JointcalCoaddTask¶
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class
lsst.jointcal.
JointcalCoaddTask
(reuse=False, **kwargs)¶ Bases:
lsst.pipe.tasks.makeCoaddTempExp.MakeCoaddTempExpTask
Attributes Summary
canMultiprocess
Methods Summary
applyJointcalResultsExposure
(dataRef[, calexp])Update an Exposure with the Wcs, from meas_jointcal (Calib and flux sacling will be also used later). 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. applySkyCorr
(dataRef, calexp)Apply correction to the sky background level emptyMetadata
()Empty (clear) the metadata for this Task and all sub-Tasks. getAllSchemaCatalogs
()Get schema catalogs for all tasks in the hierarchy, combining the results into a single dict. getBadPixelMask
()! getCalExp
(dataRef, bgSubtracted)Return one “calexp” calibrated exposure getCoaddDatasetName
([warpType])Return coadd name for given warpType and task config getFullMetadata
()Get metadata for all tasks. getFullName
()Get the task name as a hierarchical name including parent task names. getName
()Get the name of the task. getSchemaCatalogs
()Get the schemas generated by this task. getSkyInfo
(patchRef)! getTaskDict
()Get a dictionary of all tasks as a shallow copy. getTempExpDatasetName
([warpType])Return warp name for given warpType and task config getWarpTypeList
()Return list of requested warp types per the config. 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. run
(calexpRefList, skyInfo[, visitId])Create a Warp from inputs runDataRef
(patchRef[, selectDataList])!Produce <coaddName>Coadd_<warpType>Warp images by warping and optionally PSF-matching. selectExposures
(patchRef[, skyInfo, …])! 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
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canMultiprocess
= True¶
Methods Documentation
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applyJointcalResultsExposure
(dataRef, calexp=None)¶ Update an Exposure with the Wcs, from meas_jointcal (Calib and flux sacling will be also used later). If None, the calexp will be loaded from the dataRef. Otherwise it is updated in-place.
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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: - config : instance of task’s
ConfigClass
Task configuration.
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.
- config : instance of task’s
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applySkyCorr
(dataRef, calexp)¶ Apply correction to the sky background level
Sky corrections can be generated with the ‘skyCorrection.py’ executable in pipe_drivers. Because the sky model used by that code extends over the entire focal plane, this can produce better sky subtraction.
The calexp is updated in-place.
Parameters: - dataRef :
lsst.daf.persistence.ButlerDataRef
Data reference for calexp.
- calexp :
lsst.afw.image.Exposure
orlsst.afw.image.MaskedImage
Calibrated exposure.
- dataRef :
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emptyMetadata
()¶ Empty (clear) the metadata for this Task and all sub-Tasks.
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getAllSchemaCatalogs
()¶ 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.
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.- schemacatalogs :
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getBadPixelMask
()¶ ! @brief Convenience method to provide the bitmask from the mask plane names
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getCalExp
(dataRef, bgSubtracted)¶ Return one “calexp” calibrated exposure
Parameters: - dataRef
a sensor-level data reference
- bgSubtracted
return calexp with background subtracted? If False get the calexp’s background background model and add it to the calexp.
Returns: - afw.image.ExposureF
The calibrated exposure. If config.doApplyUberCal, jointcal calibrations will be applied to the returned exposure using applyMosaicResults.
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getCoaddDatasetName
(warpType='direct')¶ Return coadd name for given warpType and task config
Parameters: - warpType : string
Either ‘direct’ or ‘psfMatched’
Returns: - CoaddDatasetName :
string
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getFullMetadata
()¶ Get metadata for all tasks.
Returns: - metadata :
lsst.daf.base.PropertySet
The
PropertySet
keys are the full task name. Values are metadata for the top-level task and all subtasks, sub-subtasks, etc..
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.- metadata :
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getFullName
()¶ 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 :
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getSchemaCatalogs
()¶ 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.
See also
Task.getAllSchemaCatalogs
Notes
Warning
Subclasses that use schemas must override this method. The default implemenation 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.
- schemaCatalogs :
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getSkyInfo
(patchRef)¶ ! @brief Use @ref getSkyinfo to return the skyMap, tract and patch information, wcs and the outer bbox of the patch.
@param[in] patchRef data reference for sky map. Must include keys “tract” and “patch”
@return pipe_base Struct containing: - skyMap: sky map - tractInfo: information for chosen tract of sky map - patchInfo: information about chosen patch of tract - wcs: WCS of tract - bbox: outer bbox of patch, as an afwGeom Box2I
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getTaskDict
()¶ 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 :
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getTempExpDatasetName
(warpType='direct')¶ Return warp name for given warpType and task config
Parameters: - warpType : string
Either ‘direct’ or ‘psfMatched’
Returns: - WarpDatasetName :
string
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getWarpTypeList
()¶ Return list of requested warp types per the config.
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classmethod
makeField
(doc)¶ Make a
lsst.pex.config.ConfigurableField
for this task.Parameters: - doc :
str
Help text for the field.
Returns: - configurableField :
lsst.pex.config.ConfigurableField
A
ConfigurableField
for this task.
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("a brief description of what this task does")
- doc :
-
makeSubtask
(name, **keyArgs)¶ 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”.
Notes
The subtask must be defined by
Task.config.name
, an instance of pex_config ConfigurableField or RegistryField.- name :
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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 :
lsst.log.Log
-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.
Returns: - struct :
lsst.pipe.base.Struct
Fields are:
argumentParser
: the argument parser.parsedCmd
: the parsed command returned by the argument parser’slsst.pipe.base.ArgumentParser.parse_args
method.taskRunner
: the task runner used to run the task (an instance ofTask.RunnerClass
).
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.- args :
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run
(calexpRefList, skyInfo, visitId=0)¶ Create a Warp from inputs
We iterate over the multiple calexps in a single exposure to construct the warp (previously called a coaddTempExp) of that exposure to the supplied tract/patch.
Pixels that receive no pixels are set to NAN; this is not correct (violates LSST algorithms group policy), but will be fixed up by interpolating after the coaddition.
- @param calexpRefList: List of data references for calexps that (may)
- overlap the patch of interest
- @param skyInfo: Struct from CoaddBaseTask.getSkyInfo() with geometric
- information about the patch
- @param visitId: integer identifier for visit, for the table that will
- produce the CoaddPsf
- @return a pipeBase Struct containing:
- exposures: a dictionary containing the warps requested:
- “direct”: direct warp if config.makeDirect “psfMatched”: PSF-matched warp if config.makePsfMatched
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runDataRef
(patchRef, selectDataList=[])¶ !Produce <coaddName>Coadd_<warpType>Warp images by warping and optionally PSF-matching.
- @param[in] patchRef: data reference for sky map patch. Must include keys “tract”, “patch”,
- plus the camera-specific filter key (e.g. “filter” or “band”)
- @return: dataRefList: a list of data references for the new <coaddName>Coadd_directWarps
- if direct or both warp types are requested and <coaddName>Coadd_psfMatchedWarps if only psfMatched warps are requested.
@warning: this task assumes that all exposures in a warp (coaddTempExp) have the same filter.
@warning: this task sets the Calib of the coaddTempExp to the Calib of the first calexp with any good pixels in the patch. For a mosaic camera the resulting Calib should be ignored (assembleCoadd should determine zeropoint scaling without referring to it).
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selectExposures
(patchRef, skyInfo=None, selectDataList=[])¶ ! @brief Select exposures to coadd
Get the corners of the bbox supplied in skyInfo using @ref afwGeom.Box2D and convert the pixel positions of the bbox corners to sky coordinates using @ref skyInfo.wcs.pixelToSky. Use the @ref WcsSelectImagesTask_ “WcsSelectImagesTask” to select exposures that lie inside the patch indicated by the dataRef.
- @param[in] patchRef data reference for sky map patch. Must include keys “tract”, “patch”,
- plus the camera-specific filter key (e.g. “filter” or “band”)
@param[in] skyInfo geometry for the patch; output from getSkyInfo @return a list of science exposures to coadd, as butler data references
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timer
(name, logLevel=10000)¶ Context manager to log performance data for an arbitrary block of code.
Parameters: - name :
str
Name of code being timed; data will be logged using item name:
Start
andEnd
.- logLevel
A
lsst.log
level constant.
See also
timer.logInfo
Examples
Creating a timer context:
with self.timer("someCodeToTime"): pass # code to time
- name :
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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: -
True
: overwrite or rename the existing config, depending ondoBackup
. -False
: raiseTaskError
if this config does not match the existing config.- 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
.
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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: -
True
: overwrite or rename the existing version info, depending ondoBackup
. -False
: raiseTaskError
if this version info does not match the existing.- doBackup :
bool
, optional If
True
and clobbering, old package version files are backed up.- dataset :
str
, optional Name of dataset to read/write.
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.
- butler :
-
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: -
True
: overwrite or rename the existing schema, depending ondoBackup
. -False
: raiseTaskError
if this schema does not match the existing schema.- doBackup :
bool
, optional Set to
True
to backup the schema files if clobbering.
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.- butler :
-