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.
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 ExposurePipeline pipeline, do the following:
$ strun --save-parameters=exp_pars.asdf roman_elp r0000101001001001001_01101_0001_WFI01_uncal.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 exp_pars.asdf r0000101001001001001_01101_0001_WFI01_uncal.asdf
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
roman_elp 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: The ASDF Developers, homepage: 'http://github.com/asdf-format/asdf',
name: asdf, version: 2.13.0}
history:
extensions:
- !core/extension_metadata-1.0.0
extension_class: asdf.extension.BuiltinExtension
software: !core/software-1.0.0 {name: asdf, version: 2.13.0}
class: romancal.pipeline.exposure_pipeline.ExposurePipeline
meta:
author: <SPECIFY>
date: '2022-09-15T13:59:54'
description: Parameters for calibration step romancal.pipeline.exposure_pipeline.ExposurePipeline
instrument: {name: <SPECIFY>}
origin: <SPECIFY>
pedigree: <SPECIFY>
reftype: <SPECIFY>
telescope: <SPECIFY>
useafter: <SPECIFY>
name: ExposurePipeline
parameters:
input_dir: ''
output_dir: null
output_ext: .asdf
output_file: null
output_use_index: true
output_use_model: false
post_hooks: []
pre_hooks: []
save_calibrated_ramp: false
save_results: true
search_output_file: true
skip: false
suffix: null
steps:
- class: romancal.jump.jump_step.JumpStep
name: jump
parameters:
flag_4_neighbors: true
four_group_rejection_threshold: 190.0
input_dir: ''
max_jump_to_flag_neighbors: 1000.0
maximum_cores: none
min_jump_to_flag_neighbors: 10.0
output_dir: null
output_ext: .asdf
output_file: null
output_use_index: true
output_use_model: false
post_hooks: []
pre_hooks: []
rejection_threshold: 180.0
save_results: false
search_output_file: true
skip: false
suffix: null
three_group_rejection_threshold: 185.0
...
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: {flag_4_neighbors: true, four_group_rejection_threshold: 190.0,
max_jump_to_flag_neighbors: 1000.0, maximum_cores: none,
min_jump_to_flag_neighbors: 10.0, output_dir: null, output_ext: .asdf,
output_file: null, output_use_index: true, output_use_model: false,
rejection_threshold: 180.0, three_group_rejection_threshold: 185.0}
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 which is not currently
implemented in the Roman pipeline.
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 JumpStep example, if all that needed to change is the
rejection_threshold parameter with a setting of 80.0,
the parameters block need only contain the following:
parameters:
rejection_threshold: 80.0
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 rejection_threshold of the
JumpStep step in a ExposurePipeline parameter file, the parameter
block would look as follows:
class: romancal.pipeline.exposure_pipeline.ExposurePipeline
parameters: {}
steps:
- class: romancal.jump.jump_step.JumpStep
parameters:
rejection_threshold: 80.0
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 ExposurePipeline, 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 flatfield step,
the parameter file would look like:
class: romancal.pipeline.exposure_pipeline.ExposurePipeline
parameters: {}
steps:
- class: romancal.flatfield.flat_field_step.FlatFieldStep
name: flatfield
parameters:
skip: true
Note
In the previous examples, one may have noted the line parameters: {}. Often
when configuring a pipeline, one needs not set any 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 JumpStep, use the
following:
>>> from romancal.jump import JumpStep
>>> step = JumpStep()
>>> step.export_config('jump_step.asdf')
History¶
Parameter reference files also require at least one history entry. This can be found in the history block under entries:
history:
extensions:
- !core/extension_metadata-1.0.0
extension_class: asdf.extension.BuiltinExtension
software: !core/software-1.0.0 {name: asdf, version: 2.13.0}
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')
Roman, 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 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 explicitly 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