2025-05-13 13:55:08,482 - 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/FSlit/fs_data_01128/Obs006/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: None
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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 13:55:08,492 - 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 13:55:08,525 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_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 13:55:08,530 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits'.
2025-05-13 13:55:08,530 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits'.
2025-05-13 13:55:08,531 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-05-13 13:55:08,531 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 13:55:08,532 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 13:55:08,533 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 13:55:08,533 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits'.
2025-05-13 13:55:08,533 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0058.asdf'.
2025-05-13 13:55:08,534 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 13:55:08,534 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json'.
2025-05-13 13:55:08,535 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits'.
2025-05-13 13:55:08,535 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 13:55:08,535 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 13:55:08,536 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.asdf'.
2025-05-13 13:55:08,536 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 13:55:08,537 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 13:55:08,537 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:55:08,538 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:55:08,538 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:55:08,538 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 13:55:08,539 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 13:55:08,539 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0001.json'.
2025-05-13 13:55:08,540 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 13:55:08,540 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 13:55:08,541 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits'.
2025-05-13 13:55:08,541 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits'.
2025-05-13 13:55:08,541 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 13:55:08,542 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:55:08,542 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0149.fits'.
2025-05-13 13:55:08,542 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 13:55:08,543 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 13:55:08,543 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:55:08,544 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf'.
2025-05-13 13:55:08,544 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 13:55:08,545 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:55:08,546 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 13:55:08,552 - 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 13:55:08,552 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1
2025-05-13 13:55:08,553 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits ...
2025-05-13 13:55:08,757 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:08,887 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.13832251700000023 deg
2025-05-13 13:55:08,888 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:55:08,888 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:55:08,889 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125290031e-05 deg
2025-05-13 13:55:09,047 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS1: ['S200A1']
2025-05-13 13:55:09,047 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 1 open slitlets
2025-05-13 13:55:09,074 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.13832251700000023 deg
2025-05-13 13:55:09,074 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:55:09,075 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:55:09,076 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125290031e-05 deg
2025-05-13 13:55:09,088 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[1.66e-06, 3.17e-06]
2025-05-13 13:55:09,183 - stpipe.Spec2Pipeline.assign_wcs - INFO - Applied Barycentric velocity correction : 0.9999998742797083
2025-05-13 13:55:09,220 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 1
2025-05-13 13:55:09,221 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 2
2025-05-13 13:55:09,222 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 3
2025-05-13 13:55:09,222 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 4
2025-05-13 13:55:09,222 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 1 open slits in quadrant 5
2025-05-13 13:55:09,360 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_fixedslit 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_0058.asdf', 'fore': '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.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}
2025-05-13 13:55:09,472 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2025-05-13 13:55:09,477 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2025-05-13 13:55:09,661 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step badpix_selfcal running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1_rate.fits'], ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits']).
2025-05-13 13:55:09,662 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - Step skipped.
2025-05-13 13:55:09,840 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:09,841 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step skipped.
2025-05-13 13:55:10,020 - stpipe.Spec2Pipeline.nsclean - INFO - Step nsclean running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:10,021 - stpipe.Spec2Pipeline.nsclean - INFO - Step skipped.
2025-05-13 13:55:10,199 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs1_rate.fits>, []).
2025-05-13 13:55:10,199 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:55:10,376 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', []).
2025-05-13 13:55:10,376 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:55:10,553 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits', []).
2025-05-13 13:55:10,553 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2025-05-13 13:55:10,731 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs1_rate.fits>, ['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits', '/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits']).
2025-05-13 13:55:10,812 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00001_nrs1_rate.fits
2025-05-13 13:55:10,845 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Accumulate bkg from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00002_nrs1_rate.fits
2025-05-13 13:55:10,877 - 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 13:55:10,889 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Subtracting avg bkg from jw01128006001_0310c_00003_nrs1_rate.fits
2025-05-13 13:55:10,983 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2025-05-13 13:55:11,168 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:11,181 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_FIXEDSLIT
2025-05-13 13:55:11,182 - stpipe.Spec2Pipeline.extract_2d - INFO - All slits selected
2025-05-13 13:55:11,363 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: S200A1
2025-05-13 13:55:11,364 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 714 2048
2025-05-13 13:55:11,364 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 2 48
2025-05-13 13:55:11,536 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2025-05-13 13:55:11,537 - stpipe.Spec2Pipeline.extract_2d - INFO - xoffset, yoffset, -1.4422718289663e-06, -1.0827012648354963
2025-05-13 13:55:11,550 - stpipe.Spec2Pipeline.extract_2d - INFO - Source X/Y position in the slit: -0.061963020024758855, 0.28481080754466515
2025-05-13 13:55:11,556 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS 272.143718063 69.458712822 272.145071727 69.457830092 272.145205504 69.457855840 272.143851874 69.458738579
2025-05-13 13:55:11,557 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS 272.143718063 69.458712822 272.145071727 69.457830092 272.145205504 69.457855840 272.143851874 69.458738579
2025-05-13 13:55:11,606 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2025-05-13 13:55:11,797 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:11,803 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_FIXEDSLIT
2025-05-13 13:55:11,804 - stpipe.Spec2Pipeline.srctype - INFO - Input SRCTYAPT = UNKNOWN
2025-05-13 13:55:11,804 - stpipe.Spec2Pipeline.srctype - INFO - Exposure is nodded; setting SRCTYPE = POINT
2025-05-13 13:55:11,806 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2025-05-13 13:55:11,993 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:11,994 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step skipped.
2025-05-13 13:55:11,995 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:55:12,182 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:12,197 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf
2025-05-13 13:55:12,303 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a POINT source type in slit S200A1
2025-05-13 13:55:12,304 - stpipe.Spec2Pipeline.wavecorr - INFO - slit name S200A1
2025-05-13 13:55:12,413 - stpipe.Spec2Pipeline.wavecorr - INFO - Using wavelength zero-point correction for aperture S200A1
2025-05-13 13:55:12,460 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2025-05-13 13:55:12,656 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:12,694 - stpipe.Spec2Pipeline.flat_field - INFO - No reference found for type FLAT
2025-05-13 13:55:12,717 - stpipe.Spec2Pipeline.flat_field - INFO - Using FFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits
2025-05-13 13:55:12,774 - stpipe.Spec2Pipeline.flat_field - INFO - Using SFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0149.fits
2025-05-13 13:55:12,923 - stpipe.Spec2Pipeline.flat_field - INFO - Using DFLAT reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0001.fits
2025-05-13 13:55:13,031 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit S200A1
2025-05-13 13:55:13,563 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2025-05-13 13:55:13,758 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:13,773 - stpipe.Spec2Pipeline.pathloss - INFO - Using PATHLOSS reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits
2025-05-13 13:55:13,824 - stpipe.Spec2Pipeline.pathloss - INFO - Input exposure type is NRS_FIXEDSLIT
2025-05-13 13:55:13,945 - stpipe.Spec2Pipeline.pathloss - INFO - Working on slit S200A1
2025-05-13 13:55:13,946 - stpipe.Spec2Pipeline.pathloss - INFO - Using aperture S200A1
2025-05-13 13:55:13,996 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2025-05-13 13:55:14,193 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:14,194 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2025-05-13 13:55:14,385 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from jw01128006001_0310c_00003_nrs1_rate.fits>,).
2025-05-13 13:55:14,409 - stpipe.Spec2Pipeline.photom - INFO - Using photom reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits
2025-05-13 13:55:14,410 - stpipe.Spec2Pipeline.photom - INFO - Using area reference file: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits
2025-05-13 13:55:14,517 - stpipe.Spec2Pipeline.photom - INFO - Using instrument: NIRSPEC
2025-05-13 13:55:14,518 - stpipe.Spec2Pipeline.photom - INFO - detector: NRS1
2025-05-13 13:55:14,518 - stpipe.Spec2Pipeline.photom - INFO - exp_type: NRS_FIXEDSLIT
2025-05-13 13:55:14,519 - stpipe.Spec2Pipeline.photom - INFO - filter: F170LP
2025-05-13 13:55:14,519 - stpipe.Spec2Pipeline.photom - INFO - grating: G235M
2025-05-13 13:55:14,547 - stpipe.Spec2Pipeline.photom - INFO - Working on slit S200A1
2025-05-13 13:55:14,548 - stpipe.Spec2Pipeline.photom - INFO - PHOTMJSR value: 1
2025-05-13 13:55:14,589 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2025-05-13 13:55:14,884 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_cal.fits>,).
2025-05-13 13:55:14,885 - stpipe.Spec2Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 13:55:15,083 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_cal.fits>,).
2025-05-13 13:55:15,225 - stpipe.Spec2Pipeline.resample_spec - INFO - Reorganizing data from exposure /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_cal.fits
2025-05-13 13:55:15,604 - stpipe.Spec2Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 13:55:15,614 - stpipe.Spec2Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10551 arcsec.
2025-05-13 13:55:15,616 - stpipe.Spec2Pipeline.resample_spec - INFO - Output pixel scale: 0.10551065056099244 arcsec.
2025-05-13 13:55:15,617 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 13:55:15,617 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:55:15,618 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 13:55:15,618 - stpipe.Spec2Pipeline.resample_spec - INFO - Driz parameter weight_type: exptime
2025-05-13 13:55:15,620 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:55:15,692 - stpipe.Spec2Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:55:15,701 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:55:15,711 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:55:15,721 - stpipe.Spec2Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (36, 1334)
2025-05-13 13:55:15,839 - stpipe.Spec2Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 272.143788947 69.457819776 272.145174175 69.457819776 272.145174175 69.458723106 272.143788947 69.458723106
2025-05-13 13:55:15,980 - stpipe.Spec2Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_s2d.fits
2025-05-13 13:55:15,980 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 13:55:16,190 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from jw01128006001_0310c_00003_nrs1_s2d.fits>,).
2025-05-13 13:55:16,262 - stpipe.Spec2Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json
2025-05-13 13:55:16,271 - stpipe.Spec2Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits
2025-05-13 13:55:16,308 - stpipe.Spec2Pipeline.extract_1d - INFO - Working on slit S200A1
2025-05-13 13:55:16,309 - stpipe.Spec2Pipeline.extract_1d - WARNING - Mismatched data shapes; skipping invalid data updates for extension 'dq'
2025-05-13 13:55:16,310 - stpipe.Spec2Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = NRS_FIXEDSLIT
2025-05-13 13:55:16,313 - stpipe.Spec2Pipeline.extract_1d - INFO - Using source_xpos and source_ypos to center extraction.
2025-05-13 13:55:16,318 - stpipe.Spec2Pipeline.extract_1d - INFO - Computed source location is 9.14, at pixel 666, wavelength 2.36
2025-05-13 13:55:16,319 - stpipe.Spec2Pipeline.extract_1d - INFO - Nominal aperture start/stop: 26.50 -> 31.50 (inclusive)
2025-05-13 13:55:16,320 - stpipe.Spec2Pipeline.extract_1d - INFO - Nominal location is 29.00, so offset is -19.86 pixels
2025-05-13 13:55:16,322 - stpipe.Spec2Pipeline.extract_1d - INFO - Mean aperture start/stop from trace: 6.64 -> 11.64 (inclusive)
2025-05-13 13:55:16,325 - stpipe.Spec2Pipeline.extract_1d - INFO - Creating aperture correction.
2025-05-13 13:55:17,447 - stpipe.Spec2Pipeline.extract_1d - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_x1d.fits
2025-05-13 13:55:17,448 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 13:55:17,448 - stpipe.Spec2Pipeline - INFO - Finished processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs1
2025-05-13 13:55:17,450 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2025-05-13 13:55:17,450 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:55:17,645 - stpipe.Spec2Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_cal.fits
2025-05-13 13:55:17,646 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done
2025-05-13 13:55:17,646 - stpipe - INFO - Results used jwst version: 1.18.0
2025-05-13 13:55:17,692 - stpipe - WARNING - /usr/share/miniconda/lib/python3.13/site-packages/jwst/associations/association.py:215: UserWarning: Input association file contains path information; note that this can complicate usage and/or sharing of such files.
warnings.warn(err_str, UserWarning)
2025-05-13 13:55:17,756 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:55:17,779 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:55:17,805 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2025-05-13 13:55:17,806 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2025-05-13 13:55:17,807 - stpipe.Spec2Pipeline.badpix_selfcal - INFO - BadpixSelfcalStep instance created.
2025-05-13 13:55:17,808 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2025-05-13 13:55:17,810 - stpipe.Spec2Pipeline.nsclean - INFO - NSCleanStep instance created.
2025-05-13 13:55:17,810 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2025-05-13 13:55:17,811 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2025-05-13 13:55:17,812 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2025-05-13 13:55:17,817 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2025-05-13 13:55:17,819 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:55:17,820 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:55:17,821 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:55:17,822 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2025-05-13 13:55:17,823 - stpipe.Spec2Pipeline.master_background_mos.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:55:17,824 - stpipe.Spec2Pipeline.master_background_mos.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:55:17,826 - stpipe.Spec2Pipeline.master_background_mos.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:55:17,827 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2025-05-13 13:55:17,828 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2025-05-13 13:55:17,828 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2025-05-13 13:55:17,830 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2025-05-13 13:55:17,831 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2025-05-13 13:55:17,832 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2025-05-13 13:55:17,833 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2025-05-13 13:55:17,833 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2025-05-13 13:55:17,834 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2025-05-13 13:55:17,835 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:55:17,836 - stpipe.Spec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:55:17,838 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:55:17,839 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 13:55:17,841 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:55:18,043 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/asn/jw01128006001_0310c_00003_nrs2_l2asn.json',).
Applying Stage 2 Corrections & Calibrations to: /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs2_rate.fits
2025-05-13 13:55:18,077 - 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/FSlit/fs_data_01128/Obs006/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: None
source_ids: None
extract_orders: None
grism_objects: None
tsgrism_extract_height: None
wfss_extract_half_height: 5
wfss_mmag_extract: None
wfss_nbright: 1000
master_background_mos:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
sigma_clip: 3.0
median_kernel: 1
force_subtract: False
save_background: False
user_background: None
inverse: False
steps:
flat_field:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
save_interpolated_flat: False
user_supplied_flat: None
inverse: False
pathloss:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
user_slit_loc: None
barshadow:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
photom:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
inverse: False
source_type: None
mrs_time_correction: True
pixel_replace:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: True
suffix: None
search_output_file: True
input_dir: ''
algorithm: fit_profile
n_adjacent_cols: 3
resample_spec:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
pixfrac: 1.0
kernel: square
fillval: NaN
weight_type: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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 13:55:18,087 - 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 13:55:18,121 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_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 13:55:18,127 - stpipe.Spec2Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits'.
2025-05-13 13:55:18,127 - stpipe.Spec2Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits'.
2025-05-13 13:55:18,127 - stpipe.Spec2Pipeline - INFO - Prefetch for BARSHADOW reference file is 'N/A'.
2025-05-13 13:55:18,128 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_camera_0007.asdf'.
2025-05-13 13:55:18,128 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_collimator_0007.asdf'.
2025-05-13 13:55:18,129 - stpipe.Spec2Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 13:55:18,129 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_dflat_0002.fits'.
2025-05-13 13:55:18,130 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_disperser_0058.asdf'.
2025-05-13 13:55:18,130 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2025-05-13 13:55:18,131 - stpipe.Spec2Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json'.
2025-05-13 13:55:18,131 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fflat_0161.fits'.
2025-05-13 13:55:18,131 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2025-05-13 13:55:18,132 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2025-05-13 13:55:18,132 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fore_0048.asdf'.
2025-05-13 13:55:18,133 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_fpa_0008.asdf'.
2025-05-13 13:55:18,133 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2025-05-13 13:55:18,134 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2025-05-13 13:55:18,134 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2025-05-13 13:55:18,134 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2025-05-13 13:55:18,135 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2025-05-13 13:55:18,135 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msa_0008.asdf'.
2025-05-13 13:55:18,136 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_msaoper_0001.json'.
2025-05-13 13:55:18,136 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_ote_0010.asdf'.
2025-05-13 13:55:18,137 - stpipe.Spec2Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 13:55:18,137 - stpipe.Spec2Pipeline - INFO - Prefetch for PATHLOSS reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pathloss_0007.fits'.
2025-05-13 13:55:18,138 - stpipe.Spec2Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits'.
2025-05-13 13:55:18,138 - stpipe.Spec2Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 13:55:18,138 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2025-05-13 13:55:18,139 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_sflat_0159.fits'.
2025-05-13 13:55:18,139 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 13:55:18,140 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 13:55:18,140 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2025-05-13 13:55:18,140 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavecorr_0003.asdf'.
2025-05-13 13:55:18,141 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_wavelengthrange_0006.asdf'.
2025-05-13 13:55:18,142 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2025-05-13 13:55:18,142 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2025-05-13 13:55:18,149 - 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 13:55:18,149 - stpipe.Spec2Pipeline - INFO - Processing product /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs2
2025-05-13 13:55:18,150 - stpipe.Spec2Pipeline - INFO - Working on input /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage1/jw01128006001_0310c_00003_nrs2_rate.fits ...
2025-05-13 13:55:18,368 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(64, 2048) from jw01128006001_0310c_00003_nrs2_rate.fits>,).
2025-05-13 13:55:18,503 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.13832251700000023 deg
2025-05-13 13:55:18,504 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3156737000000005 deg
2025-05-13 13:55:18,505 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.005181671717186684 deg
2025-05-13 13:55:18,506 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: -8.010507125290031e-05 deg
2025-05-13 13:55:18,666 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit S200A1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2025-05-13 13:55:18,667 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS2: []
2025-05-13 13:55:18,668 - stpipe.Spec2Pipeline.assign_wcs - CRITICAL - No open slits fall on detector NRS2.
2025-05-13 13:55:18,668 - stpipe.Spec2Pipeline - ERROR - Assign_wcs processing was skipped.
2025-05-13 13:55:18,668 - stpipe.Spec2Pipeline - ERROR - Aborting remaining processing for this exposure.
2025-05-13 13:55:18,669 - stpipe.Spec2Pipeline - ERROR - No output product will be created.
Skipped processing jw01128006001_0310c_00003_nrs2_l2asn.json: (64, 'No open slits fall on detector NRS2.')
Spec2 has been completed for SCI data!
6.3.2 Calibrating Background Files#
Prepare background files for master background subtraction in Stage 3.
# Run Stage 2 pipeline using the custom spec2dict dictionary.
# Process dedicated background data to use in the master background step.
if dospec2bg and master_bg:
# ------------------------Background RATE files------------------------
for file in rate_bg:
try: # Create ASN files.
asnfile = os.path.join(asn_dir, os.path.basename(file).replace('rate.fits', 'l2asn.json'))
if writel2asn(file, rate_bg, [], asnfile, 'Level2', 'NRS_FIXEDSLIT'):
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 slices fall on NRS2.
print(f"Skipped processing {os.path.basename(asnfile)}: {e}")
print("Spec2 has been completed for BKG data! \n")
else:
print("Skipping Spec2 for BKG data. \n")
Skipping Spec2 for BKG data.
# Print out the time benchmarks.
time3 = time.perf_counter()
print(f"Runtime so far: {round((time3-time0)/60.0, 1):0.4f} min")
print(f"Runtime for Spec2: {round((time3-time_spec2)/60.0, 1):0.4f} min")
Runtime so far: 6.6000 min
Runtime for Spec2: 0.9000 min
# 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))
if dospec2bg:
# ----------------------------Background files---------------------------
bg_cal = sorted(glob.glob(spec2_bgdir + '*_cal.fits'))
bg_s2d = sorted(glob.glob(spec2_bgdir + '*_s2d.fits'))
bg_x1d = sorted(glob.glob(spec2_bgdir + '*_x1d.fits'))
print(f"BACKGROUND | Stage 2 CAL Products:\n{'-'*20}\n" + "\n".join(bg_cal))
print(f"BACKGROUND | Stage 2 S2D Products:\n{'-'*20}\n" + "\n".join(bg_s2d))
print(f"BACKGROUND | Stage 2 X1D Products:\n{'-'*20}\n" + "\n".join(bg_x1d))
SCIENCE | Stage 2 CAL Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_cal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_cal.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_cal.fits
SCIENCE | Stage 2 S2D Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_s2d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_s2d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_s2d.fits
SCIENCE | Stage 2 X1D Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00001_nrs1_x1d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00002_nrs1_x1d.fits
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage2/jw01128006001_0310c_00003_nrs1_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.
The Spec3Pipeline performs additional corrections (e.g., outlier detection, background subtraction) 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 FS:
assign_mtwcs: Modifies the WCS output frame in each exposure of a Moving Target (MT) observation association.
master_background: Master background subtraction.
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 FS data.
If master background subtraction was chosen above, it will be applied during this stage. 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['master_background'] = {}, {}
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'] = True
# Master background usage was set up above, propagate that here.
spec3dict['master_background']['skip'] = not master_bg
# 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'] = 'exptime'
7.2 Create Spec3Pipeline Association Files#
Stage 3 ASN files for FS data can include science and background exposure types. A Stage 3 ASN file requires at least one science file (there is usually more than one) but can contain multiple background files that enable master background subtraction in calwebb_spec3. Note that the science exposures should be in the _cal.fits format, while the background exposures must be in the _x1d.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, bgfiles):
"""
Create a Level 3 association file.
Parameters
----------
scifiles : list of str
List of all science exposure files.
bgfiles : list of str
List of background 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'), fits.getval(f, 'FXD_SLIT'))
grouped[k]['sci'].append(f)
for f in bgfiles:
k = (fits.getval(f, 'FILTER'), fits.getval(f, 'GRATING'), fits.getval(f, 'FXD_SLIT'))
grouped[k]['bg'].append(f)
# Make ASN for each FILTER/GRATING.
for (filt, grat, slit), files in grouped.items():
name = f"{slit}_{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)
for bg in files['bg']:
asn['products'][0]['members'].append({'expname': bg, 'exptype': 'background'})
with open(asnfile, 'w') as f:
f.write(asn.dump()[1])
print("Level 3 ASN creation complete!")
if dospec3:
writel3asn(sci_cal, bg_x1d if bg_dir else [])
# Get list of all spec3 ASN files.
spec3_asn = glob.glob(f"{asn_dir}*l3asn.json")
print(f"Stage 3 ASN Files:\n{'-'*20}\n" + "\n".join(spec3_asn))
2025-05-13 13:55:18,712 - 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!
Stage 3 ASN Files:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/asn/s200a1_f170lp_g235m_l3asn.json
# Open an ASN file as an example.
# Check that file paths have been correctly updated.
if dospec3:
with open(spec3_asn[0], '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 and, if available, any background 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:
# --------------------------Spec3 ASN files--------------------------
for s3_asn in spec3_asn:
print(f"Applying Stage 3 Corrections & Calibrations to: "
f"{os.path.basename(s3_asn)}")
spec3_result = Spec3Pipeline.call(s3_asn,
save_results=True,
steps=spec3dict,
output_dir=spec3_dir)
print("Spec3 has been completed! \n")
else:
print("Skipping Spec3. \n")
Applying Stage 3 Corrections & Calibrations to: s200a1_f170lp_g235m_l3asn.json
2025-05-13 13:55:19,079 - CRDS - INFO - Fetching /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-outlierdetectionstep_0007.asdf 1.6 K bytes (1 / 1 files) (0 / 1.6 K bytes)
2025-05-13 13:55:19,164 - stpipe - INFO - PARS-OUTLIERDETECTIONSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-outlierdetectionstep_0007.asdf
2025-05-13 13:55:19,178 - stpipe - INFO - PARS-RESAMPLESPECSTEP parameters found: /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_pars-resamplespecstep_0001.asdf
2025-05-13 13:55:19,207 - stpipe.Spec3Pipeline - INFO - Spec3Pipeline instance created.
2025-05-13 13:55:19,208 - stpipe.Spec3Pipeline.assign_mtwcs - INFO - AssignMTWcsStep instance created.
2025-05-13 13:55:19,209 - stpipe.Spec3Pipeline.master_background - INFO - MasterBackgroundStep instance created.
2025-05-13 13:55:19,210 - stpipe.Spec3Pipeline.mrs_imatch - INFO - MRSIMatchStep instance created.
2025-05-13 13:55:19,212 - stpipe.Spec3Pipeline.outlier_detection - INFO - OutlierDetectionStep instance created.
2025-05-13 13:55:19,213 - stpipe.Spec3Pipeline.pixel_replace - INFO - PixelReplaceStep instance created.
2025-05-13 13:55:19,214 - stpipe.Spec3Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2025-05-13 13:55:19,216 - stpipe.Spec3Pipeline.cube_build - INFO - CubeBuildStep instance created.
2025-05-13 13:55:19,217 - stpipe.Spec3Pipeline.extract_1d - INFO - Extract1dStep instance created.
2025-05-13 13:55:19,219 - stpipe.Spec3Pipeline.photom - INFO - PhotomStep instance created.
2025-05-13 13:55:19,220 - stpipe.Spec3Pipeline.combine_1d - INFO - Combine1dStep instance created.
2025-05-13 13:55:19,220 - stpipe.Spec3Pipeline.spectral_leak - INFO - SpectralLeakStep instance created.
2025-05-13 13:55:19,416 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline running with args ('/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/asn/s200a1_f170lp_g235m_l3asn.json',).
2025-05-13 13:55:19,431 - 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/FSlit/fs_data_01128/Obs006/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: True
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: exptime
output_shape: None
pixel_scale_ratio: 1.0
pixel_scale: None
output_wcs: ''
single: False
blendheaders: True
in_memory: True
cube_build:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: True
output_use_index: True
save_results: False
skip: False
suffix: s3d
search_output_file: False
input_dir: ''
channel: all
band: all
grating: all
filter: all
output_type: None
scalexy: 0.0
scalew: 0.0
weighting: drizzle
coord_system: skyalign
ra_center: None
dec_center: None
cube_pa: None
nspax_x: None
nspax_y: None
rois: 0.0
roiw: 0.0
weight_power: 2.0
wavemin: None
wavemax: None
single: False
skip_dqflagging: False
offset_file: None
debug_spaxel: -1 -1 -1
extract_1d:
pre_hooks: []
post_hooks: []
output_file: None
output_dir: None
output_ext: .fits
output_use_model: False
output_use_index: True
save_results: False
skip: False
suffix: None
search_output_file: True
input_dir: ''
subtract_background: None
apply_apcorr: True
extraction_type: box
use_source_posn: None
position_offset: 0.0
model_nod_pair: True
optimize_psf_location: True
smoothing_length: None
bkg_fit: None
bkg_order: None
log_increment: 50
save_profile: False
save_scene_model: False
save_residual_image: False
center_xy: None
ifu_autocen: 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 13:55:19,440 - 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 13:55:19,657 - stpipe.Spec3Pipeline - INFO - Prefetching reference files for dataset: 'jw01128006001_0310c_00001_nrs1_cal.fits' reftypes = ['apcorr', 'area', 'cubepar', 'extract1d', 'mrsptcorr', 'pastasoss', 'photom', 'psf', 'speckernel', 'specprofile']
2025-05-13 13:55:19,663 - stpipe.Spec3Pipeline - INFO - Prefetch for APCORR reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits'.
2025-05-13 13:55:19,664 - stpipe.Spec3Pipeline - INFO - Prefetch for AREA reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_area_0062.fits'.
2025-05-13 13:55:19,664 - stpipe.Spec3Pipeline - INFO - Prefetch for CUBEPAR reference file is 'N/A'.
2025-05-13 13:55:19,664 - stpipe.Spec3Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json'.
2025-05-13 13:55:19,665 - stpipe.Spec3Pipeline - INFO - Prefetch for MRSPTCORR reference file is 'N/A'.
2025-05-13 13:55:19,665 - stpipe.Spec3Pipeline - INFO - Prefetch for PASTASOSS reference file is 'N/A'.
2025-05-13 13:55:19,666 - stpipe.Spec3Pipeline - INFO - Prefetch for PHOTOM reference file is '/home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_photom_0014.fits'.
2025-05-13 13:55:19,666 - stpipe.Spec3Pipeline - INFO - Prefetch for PSF reference file is 'N/A'.
2025-05-13 13:55:19,667 - stpipe.Spec3Pipeline - INFO - Prefetch for SPECKERNEL reference file is 'N/A'.
2025-05-13 13:55:19,667 - stpipe.Spec3Pipeline - INFO - Prefetch for SPECPROFILE reference file is 'N/A'.
2025-05-13 13:55:19,668 - stpipe.Spec3Pipeline - INFO - Starting calwebb_spec3 ...
2025-05-13 13:55:19,677 - 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 13:55:20,318 - stpipe.Spec3Pipeline - INFO - Convert from exposure-based to source-based data.
2025-05-13 13:55:20,319 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw01128006001_0310c_00001_nrs1_cal.fits
2025-05-13 13:55:20,438 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw01128006001_0310c_00002_nrs1_cal.fits
2025-05-13 13:55:20,486 - stpipe.Spec3Pipeline - INFO - Reorganizing data from exposure jw01128006001_0310c_00003_nrs1_cal.fits
2025-05-13 13:55:21,228 - stpipe.Spec3Pipeline - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_cal.fits
2025-05-13 13:55:21,429 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection running with args (<jwst.datamodels.source_container.SourceModelContainer object at 0x7f53e26f48a0>,).
2025-05-13 13:55:21,430 - stpipe.Spec3Pipeline.outlier_detection - INFO - Outlier Detection mode: spec
2025-05-13 13:55:21,431 - stpipe.Spec3Pipeline.outlier_detection - INFO - Outlier Detection asn_id: None
2025-05-13 13:55:21,840 - stpipe.Spec3Pipeline.outlier_detection - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 13:55:21,853 - stpipe.Spec3Pipeline.outlier_detection - INFO - Computed output pixel scale: 0.10551 arcsec.
2025-05-13 13:55:21,855 - stpipe.Spec3Pipeline.outlier_detection - INFO - Output pixel scale: 0.10551065062190848 arcsec.
2025-05-13 13:55:21,856 - stpipe.Spec3Pipeline.outlier_detection - INFO - Driz parameter kernel: square
2025-05-13 13:55:21,857 - stpipe.Spec3Pipeline.outlier_detection - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:55:21,857 - stpipe.Spec3Pipeline.outlier_detection - INFO - Driz parameter fillval: NaN
2025-05-13 13:55:21,858 - stpipe.Spec3Pipeline.outlier_detection - INFO - Driz parameter weight_type: ivm
2025-05-13 13:55:21,859 - stpipe.Spec3Pipeline.outlier_detection - INFO - 1 exposures to drizzle together
2025-05-13 13:55:21,923 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 13:55:22,031 - stpipe.Spec3Pipeline.outlier_detection - INFO - 1 exposures to drizzle together
2025-05-13 13:55:22,097 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 13:55:22,206 - stpipe.Spec3Pipeline.outlier_detection - INFO - 1 exposures to drizzle together
2025-05-13 13:55:22,272 - stpipe.Spec3Pipeline.outlier_detection - INFO - Resampling science and variance data
2025-05-13 13:55:22,500 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (46, 1334) <-- (54, 1334)
2025-05-13 13:55:22,568 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (46, 1334) <-- (54, 1334)
2025-05-13 13:55:22,572 - stpipe.Spec3Pipeline.outlier_detection - INFO - 1934 pixels marked as outliers
2025-05-13 13:55:22,642 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (46, 1334) <-- (54, 1334)
2025-05-13 13:55:22,710 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (46, 1334) <-- (54, 1334)
2025-05-13 13:55:22,714 - stpipe.Spec3Pipeline.outlier_detection - INFO - 3557 pixels marked as outliers
2025-05-13 13:55:22,782 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (46, 1334) <-- (54, 1334)
2025-05-13 13:55:22,853 - stpipe.Spec3Pipeline.outlier_detection - INFO - Blotting (46, 1334) <-- (54, 1334)
2025-05-13 13:55:22,857 - stpipe.Spec3Pipeline.outlier_detection - INFO - 1807 pixels marked as outliers
2025-05-13 13:55:23,345 - stpipe.Spec3Pipeline.outlier_detection - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_crf.fits
2025-05-13 13:55:23,346 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection done
2025-05-13 13:55:23,557 - stpipe.Spec3Pipeline.pixel_replace - INFO - Step pixel_replace running with args (<jwst.datamodels.source_container.SourceModelContainer object at 0x7f53e26f48a0>,).
2025-05-13 13:55:23,558 - stpipe.Spec3Pipeline.pixel_replace - INFO - Step skipped.
2025-05-13 13:55:23,761 - stpipe.Spec3Pipeline.resample_spec - INFO - Step resample_spec running with args (<jwst.datamodels.source_container.SourceModelContainer object at 0x7f53e26f48a0>,).
2025-05-13 13:55:24,545 - stpipe.Spec3Pipeline.resample_spec - INFO - Specified output pixel scale ratio: 1.0.
2025-05-13 13:55:24,555 - stpipe.Spec3Pipeline.resample_spec - INFO - Computed output pixel scale: 0.10551 arcsec.
2025-05-13 13:55:24,557 - stpipe.Spec3Pipeline.resample_spec - INFO - Output pixel scale: 0.10551065053493572 arcsec.
2025-05-13 13:55:24,558 - stpipe.Spec3Pipeline.resample_spec - INFO - Driz parameter kernel: square
2025-05-13 13:55:24,558 - stpipe.Spec3Pipeline.resample_spec - INFO - Driz parameter pixfrac: 1.0
2025-05-13 13:55:24,559 - stpipe.Spec3Pipeline.resample_spec - INFO - Driz parameter fillval: NaN
2025-05-13 13:55:24,559 - stpipe.Spec3Pipeline.resample_spec - INFO - Driz parameter weight_type: exptime
2025-05-13 13:55:24,560 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:55:24,627 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:55:24,637 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:24,647 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:24,656 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:24,796 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:55:24,805 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:24,815 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:24,825 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:24,907 - stpipe.Spec3Pipeline.resample_spec - INFO - Resampling science and variance data
2025-05-13 13:55:24,917 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:24,927 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:24,936 - stpipe.Spec3Pipeline.resample_spec - INFO - Drizzling (46, 1334) --> (54, 1334)
2025-05-13 13:55:25,241 - stpipe.Spec3Pipeline.resample_spec - INFO - Update S_REGION to POLYGON ICRS 272.143799606 69.457348283 272.145897188 69.457348283 272.145897188 69.458716188 272.143799606 69.458716188
2025-05-13 13:55:25,483 - stpipe.Spec3Pipeline.resample_spec - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_s2d.fits
2025-05-13 13:55:25,483 - stpipe.Spec3Pipeline.resample_spec - INFO - Step resample_spec done
2025-05-13 13:55:25,691 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d running with args (<SlitModel(54, 1334) from s200a1_f170lp_g235m_s200a1_s000000001_s2d.fits>,).
2025-05-13 13:55:25,804 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_extract1d_0008.json
2025-05-13 13:55:25,858 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits
2025-05-13 13:55:25,943 - stpipe.Spec3Pipeline.extract_1d - INFO - Processing spectral order -1
2025-05-13 13:55:25,944 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = NRS_FIXEDSLIT
2025-05-13 13:55:25,947 - stpipe.Spec3Pipeline.extract_1d - INFO - Using source_xpos and source_ypos to center extraction.
2025-05-13 13:55:25,952 - stpipe.Spec3Pipeline.extract_1d - INFO - Computed source location is 27.41, at pixel 666, wavelength 2.36
2025-05-13 13:55:25,954 - stpipe.Spec3Pipeline.extract_1d - INFO - Nominal aperture start/stop: 26.50 -> 31.50 (inclusive)
2025-05-13 13:55:25,955 - stpipe.Spec3Pipeline.extract_1d - INFO - Nominal location is 29.00, so offset is -1.59 pixels
2025-05-13 13:55:25,956 - stpipe.Spec3Pipeline.extract_1d - INFO - Mean aperture start/stop from trace: 24.91 -> 29.91 (inclusive)
2025-05-13 13:55:25,960 - stpipe.Spec3Pipeline.extract_1d - INFO - Creating aperture correction.
2025-05-13 13:55:27,079 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_x1d.fits
2025-05-13 13:55:27,079 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d done
2025-05-13 13:55:27,081 - stpipe.Spec3Pipeline - INFO - Ending calwebb_spec3
2025-05-13 13:55:27,084 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline done
2025-05-13 13:55:27,084 - stpipe - INFO - Results used jwst version: 1.18.0
Spec3 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: 6.8000 min
Runtime for Spec3: 0.1000 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/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_cal.fits
Stage 3 S3D Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_s2d.fits
Stage 3 X1D Products:
--------------------
/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_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.
# Function to display the rate files produced by Stage 1 in the
# JWST Calibration Pipeline.
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)
# ----------------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)
# -----------------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
x = slit.xstart if 'nrs1' in rate else slit.xstart + slit.xsize
ha = 'right' if 'nrs1' in rate else 'left'
plt.text(x, 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'))
# -----------------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 display the spectra generated in stage 2/3 of the
# JWST Calibration Pipeline.
def display_spectra(spectra,
compare_x1d=None,
compare_mast=None,
integration=None,
extname='data',
source_id=1,
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 str, optional
Identifier for the source/slit to be displayed. Default is 1.
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
# 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 source_id.lower() in f and ('FXD_SLIT' not in fits.getheader(f, ext=0) or fits.getheader(f, ext=0)['FXD_SLIT'].lower() == source_id.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 in {os.path.basename(product)}")
print(f"Available source_ids: {[s.source_id for s in slits][:5]}")
continue
# 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 prods_1d, prefix in [(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(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)
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=-0.1, vmax=1, scale='asinh',
aspect=10, title_prefix='REPROCESSED') # , extname='dq')
2025-05-13 13:55:27,172 - 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#
Inspect the Stage 2 calibrated spectra. Use Jdaviz Specviz2D 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 2 FS spectra with Specviz2D.
if doviz:
try:
specviz2d = Specviz2d()
spectrum_1d = sorted(glob.glob(spec2_dir + '*x1d.fits'))[1]
spectrum_2d = sorted(glob.glob(spec2_dir + '*s2d.fits'))[1]
specviz2d.load_data(spectrum_1d)
specviz2d.show()
except Exception as e:
print(f"Unable to run Specviz2D, using matplotlib instead. {e}")
display_spectra(sci_s2d + sci_x1d, source_id='S200A1', scale='log',
vmin=-0.1e-9, vmax=3e-8, title_prefix='REPROCESSED')
2025-05-13 13:55:28,380 - 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 13:55:28,436 - stpipe - WARNING - /tmp/ipykernel_2206/3679232725.py:253: 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)
Unable to run Specviz2D, using matplotlib instead. list index out of range
2025-05-13 13:55:28,547 - 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 13:55:28,602 - stpipe - WARNING - /tmp/ipykernel_2206/3679232725.py:253: 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)
2025-05-13 13:55:28,709 - 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 13:55:28,765 - stpipe - WARNING - /tmp/ipykernel_2206/3679232725.py:253: 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)
8.3 Display Spec3Pipeline Products#
Inspect the Stage 3 combined calibrated spectra.
# Plot the Stage 3 FS spectra with Specviz2D.
if doviz:
try:
specviz2d = Specviz2d()
spectrum_1d = sorted(glob.glob(spec3_dir + '*x1d.fits'))[0]
spectrum_2d = sorted(glob.glob(spec3_dir + '*s2d.fits'))[0]
specviz2d.load_data(spectrum_2d=spectrum_2d, spectrum_1d=spectrum_1d)
specviz2d.show()
except ValueError:
print("Unable to display spectra with Specviz2d")
display_spectra(stage3_s2d + stage3_x1d, source_id='S200A1', scale='log',
vmin=-0.1e-9, vmax=3e-8, title_prefix='REPROCESSED', is_stage3=True)
2025-05-13 13:55:30,763 - 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 13:55:30,818 - stpipe - WARNING - /tmp/ipykernel_2206/3679232725.py:253: 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)
Unable to display spectra with Specviz2d
9. Modifying the EXTRACT1D Reference File (as needed)#
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 do this.
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; 5 for S1600A1) 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_0008.json'])
extract_1d_ref = refs['jwst_nirspec_extract1d_0008.json']
# Open EXTRACT1D reference file in read-mode.
with open(extract_1d_ref, "r") as ref_file:
params = json.load(ref_file)
yshift = -4 # Applied shift in pixels as example.
# S200A1
params["apertures"][0]["extract_width"] = 6
params["apertures"][0]["ystart"] += yshift
params["apertures"][0]["ystop"] += yshift
# S200B1
params["apertures"][1]["extract_width"] = 6
params["apertures"][1]["ystart"] = 26.5
params["apertures"][1]["ystop"] = 31.5
# S200A2
params["apertures"][2]["extract_width"] = 6
params["apertures"][2]["ystart"] = 26.5
params["apertures"][2]["ystop"] = 31.5
# S400A1
params["apertures"][3]["extract_width"] = 6
params["apertures"][3]["ystart"] = 31
params["apertures"][3]["ystop"] = 36
# S1600A1
params["apertures"][4]["extract_width"] = 5
params["apertures"][4]["ystart"] = 14
params["apertures"][4]["ystop"] = 18
# 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(basedir, basename + "_fs.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>
Now, we re-extract the 1D spectrum by running the Extract1dStep and overriding the reference file.
Extract1dStep.call(stage3_s2d,
save_results=True,
output_dir=spec3_dir,
output_use_model=True,
suffix='x1d_mod', # Change suffix to easily find modified file.
use_source_posn=False,
override_extract1d=extract_1d_ref_mod)
2025-05-13 13:55:31,577 - stpipe.Extract1dStep - INFO - Extract1dStep instance created.
2025-05-13 13:55:31,796 - stpipe.Extract1dStep - INFO - Step Extract1dStep running with args (['/home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_s2d.fits'],).
2025-05-13 13:55:31,800 - 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/FSlit/fs_data_01128/Obs006/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 13:55:31,974 - stpipe.Extract1dStep - INFO - Using EXTRACT1D reference file /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/jwst_nirspec_extract1d_0008_fs.json
2025-05-13 13:55:32,028 - stpipe.Extract1dStep - INFO - Using APCORR file /home/runner/crds_cache/references/jwst/nirspec/jwst_nirspec_apcorr_0003.fits
2025-05-13 13:55:32,112 - stpipe.Extract1dStep - INFO - Processing spectral order -1
2025-05-13 13:55:32,114 - stpipe.Extract1dStep - INFO - Aperture start/stop: 22.50 -> 27.50 (inclusive)
2025-05-13 13:55:32,118 - stpipe.Extract1dStep - INFO - Creating aperture correction.
2025-05-13 13:55:33,178 - stpipe.Extract1dStep - INFO - Results used CRDS context: jwst_1364.pmap
2025-05-13 13:55:33,243 - stpipe.Extract1dStep - INFO - Saved model in /home/runner/work/jwst-pipeline-notebooks/jwst-pipeline-notebooks/notebooks/NIRSPEC/FSlit/fs_data_01128/Obs006/stage3/s200a1_f170lp_g235m_s200a1_s000000001_x1d_mod.fits
2025-05-13 13:55:33,244 - stpipe.Extract1dStep - INFO - Step Extract1dStep done
2025-05-13 13:55:33,244 - stpipe - INFO - Results used jwst version: 1.18.0
<MultiSpecModel from s200a1_f170lp_g235m_s200a1_s000000001_x1d_mod.fits>
stage3_x1ds_mod = sorted(glob.glob(spec3_dir + '*_x1d_mod.fits'))
display_spectra(stage3_s2d + stage3_x1d, compare_x1d=stage3_x1ds_mod, source_id='S200A1',
scale='log', vmin=-0.1e-9, vmax=3e-8,
title_prefix='REPROCESSED', is_stage3=True)
2025-05-13 13:55:33,478 - 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 13:55:33,537 - stpipe - WARNING - /tmp/ipykernel_2206/3679232725.py:253: 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)
As expected, the demo spectrum extracted in the shifted location has lower flux that the spectrum extracted in the center of the 2D spectral trace.
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