Introduction

This document provides instructions on running the JWST Science Calibration Pipeline (referred to as “the pipeline”) and individual pipeline steps.

Pipeline modules are available for detector-level (stage 1) processing of data from all observing modes, stage 2 processing for imaging and spectroscopic modes, and stage 3 processing for imaging, spectroscopic, coronagraphic, Aperture Masking Interferometry (AMI), and Time Series Observations (TSO).

Stage 1 processing consists of detector-level corrections that must be performed on a group-by-group basis before ramp fitting is applied. The output of stage 1 processing is a countrate image per exposure or per integration for some modes. Details of this pipeline can be found at Stage 1 Pipeline Step Flow (calwebb_detector1).

Stage 2 processing consists of additional corrections and calibrations to produce fully calibrated exposures. The details differ for imaging and spectroscopic exposures, and there are some corrections that are unique to certain instruments or modes. Details are at Stage 2 Imaging Pipeline Step Flow (calwebb_image2) and Stage 2 Spectroscopic Pipeline Step Flow (calwebb_spec2).

Stage 3 processing consists of routines that work with multiple exposures and in most cases produce some kind of combined product. There are dedicated (and unique) pipeline modules for stage 3 processing of imaging, spectroscopic, coronagraphic, AMI, and TSO observations. Details of each are available at Stage 3 Imaging Pipeline Step Flow (calwebb_image3), Stage 3 Spectroscopic Pipeline Step Flow (calwebb_spec3), Stage 3 Coronagraphic Pipeline Step Flow (calwebb_coron3), Stage 3 Aperture Masking Interferometry (AMI) Pipeline Step Flow (calwebb_ami3), and Stage 3 Time-Series Observation(TSO) Pipeline Step Flow (calwebb_tso3).

The remainder of this document discusses pipeline configuration files and gives examples of running pipelines as a whole or in individual steps.

Reference Files

Many pipeline steps rely on the use of a set of reference files essential to ensure the correct and accurate process of the data. The reference files are instrument-specific, and are periodically updated as the data process evolves and the understanding of the instruments improves. They are created, tested and validated by the JWST Instrument Teams. They ensure all the files are in the correct format and have all required header keywords. The files are then delivered to the Reference Data for Calibration and Tools (ReDCaT) Management Team. The result of this process is the files being ingested into CRDS (the JWST Calibration Reference Data System), and made available to the pipeline team and any other ground-subsystem that needs access to them.

Information about all the reference files used by the Calibration Pipeline can be found at reference-file-formats-documentation as well as in the documentation for the Calibration Step using them.

CRDS

CRDS reference file mappings are usually set by default to always give access to the most recent reference file deliveries and selection rules. On occasion it might be necessary or desirable to use one of the non-default mappings in order to, for example, run different versions of the pipeline software or use older versions of the reference files. This can be accomplished by setting the environment variable CRDS_CONTEXT to the desired project mapping version, e.g.

$ export CRDS_CONTEXT='jwst_0421.pmap'

The current storage location for all JWST CRDS reference files is:

/grp/crds/jwst/references/jwst/

Each pipeline step records the reference file that it used in the value of a header keyword in the output data file. The keyword names use the syntax “R_<ref>”, where <ref> corresponds to a 6-character version of the reference file type, such as R_DARK, R_LINEAR, and R_PHOTOM.

Running From the Command Line

Individual steps and pipelines (consisting of a series of steps) can be run from the command line using the strun command:

$ strun <class_name or cfg_file> <input_file>

The first argument to strun must be either the python class name of the step or pipeline to be run, or the name of a configuration (.cfg) file for the desired step or pipeline (see Configuration Files below for more details). The second argument to strun is the name of the input data file to be processed.

For example, running the full stage 1 pipeline or an individual step by referencing their class names is done as follows:

$ strun jwst.pipeline.Detector1Pipeline jw00017001001_01101_00001_nrca1_uncal.fits
$ strun jwst.dq_init.DQInitStep jw00017001001_01101_00001_nrca1_uncal.fits

When a pipeline or step is executed in this manner (i.e. by referencing the class name), it will be run using all default parameter values. The same thing can be accomplished by using the default configuration file corresponding to each:

$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
$ strun dq_init.cfg jw00017001001_01101_00001_nrca1_uncal.fits

If you want to use non-default parameter values, you can specify them as keyword arguments on the command line or set them in the appropriate cfg file. To specify parameter values for an individual step when running a pipeline use the syntax --steps.<step_name>.<parameter>=value. For example, to override the default selection of a dark current reference file from CRDS when running a pipeline:

$ strun jwst.pipeline.Detector1Pipeline jw00017001001_01101_00001_nrca1_uncal.fits
      --steps.dark_current.override_dark='my_dark.fits'
$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
      --steps.dark_current.override_dark='my_dark.fits'

You can get a list of all the available arguments for a given pipeline or step by using the ‘-h’ (help) argument to strun:

$ strun dq_init.cfg -h
$ strun jwst.pipeline.Detector1Pipeline -h

If you want to consistently override the default values of certain arguments and don’t want to specify them on the command line every time you execute strun, you can specify them in the configuration (.cfg) file for the pipeline or the individual step. For example, to always run Detector1Pipeline using the override in the previous example, you could edit your calwebb_detector1.cfg file to contain the following:

name = "Detector1Pipeline"
class = "jwst.pipeline.Detector1Pipeline"

   [steps]
     [[dark_current]]
       override_dark = 'my_dark.fits'

Note that simply removing the entry for a step from a pipeline cfg file will NOT cause that step to be skipped when you run the pipeline (it will simply run the step with all default parameters). In order to skip a step you must use the skip = True argument for that step (see Skip below).

Alternatively, you can specify arguments for individual steps within the step’s configuration file and then reference those step cfg files in the pipeline cfg file, such as:

name = "Detector1Pipeline"
class = "jwst.pipeline.Detector1Pipeline"

   [steps]
     [[dark_current]]
       config_file = my_dark_current.cfg

where my_dark_current.cfg contains:

name = "dark_current"
class = "jwst.dark_current.DarkCurrentStep"
override_dark = 'my_dark.fits'

Exit Status

strun produces the following exit status codes:

• 0: Successful completion of the step/pipeline
• 1: General error occurred
• 64: No science data found

The “No science data found” condition is returned by the assign_wcs step of calwebb_spec2 when, after successfully determining the WCS solution for a file, the WCS indicates that no science data will be found. This condition is most often found with NIRSpec’s NRS2 detector. There are certain optical and MSA configurations in which dispersion will not cross to the NRS2 detector.

Running From Within Python

You can execute a pipeline or a step from within python by using the call method of the class:

from jwst.pipeline import Detector1Pipeline
result = Detector1Pipeline.call('jw00017001001_01101_00001_nrca1_uncal.fits')

from jwst.linearity import LinearityStep
result = LinearityStep.call('jw00001001001_01101_00001_mirimage_uncal.fits')

The easiest way to use optional arguments when calling a pipeline from within python is to set those parameters in the pipeline cfg file and then supply the cfg file as a keyword argument:

Detector1Pipeline.call('jw00017001001_01101_00001_nrca1_uncal.fits', config_file='calwebb_detector1.cfg')

Universal Parameters

Output Directory

By default, all pipeline and step outputs will drop into the current working directory, i.e., the directory in which the process is running. To change this, use the output_dir argument. For example, to have all output from calwebb_detector1, including any saved intermediate steps, appear in the sub-directory calibrated, use

$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
    --output_dir=calibrated

output_dir can be specified at the step level, overriding what was specified for the pipeline. From the example above, to change the name and location of the dark_current step, use the following

$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
    --output_dir=calibrated
    --steps.dark_current.output_file='dark_sub.fits'
    --steps.dark_current.output_dir='dark_calibrated'

Output File

When running a pipeline, the stpipe infrastructure automatically passes the output data model from one step to the input of the next step, without saving any intermediate results to disk. If you want to save the results from individual steps, you have two options:

• Specify save_results

  This option will save the results of the step, using a filename created by the step.

• Specify a file name using output_file

  This option will save the step results using the name specified.

For example, to save the result from the dark current step of calwebb_detector1 in a file named dark_sub.fits, use

$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
    --steps.dark_current.output_file='dark_sub.fits'

You can also specify a particular file name for saving the end result of the entire pipeline using the --output_file argument also

$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
    --output_file='detector1_processed.fits'

Output File and Associations

Stage 2 pipelines can take an individual file or an association as input. Nearly all Stage 3 pipelines require an associaiton as input. Normally, the output file is defined in each association’s product_name.

If there is need to produce multiple versions of a calibration based on an association, it is highly suggested to use output_dir to place the results in a different directory instead of using output_file to rename the output files. Stage 2 pipelines do not allow the override of the output using output_file. Stage 3 pipelines do. However, since Stage 3 pipelines generally produce many files per association, using different directories via output_dir will make file keeping simpler.

Override Reference File

For any step that uses a calibration reference file you always have the option to override the automatic selection of a reference file from CRDS and specify your own file to use. Arguments for this are of the form --override_<ref_type>, where ref_type is the name of the reference file type, such as mask, dark, gain, or linearity. When in doubt as to the correct name, just use the -h argument to strun to show you the list of available override arguments.

To override the use of the default linearity file selection, for example, you would use:

$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
        --steps.linearity.override_linearity='my_lin.fits'

Skip

Another argument available to all steps in a pipeline is skip. If skip=True is set for any step, that step will be skipped, with the output of the previous step being automatically passed directly to the input of the step following the one that was skipped. For example, if you want to skip the linearity correction step, edit the calwebb_detector1.cfg file to contain:

[steps]
   [[linearity]]
     skip = True
   ...

Alternatively you can specify the skip argument on the command line:

$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
    --steps.linearity.skip=True

Logging Configuration

If there’s no stpipe-log.cfg file in the working directory, which specifies how to handle process log information, the default is to display log messages to stdout. If you want log information saved to a file, you can specify the name of a logging configuration file either on the command line or in the pipeline cfg file.

For example:

$ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
    --logcfg=pipeline-log.cfg

and the file pipeline-log.cfg contains:

[*]
handler = file:pipeline.log
level = INFO

In this example log information is written to a file called pipeline.log. The level argument in the log cfg file can be set to one of the standard logging level designations of DEBUG, INFO, WARNING, ERROR, and CRITICAL. Only messages at or above the specified level will be displayed.

Input Files

There are two general types of input to any stage: references files and data files. The references files, unless explicitly overridden, are provided through CRDS.

The input data files - the exposure FITS files, association JSON files and input catalogs - are presumed to all be in the same directory as the primary input file. Sometimes the primary input is an association JSON file, and sometimes it is an exposure FITS file.

Output File Names

File names for the outputs from pipelines and steps come from three different sources:

• The name of the input file
• The product name defined in an association
• As specified by the output_file argument

Regardless of the source, each pipeline/step uses the name as a “base name”, on to which several different suffixes are appended, which indicate the type of data in that particular file.

Pipeline/Step Suffix Definitions

However the file name is determined (see above), the various stage 1, 2, and 3 pipeline modules will use that file name, along with a set of predetermined suffixes, to compose output file names. The output file name suffix will always replace any existing suffix of the input file name. Each pipeline module uses the appropriate suffix for the product(s) it is creating. The list of suffixes is shown in the following table.

Product	Suffix
Uncalibrated raw input	uncal
Corrected ramp data	ramp
Corrected countrate image	rate
Corrected countrate per integration	rateints
Optional fitting results from ramp_fit step	fitopt
Background-subtracted image	bsub
Per integration background-subtracted image	bsubints
Calibrated image	cal
Calibrated per integration images	calints
CR-flagged image	crf
CR-flagged per integration images	crfints
1D extracted spectrum	x1d
1D extracted spectra per integration	x1dints
Resampled 2D image	i2d
Resampled 2D spectrum	s2d
Resampled 3D IFU cube	s3d
Source catalog	cat
Time Series photometric catalog	phot
Time Series white-light catalog	whtlt
Coronagraphic PSF image stack	psfstack
Coronagraphic PSF-aligned images	psfalign
Coronagraphic PSF-subtracted images	psfsub
AMI fringe and closure phases	ami
AMI averaged fringe and closure phases	amiavg
AMI normalized fringe and closure phases	aminorm

Individual Step Outputs

If individual steps are executed without an output file name specified via the output_file argument, the stpipe infrastructure automatically uses the input file name as the root of the output file name and appends the name of the step as an additional suffix to the input file name. If the input file name already has a known suffix, that suffix will be replaced. For example:

$ strun dq_init.cfg jw00017001001_01101_00001_nrca1_uncal.fits

produces an output file named jw00017001001_01101_00001_nrca1_dq_init.fits.

Configuration Files

Configuration (.cfg) files can be used to specify parameter values when running a pipeline or individual steps, as well as for specifying logging options.

You can use the collect_pipeline_cfgs task to get copies of all the cfg files currently in use by the jwst pipeline software. The task takes a single argument, which is the name of the directory to which you want the cfg files copied. Use ‘.’ to specify the current working directory, e.g.

$ collect_pipeline_cfgs .

Each step and pipeline has their own cfg file, which are used to specify relevant parameter values. For each step in a pipeline, the pipeline cfg file specifies either the step’s arguments or the cfg file containing the step’s arguments.

The name of a file in which to save log information, as well as the desired level of logging messages, can be specified in an optional configuration file “stpipe-log.cfg”. This file must be in the same directory in which you run the pipeline in order for it to be used. If this file does not exist, the default logging mechanism is STDOUT, with a level of INFO. An example of the contents of the stpipe-log.cfg file is:

[*]
handler = file:pipeline.log
level = INFO

which specifies that all log messages will be directed to a file called “pipeline.log” and messages at a severity level of INFO and above will be recorded.

For a given step, the step’s cfg file specifies parameters and their default values; it includes parameters that are typically not changed between runs. Parameters that are usually reset for each run are not included in the cfg file, but instead specified on the command line. An example of a cfg file for the jump detection step is:

name = "jump"
class = "jwst.jump.JumpStep"
rejection_threshold = 4.0

You can list all of the parameters for this step using:

$ strun jump.cfg -h

which gives the usage, the positional arguments, and the optional arguments. More information on configuration files can be found in the stpipe User’s Guide at For Users.

Available Pipelines

There are many pre-defined pipeline modules for processing data from different instrument observing modes through each of the 3 stages of calibration. For all of the details see Pipeline Modules.

For More Information

More information on logging and running pipelines can be found in the stpipe User’s Guide at For Users.

More detailed information on writing pipelines can be found in the stpipe Developer’s Guide at For Developers.