ApPipeTask¶
- class lsst.ap.pipe.ApPipeTask(butler, *args, **kwargs)¶
Bases:
CmdLineTask
Command-line task representing the entire AP pipeline.
ApPipeTask
processes raw DECam images from basic processing through source association. Other observatories will be supported in the future.ApPipeTask
can be run from the command line, but it can also be called from other pipeline code. It provides public methods for executing each major step of the pipeline by itself.- Parameters:
- butler
lsst.daf.persistence.Butler
A Butler providing access to the science, calibration, and (unless
config.differencer.getTemplate
is overridden) template data to be processed. Its output repository must be both readable and writable.
- butler
Attributes Summary
Methods Summary
applyOverrides
(config)A hook to allow a task to change the values of its config after the camera-specific overrides are loaded but before any command-line overrides are applied.
Empty (clear) the metadata for this Task and all sub-Tasks.
Get schema catalogs for all tasks in the hierarchy, combining the results into a single dict.
Get metadata for all tasks.
Get the task name as a hierarchical name including parent task names.
getName
()Get the name of the task.
Get the schemas generated by this task.
Get a dictionary of all tasks as a shallow copy.
makeField
(doc)Make a
lsst.pex.config.ConfigurableField
for this task.makeSubtask
(name, **keyArgs)Create a subtask as a new instance as the
name
attribute of this task.parseAndRun
([args, config, log, doReturnResults])Parse an argument list and run the command.
runAssociation
(sensorRef)Do source association.
runDataRef
(rawRef[, templateIds, reuse])Execute the ap_pipe pipeline on a single image.
runDiffIm
(sensorRef[, templateIds])Do difference imaging with a template and a science image
runProcessCcd
(sensorRef)Perform ISR with ingested images and calibrations via processCcd.
timer
(name[, logLevel])Context manager to log performance data for an arbitrary block of code.
writeConfig
(butler[, clobber, doBackup])Write the configuration used for processing the data, or check that an existing one is equal to the new one if present.
writeMetadata
(dataRef)Write the metadata produced from processing the data.
writePackageVersions
(butler[, clobber, ...])Compare and write package versions.
writeSchemas
(butler[, clobber, doBackup])Write the schemas returned by
lsst.pipe.base.Task.getAllSchemaCatalogs
.Attributes Documentation
- canMultiprocess = True¶
Methods Documentation
- classmethod applyOverrides(config)¶
A hook to allow a task to change the values of its config after the camera-specific overrides are loaded but before any command-line overrides are applied.
- Parameters:
- configinstance of task’s
ConfigClass
Task configuration.
- configinstance of task’s
Notes
This is necessary in some cases because the camera-specific overrides may retarget subtasks, wiping out changes made in ConfigClass.setDefaults. See LSST Trac ticket #2282 for more discussion.
Warning
This is called by CmdLineTask.parseAndRun; other ways of constructing a config will not apply these overrides.
- getAllSchemaCatalogs() Dict[str, Any] ¶
Get schema catalogs for all tasks in the hierarchy, combining the results into a single dict.
- Returns:
- schemacatalogs
dict
Keys are butler dataset type, values are a empty catalog (an instance of the appropriate
lsst.afw.table
Catalog type) for all tasks in the hierarchy, from the top-level task down through all subtasks.
- schemacatalogs
Notes
This method may be called on any task in the hierarchy; it will return the same answer, regardless.
The default implementation should always suffice. If your subtask uses schemas the override
Task.getSchemaCatalogs
, not this method.
- getFullMetadata() TaskMetadata ¶
Get metadata for all tasks.
- Returns:
- metadata
TaskMetadata
The keys are the full task name. Values are metadata for the top-level task and all subtasks, sub-subtasks, etc.
- metadata
Notes
The returned metadata includes timing information (if
@timer.timeMethod
is used) and any metadata set by the task. The name of each item consists of the full task name with.
replaced by:
, followed by.
and the name of the item, e.g.:topLevelTaskName:subtaskName:subsubtaskName.itemName
using
:
in the full task name disambiguates the rare situation that a task has a subtask and a metadata item with the same name.
- getFullName() str ¶
Get the task name as a hierarchical name including parent task names.
- Returns:
- fullName
str
The full name consists of the name of the parent task and each subtask separated by periods. For example:
The full name of top-level task “top” is simply “top”.
The full name of subtask “sub” of top-level task “top” is “top.sub”.
The full name of subtask “sub2” of subtask “sub” of top-level task “top” is “top.sub.sub2”.
- fullName
- getSchemaCatalogs() Dict[str, Any] ¶
Get the schemas generated by this task.
- Returns:
- schemaCatalogs
dict
Keys are butler dataset type, values are an empty catalog (an instance of the appropriate
lsst.afw.table
Catalog type) for this task.
- schemaCatalogs
See also
Task.getAllSchemaCatalogs
Notes
Warning
Subclasses that use schemas must override this method. The default implementation returns an empty dict.
This method may be called at any time after the Task is constructed, which means that all task schemas should be computed at construction time, not when data is actually processed. This reflects the philosophy that the schema should not depend on the data.
Returning catalogs rather than just schemas allows us to save e.g. slots for SourceCatalog as well.
- getTaskDict() Dict[str, ReferenceType[Task]] ¶
Get a dictionary of all tasks as a shallow copy.
- Returns:
- taskDict
dict
Dictionary containing full task name: task object for the top-level task and all subtasks, sub-subtasks, etc.
- taskDict
- classmethod makeField(doc: str) ConfigurableField ¶
Make a
lsst.pex.config.ConfigurableField
for this task.- Parameters:
- doc
str
Help text for the field.
- doc
- Returns:
- configurableField
lsst.pex.config.ConfigurableField
A
ConfigurableField
for this task.
- configurableField
Examples
Provides a convenient way to specify this task is a subtask of another task.
Here is an example of use:
class OtherTaskConfig(lsst.pex.config.Config): aSubtask = ATaskClass.makeField("brief description of task")
- makeSubtask(name: str, **keyArgs: Any) None ¶
Create a subtask as a new instance as the
name
attribute of this task.- Parameters:
- name
str
Brief name of the subtask.
- keyArgs
Extra keyword arguments used to construct the task. The following arguments are automatically provided and cannot be overridden:
“config”.
“parentTask”.
- name
Notes
The subtask must be defined by
Task.config.name
, an instance ofConfigurableField
orRegistryField
.
- classmethod parseAndRun(args=None, config=None, log=None, doReturnResults=False)¶
Parse an argument list and run the command.
- Parameters:
- args
list
, optional - config
lsst.pex.config.Config
-type, optional Config for task. If
None
useTask.ConfigClass
.- log
logging.Logger
-type, optional Log. If
None
use the default log.- doReturnResults
bool
, optional If
True
, return the results of this task. Default isFalse
. This is only intended for unit tests and similar use. It can easily exhaust memory (if the task returns enough data and you call it enough times) and it will fail when using multiprocessing if the returned data cannot be pickled.
- args
- Returns:
- struct
lsst.pipe.base.Struct
Fields are:
argumentParser
the argument parser (
lsst.pipe.base.ArgumentParser
).parsedCmd
the parsed command returned by the argument parser’s
parse_args
method (argparse.Namespace
).taskRunner
the task runner used to run the task (an instance of
Task.RunnerClass
).resultList
results returned by the task runner’s
run
method, one entry per invocation (list
). This will typically be a list ofStruct
, each containing at least anexitStatus
integer (0 or 1); seeTask.RunnerClass
(TaskRunner
by default) for more details.
- struct
Notes
Calling this method with no arguments specified is the standard way to run a command-line task from the command-line. For an example see
pipe_tasks
bin/makeSkyMap.py
or almost any other file in that directory.If one or more of the dataIds fails then this routine will exit (with a status giving the number of failed dataIds) rather than returning this struct; this behaviour can be overridden by specifying the
--noExit
command-line option.
- runAssociation(sensorRef)¶
Do source association.
This method writes an
apdb_marker
dataset once all changes related to the current exposure have been committed.- Parameters:
- sensorRef
lsst.daf.persistence.ButlerDataRef
Data reference for multiple input dataset types.
- sensorRef
- Returns:
- result
lsst.pipe.base.Struct
Result struct with components:
- apdb
lsst.dax.apdb.Apdb
Initialized association database containing final association results.
- apdb
taskResults : output of
config.diaPipe.run
(lsst.pipe.base.Struct
).
- result
- runDataRef(rawRef, templateIds=None, reuse=None)¶
Execute the ap_pipe pipeline on a single image.
- Parameters:
- rawRef
lsst.daf.persistence.ButlerDataRef
A reference to the raw data to process.
- templateIds
list
ofdict
, optional A list of parsed data IDs for templates to use. Only used if
config.differencer
is configured to do so.differencer
or its subtasks may restrict the allowed IDs.- reuse
list
ofstr
, optional The names of all subtasks that may be skipped if their output is present. Defaults to skipping nothing.
- rawRef
- Returns:
- result
lsst.pipe.base.Struct
Result struct with components:
- l1Databasehandle for accessing the final association database, conforming to
ap_association
’s DB access API
ccdProcessor : output of
config.ccdProcessor.runDataRef
(lsst.pipe.base.Struct
orNone
).differencer : output of
config.differencer.runDataRef
(lsst.pipe.base.Struct
orNone
).diaPipe : output of
config.diaPipe.run
(lsst.pipe.base.Struct
orNone
).
- result
- runDiffIm(sensorRef, templateIds=None)¶
Do difference imaging with a template and a science image
The output repository associated with
sensorRef
will be populated with difference images and catalogs of detected sources (diaSrc, diffexp, and metadata files)- Parameters:
- sensorRef
lsst.daf.persistence.ButlerDataRef
Data reference for multiple dataset types, both input and output.
- templateIds
list
ofdict
, optional A list of parsed data IDs for templates to use. Only used if
config.differencer
is configured to do so.differencer
or its subtasks may restrict the allowed IDs.
- sensorRef
- Returns:
- result
lsst.pipe.base.Struct
Output of
config.differencer.runDataRef
.
- result
- runProcessCcd(sensorRef)¶
Perform ISR with ingested images and calibrations via processCcd.
The output repository associated with
sensorRef
will be populated with the usual post-ISR data (bkgd, calexp, icExp, icSrc, postISR).- Parameters:
- sensorRef
lsst.daf.persistence.ButlerDataRef
Data reference for raw data.
- sensorRef
- Returns:
- result
lsst.pipe.base.Struct
Output of
config.ccdProcessor.runDataRef
.
- result
Notes
The input repository corresponding to
sensorRef
must already contain the refcats.
- timer(name: str, logLevel: int = 10) Iterator[None] ¶
Context manager to log performance data for an arbitrary block of code.
- Parameters:
See also
timer.logInfo
Examples
Creating a timer context:
with self.timer("someCodeToTime"): pass # code to time
- writeConfig(butler, clobber=False, doBackup=True)¶
Write the configuration used for processing the data, or check that an existing one is equal to the new one if present.
- Parameters:
- butler
lsst.daf.persistence.Butler
Data butler used to write the config. The config is written to dataset type
CmdLineTask._getConfigName
.- clobber
bool
, optional A boolean flag that controls what happens if a config already has been saved:
- doBackup
bool
, optional Set to
True
to backup the config files if clobbering.
- butler
- writeMetadata(dataRef)¶
Write the metadata produced from processing the data.
- Parameters:
- dataRef
Butler data reference used to write the metadata. The metadata is written to dataset type
CmdLineTask._getMetadataName
.
- writePackageVersions(butler, clobber=False, doBackup=True, dataset='packages')¶
Compare and write package versions.
- Parameters:
- butler
lsst.daf.persistence.Butler
Data butler used to read/write the package versions.
- clobber
bool
, optional A boolean flag that controls what happens if versions already have been saved:
- doBackup
bool
, optional If
True
and clobbering, old package version files are backed up.- dataset
str
, optional Name of dataset to read/write.
- butler
- Raises:
- TaskError
Raised if there is a version mismatch with current and persisted lists of package versions.
Notes
Note that this operation is subject to a race condition.
- writeSchemas(butler, clobber=False, doBackup=True)¶
Write the schemas returned by
lsst.pipe.base.Task.getAllSchemaCatalogs
.- Parameters:
- butler
lsst.daf.persistence.Butler
Data butler used to write the schema. Each schema is written to the dataset type specified as the key in the dict returned by
getAllSchemaCatalogs
.- clobber
bool
, optional A boolean flag that controls what happens if a schema already has been saved:
- doBackup
bool
, optional Set to
True
to backup the schema files if clobbering.
- butler
Notes
If
clobber
isFalse
and an existing schema does not match a current schema, then some schemas may have been saved successfully and others may not, and there is no easy way to tell which is which.