Configuring tasks from the command line

Generally, configuring tasks for pipeline processing should happen either in the pipeline definition itself or in obs package overrides. There are, though, situations where a specific override needs to be used when running using the pipetask command-line tool.

This page describes how to review configurations with --show config and --show tasks, and change configurations on the command line with --config or --config-file

How to show a task’s current configuration

The --show argument allows you to review the current configuration details for a pipeline.

Tip

--show works for the build, qgraph, and run subcommands but will stop processing once the show options have been handled. If run or qgraph are used but with --show options that only refer to the build stage then only pipetask build will execute. If any show option is given with pipetask run, the command will finish after either the pipeline build or quantum graph construction phase.

Viewing all configurations

Use --show config to see all current configurations for a command-line. For example, using the RC2 subset test repository from the tutorial the first few lines of output are:

pipetask build  -p $DRP_PIPE_DIR/pipelines/HSC/DRP-RC2_subset.yaml#singleFrame --show config

### Configuration for task `isr'
# Flag to enable/disable metadata saving for a task, enabled by default.
config.saveMetadata=True

# Flag to enable/disable saving of log output for a task, enabled by default.
config.saveLogOutput=True

# Dataset type for input data; users will typically leave this alone, but camera-specific ISR tasks will override it
config.datasetType='raw'

# Fallback default filter name for calibrations.
config.fallbackFilterName='HSC-R'

...

This pipeline does know about the instrument overrides from obs packages because it is defined to work specifically for HSC.

The --show dump-config option reports the full config as reported by --show config but also includes all the associated import statements.

Viewing a subset of configurations

To filter the --show config output, include a search term with wildcard matching (*) characters (quoting to escape the wildcard from the shell). For example, this will show any configuration that start with the string mesh:

pipetask build -p ${DRP_PIPE_DIR}/pipelines/HSC/pipelines_check.yaml --show config="mesh*"

### Configuration for task `isr'
# Mesh size in X for flatness statistics
config.qa.flatness.meshX=256

# Mesh size in Y for flatness statistics
config.qa.flatness.meshY=256

### Configuration for task `characterizeImage'
### Configuration for task `calibrate'

This has checked all the configurations for all tasks, but if you want to restrict your search to a specific task use task:::

pipetask build -p ${DRP_PIPE_DIR}/pipelines/HSC/pipelines_check.yaml --show config="isr::mesh*"

### Configuration for task `isr'
# Mesh size in X for flatness statistics
config.qa.flatness.meshX=256

# Mesh size in Y for flatness statistics
config.qa.flatness.meshY=256

How to view the current pipeline

A pipeline can be built up from many ingredients and it can be hard to determine exactly the pipeline that you are going to execute. For example the pipeline used for the pipeline_check package, $DRP_PIPE_DIR/pipelines/HSC/pipelines_check.yaml, currently looks like:

description: |
  A tiny subset of the DRP pipeline used by the pipelines_check CI package.
instrument: lsst.obs.subaru.HyperSuprimeCam
imports:
  location: "$DRP_PIPE_DIR/pipelines/_ingredients/HSC/DRP.yaml"
  include:
    - processCcd

but you have to look in another place to see what is really going to be executed. The --show pipeline option can be used to see exactly the pipeline that will be run:

$ pipetask build -p ${DRP_PIPE_DIR}/pipelines/HSC/pipelines_check.yaml --show pipeline

which currently results in this more detailed output:

description: 'A tiny subset of the DRP pipeline used by the pipelines_check CI package.'
instrument: lsst.obs.subaru.HyperSuprimeCam
parameters:
  band: i
tasks:
  isr:
    class: lsst.ip.isr.IsrTask
  characterizeImage:
    class: lsst.pipe.tasks.characterizeImage.CharacterizeImageTask
    config:
    - python: |
        import lsst.meas.extensions.piff.piffPsfDeterminer
        config.measurePsf.psfDeterminer = "piff"
  calibrate:
    class: lsst.pipe.tasks.calibrate.CalibrateTask
subsets:
  processCcd:
    subset:
    - isr
    - calibrate
    - characterizeImage
    description: 'Set of tasks to run when doing single frame processing, without
      any conversions to Parquet/DataFrames or visit-level summaries.'

showing that this pipeline consists of three main tasks: isr, characterizeImage and calibrate, and that characterizeImage has been configured to use piff.

How to view retargeted subtasks

To see what subtasks are currently configured to run with the specified pipeline, use the --show tasks argument. For example:

pipetask build -p ${DRP_PIPE_DIR}/pipelines/HSC/pipelines_check.yaml --show tasks

An example of the printed output is:

### Subtasks for task `lsst.ip.isr.isrTask.IsrTask'
ampOffset: lsst.obs.subaru.ampOffset.SubaruAmpOffsetTask
...
### Subtasks for task `lsst.pipe.tasks.characterizeImage.CharacterizeImageTask'
applyApCorr: lsst.meas.base.applyApCorr.ApplyApCorrTask
background: lsst.meas.algorithms.subtractBackground.SubtractBackgroundTask
...
### Subtasks for task `lsst.pipe.tasks.calibrate.CalibrateTask'
applyApCorr: lsst.meas.base.applyApCorr.ApplyApCorrTask
astrometry: lsst.meas.astrom.astrometry.AstrometryTask
astrometry.matcher: lsst.meas.astrom.matchPessimisticB.MatchPessimisticBTask
...

This subtask hierarchy is interpreted as follows:

Note that if the calibrate.astrometry task is retargeted to a different task class, the subtask of calibrate.astrometry may change (for example, calibrate.astrometry.matcher may no longer exist).

How to set configurations with command-line arguments

Pipelines can be configured through a combination of two mechanisms: arguments on the command line (--config) or through configuration files (--config-file). In general, simple configurations can be made through the command line, while complex configurations and subtask retargeting must done through configuration files (see How to use configuration files).

To change a configuration value on the command line, pass that configuration task label, name and value to the --config argument. For example, change the mesh value from the previous example:

pipetask build -p ${DRP_PIPE_DIR}/pipelines/HSC/pipelines_check.yaml --show config="isr::mesh*" --config isr:qa.flatness.meshY=512

### Configuration for task `isr'
# Mesh size in X for flatness statistics
config.qa.flatness.meshX=256

# Mesh size in Y for flatness statistics
config.qa.flatness.meshY=512

You can provide multiple --config arguments on the same command line as distinct --config options:

pipetask build -p ${DRP_PIPE_DIR}/pipelines/HSC/pipelines_check.yaml --show config="isr::mesh*" --config isr:qa.flatness.meshY=512 -c isr:qa.flatness.meshX=128

### Configuration for task `isr'
# Mesh size in X for flatness statistics
config.qa.flatness.meshX=128

# Mesh size in Y for flatness statistics
config.qa.flatness.meshY=512

Only simple configuration values can be set through --config arguments, such as:

  • String values. For example: --config task:configName="value".

  • Scalar numbers. For example: --config task:configName=2.5.

  • Lists of integers. For example: --config task:intList=[2,4,-87].

  • Lists of floating point numbers. For example: --config task:floatList=[3.14,-5.6e7].

  • Lists of strings, For example: --config task:strList=[BAD,GOOD].

  • Boolean values. For example: --config task:configName=True configName2=False.

The [] are optional when specifying lists.

Specific types of configurations you cannot perform with the --config argument are:

  • You cannot retarget a subtask specified by a lsst.pex.config.ConfigurableField (which is the most common case).

  • For items in registries, you can only specify values for the active (current) item.

  • You cannot specify a subset of a list. You must specify all values at once.

For these more complex configuration types you must use configuration files, which are evaluated as Python code.

How to use configuration files

You can also provide configurations to a command-line through a configuration file. In fact, configuration files are Python modules; anything you can do in Python you can do in a configuration file.

Configuration files give you full access to the configuration API, allowing you to import and retarget subtasks, and set configurations with complex types. These configurations can only be done through configuration files, not through command-line arguments.

Use a configuration file by providing its file path through a -C / --config-file argument:

pipetask build --config-file isr:myisr.py

The task label must be associated with the configuration file to let the command know which task is being over-ridden.

Multiple configuration files can be provided through the same --config-file argument by separating with commas, and the --config-file argument itself can be repeated. The configuration parameters are applied in the order they appear on the command line.

In a configuration file, configurations are attributes of a config object. If on the command line you set a configuration with a --config task:skyMap.projection="TAN" argument, in a configuration file the equivalent statement is:

config.skyMap.projection = "TAN"

config is the root configuration object for the pipeline task. Settings for the task itself are attributes of config. In that example, config.skyMap is a subtask and projection is a configuration of that skyMap subtask.

About configuration defaults and instrument configuration override files

Command-line configurations are a combination of configurations you provide and defaults from the observatory package and the task itself.

When a command-line is run, it loads two instrument-specific configuration files, if found: one for the observatory package, and one for a specific camera defined in that observatory package. For an example observatory package named obs_package, these configuration override files are, in order:

  • obs_package/config/taskName.py (overrides for an observatory package in general).

  • obs_package/config/cameraName/taskName.py (overrides for a specific instrument, named “cameraName”).

The taskName is the pipeline task label and can either come from the name set in the task itself, or from an override in the pipeline definition.

Here are two examples:

  • obs_lsst/config/makeWarp.py: specifies which parameters are preferred when warping images using the obs_lsst observatory package.

  • obs_lsst/config/latiss/isr.py`: provides overrides for the instrument signature removal (aka detrending) task for the latiss camera in the obs_lsst observatory package.

Overall, the priority order for setting task configurations is configurations is (highest priority first):

  1. User-provided --config and --config-file arguments (computed left-to-right).

  2. Directly in a pipeline YAML definition.

  3. Camera specific configuration override file in an observatory package.

  4. General configuration override file in an observatory package.

  5. Task defaults.

Determining the history of a config parameter

Sometimes you aren’t sure where a value for a configuration parameter is coming from, given all the many places where a parameter can be overridden. To investigate the history of a parameter you can use the --show history option. This option takes a task label and a pattern to use to match a configuration parameter. The output is quite verbose since it reports the entire code hierarchy involved in setting the parameter. In this example we show how the assembleCcd.keysToRemove parameter defaults to an empty list, then values are set from the obs_subaru override, and then finally the command-line value overrides everything:

pipetask build -p ${DRP_PIPE_DIR}/pipelines/HSC/pipelines_check.yaml --show "history=isr::*keysToRemove" -c "isr:assembleCcd.keysToRemove=[A,B]"
### Configuration field for task `isr'
assembleCcd.keysToRemove
[]                                               $CTRL_MPEXEC_DIR/bin/pipetask:29                                                     sys.exit(main())
                                                ctrl/mpexec/cli/pipetask.py:51
                                                daf/butler/cli/utils.py:1069
                                                ctrl/mpexec/cli/cmd/commands.py:106
                                                ctrl/mpexec/cli/script/build.py:89
                                                ctrl/mpexec/showInfo.py:138
                                                ctrl/mpexec/showInfo.py:226
                                                ctrl/mpexec/util.py:143
                                                pipe/base/pipeline.py:668
                                                pipe/base/pipeline.py:691
                                                pex/config/configurableField.py:421
                                                pex/config/configurableField.py:421
                                                ip/isr/assembleCcdTask.py:39
[]                                               $CTRL_MPEXEC_DIR/bin/pipetask:29                                                     sys.exit(main())
                                                ctrl/mpexec/cli/pipetask.py:51
                                                daf/butler/cli/utils.py:1069
                                                ctrl/mpexec/cli/cmd/commands.py:106
                                                ctrl/mpexec/cli/script/build.py:89
                                                ctrl/mpexec/showInfo.py:138
                                                ctrl/mpexec/showInfo.py:226
                                                ctrl/mpexec/util.py:143
                                                pipe/base/pipeline.py:668
                                                pipe/base/pipeline.py:691
                                                pex/config/configurableField.py:421
                                                pex/config/configurableField.py:421
['PC001001', 'PC001002', 'PC002001', 'PC002002'] $CTRL_MPEXEC_DIR/bin/pipetask:29                                                     sys.exit(main())
                                                ctrl/mpexec/cli/pipetask.py:51
                                                daf/butler/cli/utils.py:1069
                                                ctrl/mpexec/cli/cmd/commands.py:106
                                                ctrl/mpexec/cli/script/build.py:89
                                                ctrl/mpexec/showInfo.py:138
                                                ctrl/mpexec/showInfo.py:226
                                                ctrl/mpexec/util.py:143
                                                pipe/base/pipeline.py:668
                                                pipe/base/pipeline.py:711
                                                pipe/base/configOverrides.py:299
                                                pipe/base/_instrument.py:298
                                                pex/config/config.py:1167
                                                pex/config/config.py:1251
                                                $EUPS_PATH/Darwin/obs_subaru/g56afc215e3+576f275b99/config/isr.py:33    config.assembleCcd.keysToRemove = ["PC001001", "PC001002", "PC002001", "PC002002"]
['A', 'B']                                       $CTRL_MPEXEC_DIR/bin/pipetask:29                                                     sys.exit(main())
                                                ctrl/mpexec/cli/pipetask.py:51
                                                daf/butler/cli/utils.py:1069
                                                ctrl/mpexec/cli/cmd/commands.py:106
                                                ctrl/mpexec/cli/script/build.py:89
                                                ctrl/mpexec/showInfo.py:138
                                                ctrl/mpexec/showInfo.py:226
                                                ctrl/mpexec/util.py:143
                                                pipe/base/pipeline.py:668
                                                pipe/base/pipeline.py:711
                                                pipe/base/configOverrides.py:285