# Introduction¶

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

Multiple pipeline modules are used for different stages of processing and for different JWST observing modes. The modules are broken into 3 stages:

• Stage 1: Detector-level corrections and ramp fitting for individual exposures

• Stage 2: Instrument-mode calibrations for individual exposures

• Stage 3: Combining data from multiple exposures within an observation

Stage 1 corrections are applied nearly universally for all instruments and modes. Stage 2 is divided into separate modules for imaging and spectroscopic modes. Stage 3 is divided into five separate modules for imaging, spectroscopic, coronagraphic, Aperture Masking Interferometry (AMI), and Time Series Observation (TSO) modes.

Details of all the pipeline modules can be found at Pipeline Modules. 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 reference files that contain different types of calibration data or information necessary for processing the data. The reference files are instrument-specific and are periodically updated as the data processing 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 the JWST Calibration Reference Data System (CRDS), 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 Information, as well as in the documentation for each Calibration Step that uses a reference file.

# 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'  Within STScI, 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')


# Input and Output File Conventions¶

## Input Files¶

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

Data files are the science input, such as exposure FITS files and association files. All files are assumed to be co-resident in the directory where the primary input file is located. This is particularly important for associations: JWST associations contain file names only. All files referred to by an association are expected to be located in the directory in which the association file is located.

## Output Files¶

Output files will be created either in the current working directory, or where specified by the output_dir configuration parameter.

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”, onto which several different suffixes are appended, which indicate the type of data in that particular file. A list of the main suffixes can be found below.

The pipelines do not manage versions. When re-running a pipeline, previous files will be overwritten.

### 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” which defines the basename that will be used for output file naming.

Often, one may reprocess the same set of data multiple times, such as to change reference files or parameters in configuration parameters. When doing so, 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. Most pipelines and steps create a set of output files. Separating runs by directory may be much easier to manage.

### 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. See Pipeline/Step Suffix Definitions for a list of the more common suffixes used. # 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 <basename> 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 based on intermediate, use $ strun calwebb_detector1.cfg jw00017001001_01101_00001_nrca1_uncal.fits
--steps.dark_current.output_file='intermediate'


A file, intermediate_dark_current.fits, will then be created. Note that the suffix of the step is always appended to any given name.

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='stage1_processed'  In this situation, using the default configuration, three files are created: • stage1_processed_trapsfilled.fits • stage1_processed_rate.fits • stage1_processed_rateints.fits ## 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'


## 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. # 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 Stages.

## Pipeline/Step Suffix Definitions¶

However the output 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 known 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. Replacement occurs only if the suffix is one known to the calibration code. Otherwise, the new suffix will simply be appended to the basename of the file.

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

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.