Parameters

Parameters, which exist at both the step level and the global pipeline level, can be set to change various aspects of processing. Parameters can be set in a parameter file, on the command line, or passed in as an argument when running in Python. Note that because there are multiple ways to set parameters, there is a hierarchy involved - overrides set on a pipeline or step object will take precedence over values in a parameter file. See Parameter Precedence for a full description of how a parameter gets its final value.

If there is need to re-use a set of parameters often, parameters can be stored in parameter files. See Parameter Files for more information.

To see what parameters are available for any given pipeline or step, use the -h option on strun. Some examples are:

$ strun calwebb_detector1 -h
$ strun jwst.dq_init.DQInitStep -h

Universal Parameters

The set of parameters that are common to all pipelines and steps are referred to as universal parameters and are described below. When these parameters are set at the pipeline level, they will apply to all steps within that pipeline, unless explicitly overridden for a specific step.

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 parameter. See .. _python_output_directory: for instructions when running in Python, and .. _cli_output_directory: for instructions using the command line interface.

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.

To do this using the Python pipeline interface, see .. _python_output_file:. To do this when using the command line interface, see .. _cli_output_file:.

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. Parameters 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 parameters.

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

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

Skip

Another parameter 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, one can specify the skip parameter for the strun command:

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

Alternatively, if using a parameter file, edit the file to add the following snippet:

steps:
- class: jwst.linearity.linearity_step.LinearityStep
  parameters:
    skip: true

Pipeline/Step Parameters

All pipelines and steps have parameters that can be set to change various aspects of how they execute. To see what parameters are available for any given pipeline or step, use the -h option on strun. Some examples are:

$ strun calwebb_detector1 -h
$ strun jwst.dq_init.DQInitStep -h

To set a parameter, simply specify it on the command line. For example, to have calwebb_detector1 save the calibrated ramp files, the strun command would be as follows:

$ strun calwebb_detector1 jw00017001001_01101_00001_nrca1_uncal.fits --save_calibrated_ramp=true

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 calwebb_detector1 jw00017001001_01101_00001_nrca1_uncal.fits
      --steps.dark_current.override_dark='my_dark.fits'

If there is need to re-use a set of parameters often, parameters can be stored in parameter files. See Parameter Files for more information.