ASDF Parameter Files

ASDF is the format of choice for parameter files. ASDF stands for “Advanced Scientific Data Format”, a general purpose, non-proprietary, and system-agnostic format for the dissemination of data. Built on YAML, the most basic file is text-based requiring minimal formatting.

ASDF replaces the original CFG format for step configuration. Using ASDF allows the configurations to be stored and retrieved from CRDS, selecting the best parameter file for a given set of criteria, such as instrument and observation mode.

To create a parameter file, the most direct way is to choose the Pipeline class, Step class, or already existing .asdf or .cfg file, and run that step using the --save-parameters option. For example, to get the parameters for the Spec2Pipeline pipeline, do the following:

$ strun jwst.pipeline.Spec2Pipeline jw00017001001_01101_00001_nrs1_uncal.fits --save-parameters my_spec2.asdf

Once created and modified as necessary, the file can now be used by strun to run the step/pipeline with the desired parameters:

$ strun my_spec2.asdf jw00017001001_01101_00001_nrs1_uncal.fits

The remaining sections will describe the file format and contents.

File Contents

To describe the contents of an ASDF file, the configuration for the step CubeBuildStep will be used as the example:

#ASDF 1.0.0
#ASDF_STANDARD 1.5.0
%YAML 1.1
%TAG ! tag:stsci.edu:asdf/
--- !core/asdf-1.1.0
asdf_library: !core/software-1.0.0 {author: Space Telescope Science Institute, homepage: 'http://github.com/spacetelescope/asdf',
  name: asdf, version: 2.7.3}
history:
  extensions:
  - !core/extension_metadata-1.0.0
    extension_class: asdf.extension.BuiltinExtension
    software: !core/software-1.0.0 {name: asdf, version: 2.7.3}
class: jwst.cube_build.cube_build_step.CubeBuildStep
name: CubeBuildStep
parameters:
  band: all
  channel: all
  coord_system: skyalign
  filter: all
  grating: all
  input_dir: ''
  output_ext: .fits
  output_type: band
  output_use_index: true
  output_use_model: true
  post_hooks: []
  pre_hooks: []
  rois: 0.0
  roiw: 0.0
  save_results: false
  scale1: 0.0
  scale2: 0.0
  scalew: 0.0
  search_output_file: false
  single: false
  skip: false
  skip_dqflagging: false
  weight_power: 2.0
  weighting: emsm
  ...

Required Components

Preamble

The first 5 lines, up to and including the “—” line, define the file as an ASDF file. The rest of the file is formatted as one would format YAML data. Being YAML, the last line, containing the three ... is essential.

class and name

There are two required keys at the top level: class and parameters. parameters is discussed below.

class specifies the Python class to run. It should be a fully-qualified Python path to the class. Step classes can ship with stpipe itself, they may be part of other Python packages, or they exist in freestanding modules alongside the configuration file. For example, to use the SystemCall step included with stpipe, set class to stpipe.subprocess.SystemCall. To use a class called Custom defined in a file mysteps.py in the same directory as the configuration file, set class to mysteps.Custom.

name defines the name of the step. This is distinct from the class of the step, since the same class of Step may be configured in different ways, and it is useful to be able to have a way of distinguishing between them. For example, when Steps are combined into Pipelines, a Pipeline may use the same Step class multiple times, each with different configuration parameters.

Parameters

parameters contains all the parameters to pass onto the step. The order of the parameters does not matter. It is not necessary to specify all parameters either. If not defined, the default, as defined in the code or values from CRDS parameter references, will be used.

Formatting

YAML has two ways of formatting a list of key/value pairs. In the above example, each key/value pair is on separate line. The other way is using a form that is similar to a Python dict. For example, the parameters block above could also have been formatted as:

parameters: {band: all, channel: all, coord_system: world, filter: all,
  grating: all, output_type: band, output_use_model: true, rois: 0.0,
  roiw: 0.0, scale1: 0.0, scale2: 0.0, scalew: 0.0, search_output_file: false,
  single: false, skip_dqflagging: false, weight_power: 2.0, weighting: msm}

Optional Components

The asdf_library and history blocks are necessary only when a parameter file is to be used as a parameter reference file in CRDS. See Parameter Files as Reference Files below.

Completeness

For any parameter file, it is not necessary to specify all step/pipeline parameters. Any parameter left unspecified will get, at least, the default value define in the step’s code. If a parameter is defined without a default value, and the parameter is never assigned a value, an error will be produced when the step is executed.

Remember that parameter values can come from numerous sources. Refer to Parameter Precedence for a full listing of how parameters can be set.

From the CubeBuildStep example, if all that needed to change is the weight_power parameter with a setting of 4.0, the parameters block need only contain the following:

parameters:
  weight_power: 4.0

Pipeline Configuration

Pipelines are essentially steps that refer to sub-steps. As in the original cfg format, parameters for sub-steps can also be specified. All sub-step parameters appear in a key called steps. Sub-step parameters are specified by using the sub-step name as the key, then underneath and indented, the parameters to change for that sub-step. For example, to define the weight_power of the cube_build step in a Spec2Pipeline parameter file, the parameter block would look as follows:

class: jwst.pipeline.Spec2Pipeline
parameters: {}
steps:
- class: jwst.cube_build.cube_build_step.CubeBuildStep
  parameters:
    weight_power: 4.0

As with step parameter files, not all sub-steps need to be specified. If left unspecified, the sub-steps will be run with their default parameter sets. For the example above, the other steps of Spec2Pipeline, such as assign_wcs and photom would still be executed.

Similarly, to skip a particular step, one would specify skip: true for that substep. Continuing from the above example, to skip the msa_flagging step, the parameter file would look like:

class: jwst.pipeline.Spec2Pipeline
parameters: {}
steps:
- class: jwst.msaflagopen.msaflagopen_step.MSAFlagOpenStep
  parameters:
    skip: true
- class: jwst.cube_build.cube_build_step.CubeBuildStep
  parameters:
    weight_power: 4.0

Note

In the previous examples, one may have noted the line parameters: {}. In neither example, and is a common situation when defining pipeline configurations, there is no need to set any of the parameters for the pipeline itself. However, the keyword parameters is required. As such, the value for parameters is defined as an empty dictionary, {}.

Python API

There are a number of ways to create an ASDF parameter file. From the command line utility strun, the option --save-parameters can be used.

Within a Python script, the method Step.export_config(filename: str) can be used. For example, to create a parameter file for CubeBuildStep, use the following:

>>> from jwst.cube_build import CubeBuildStep
>>> step = CubeBuildStep()
>>> step.export_config('cube_build.asdf')

Parameter Files as Reference Files

ASDF-formatted parameter files are the basis for the parameter reference reftypes in CRDS. There are two more keys that are needed to be added which CRDS requires: meta and history.

The direct way of creating a parameter reference file is through the Step.export_config method, just as one would to get a basic parameter file. The only addition is the argument include_meta=True. For example, to get a reference-file ready version of the CubeBuildStep, use the following Python code:

>>> from jwst.cube_build import CubeBuildStep
>>> step = CubeBuildStep()
>>> step.export_config('pars-cubebuildstep.asdf', include_meta=True)

The explanations for the meta and history blocks are given below.

META Block

When a parameter file is to be ingested into CRDS, there is another key required, meta, which defines the information needed by CRDS parameter file selection. A basic reference parameter file will look as follows:

#ASDF 1.0.0
#ASDF_STANDARD 1.3.0
%YAML 1.1
%TAG ! tag:stsci.edu:asdf/
--- !core/asdf-1.1.0
history:
  entries:
  - !core/history_entry-1.0.0 {description: Base values, time: !!timestamp '2019-10-29
      21:20:50'}
  extensions:
  - !core/extension_metadata-1.0.0
    extension_class: asdf.extension.BuiltinExtension
    software: {name: asdf, version: 2.4.2}
meta:
   author: Alfred E. Neuman
   date: '2019-07-17T10:56:23.456'
   description: MakeListStep parameters
   instrument: {name: MIRI}
   pedigree: GROUND
   reftype: pars-spec2pipeline
   telescope: JWST
   title: Spec2Pipeline default parameters
   useafter: '1990-04-24T00:00:00'
class: jwst.pipeline.calwebb_spec2.Spec2Pipeline
parameters: {}
...

All of the keys under meta are required, most of which are self-explanatory. For more information, refer to the CRDS documentation.

The one keyword to explain further is reftype. This is what CRDS uses to determine which parameter file is being sought after. This has the format pars-<step_name> where <step_name> is the Python class name, in lowercase.

History

Parameter reference files also require at least one history entry. This can be found in the history block under entries:

history:
  entries:
  - !core/history_entry-1.0.0 {description: Base values, time: !!timestamp '2019-10-29
      21:20:50'}

It is highly suggested to use the ASDF API to add history entries:

>>> import asdf
>>> cfg = asdf.open('config.asdf')
    #
    # Modify `parameters` and `meta` as necessary.
    #
>>> cfg.add_history_entry('Parameters modified for some reason')
>>> cfg.write_to('config_modified.asdf')

JWST, Parameters and Parameter References

In general, the default parameters for any pipeline or step are valid for nearly all instruments and observing modes. This means that when a pipeline or step is run without any explicit parameter setting, that pipeline or step will usually do the desired operation. Hence, most of the time there is no need for a parameter reference to be available in CRDS, or provided by the user. Only for a small set of observing mode/step combinations, will there be need to create a parameter reference. Even then, nearly all cases will involve changing a subset of a pipeline or step parameters.

Keeping this sparse-population philosophy in mind, for most parameter references, only those parameters that are explicilty changed should be specified in the reference. If adhered to, when a pipeline/step default value for a particular parameter needs to change, the change will be immediately available. Otherwise, all references that mistakenly set said parameter will need to be updated. See Completeness for more information.

Furthermore, every pipeline/step have a common set of parameters, listed below. These parameters generally affect the infrastructure operation of pipelines/steps, and should not be included in a parameter reference.

  • input_dir

  • output_ext

  • output_use_index

  • output_use_model

  • post_hooks

  • pre_hooks

  • save_results

  • search_output_file