Pipelines¶

It is important to note that a Pipeline is also a Step, so everything that applies to a Step in the For Users chapter also applies to Pipelines.

Configuring a Pipeline¶

This section describes how to set parameters on the individual steps in a pipeline. To change the order of steps in a pipeline, one must write a Pipeline subclass in Python. That is described in the Pipelines section of the developer documentation.

Just as with Steps, Pipelines can by configured either by a parameter file or directly from Python.

From a parameter file¶

A Pipeline parameter file follows the same format as a Step parameter file: ASDF Parameter Files

Here is an example pipeline parameter file for the ExposurePipeline class:

#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.dq_init.dq_init_step.DQInitStep
name: dq_init
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_results: false
search_output_file: true
skip: false
suffix: null
- class: romancal.saturation.saturation_step.SaturationStep
...

Just like a Step, it must have name and class values. Here the class must refer to a subclass of stpipe.Pipeline.

Following name and class is the steps section. Under this section is a subsection for each step in the pipeline. The easiest way to get started on a parameter file is to call Step.export_config and then edit the file that is created. This will generate an ASDF config file that includes every available parameter, which can then be trimmed to the parameters that require customization.

For each Step’s section, the parameters for that step may either be specified inline, or specified by referencing an external parameter file just for that step. For example, a pipeline parameter file that contains:

- 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

is equivalent to:

steps:
- class: romancal.jump.jump_step.JumpStep
  name: jump
  parameters:
     config_file = myjump.asdf

with the file myjump.asdf. in the same directory:

class: romancal.jump.jump_step.JumpStep
name: jump
parameters:
  flag_4_neighbors: true
  four_group_rejection_threshold: 190.0

If both a config_file and additional parameters are specified, the config_file is loaded, and then the local parameters override them.

Any optional parameters for each Step may be omitted, in which case defaults will be used.

From Python¶

A pipeline may be configured from Python by passing a nested dictionary of parameters to the Pipeline’s constructor. Each key is the name of a step, and the value is another dictionary containing parameters for that step. For example, the following is the equivalent of the parameter file above:

from stpipe.pipeline import Image2Pipeline

steps = {
    'jump':{'rejection_threshold': 180.,
            'three_group_rejection_threshold': 190.,
            'four_group_rejection_threshold':195.
}

pipe = ExposurePipeline(steps=steps)

Running a Pipeline¶

From the commandline¶

The same strun script used to run Steps from the commandline can also run Pipelines.

The only wrinkle is that any parameters overridden from the commandline use dot notation to specify the parameter name. For example, to override the rejection_threshold value on the jump step in the example above, one can do:

> strun romancal.pipeline.ExposurePipeline --steps.jump.rejection_threshold=180.

From Python¶

Once the pipeline has been configured (as above), just call the instance to run it.

pipe(input_data)

Caching details¶

The results of a Step are cached using Python pickles. This allows virtually most of the standard Python data types to be cached. In addition, any ASDF models that are the result of a step are saved as standalone ASDF files to make them more easily used by external tools. The filenames are based on the name of the substep within the pipeline.

Hooks¶

Each Step in a pipeline can also have pre- and post-hooks associated. Hooks themselves are Step instances, but there are some conveniences provided to make them easier to specify in a parameter file.

Pre-hooks are run right before the Step. The inputs to the pre-hook are the same as the inputs to their parent Step. Post-hooks are run right after the Step. The inputs to the post-hook are the return value(s) from the parent Step. The return values are always passed as a list. If the return value from the parent Step is a single item, a list of this single item is passed to the post hooks. This allows the post hooks to modify the return results, if necessary.

Hooks are specified using the pre_hooks and post_hooks parameters associated with each step. More than one pre- or post-hook may be assigned, and they are run in the order they are given. There can also be pre_hooks and post_hooks on the Pipeline as a whole (since a Pipeline is also a Step). Each of these parameters is a list of strings, where each entry is one of:

An external commandline application. The arguments can be accessed using {0}, {1} etc. (See stpipe.subproc.SystemCall).

A dot-separated path to a Python Step class.

A dot-separated path to a Python function.