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#!/usr/bin/env python # # LSST Data Management System # Copyright 2008-2015 AURA/LSST. # # This product includes software developed by the # LSST Project (http://www.lsst.org/). # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the LSST License Statement and # the GNU General Public License along with this program. If not, # see <https://www.lsstcorp.org/LegalNotices/>. # PipelineTask, PipelineTaskConfig, InitInputDatasetField, InitOutputDatasetField, InputDatasetField, OutputDatasetField)
""" New set types: * deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter) * deepCoadd_mergeDet: merged detections (tract, patch) * deepCoadd_meas: measurements of merged detections (tract, patch, filter) * deepCoadd_ref: reference sources (tract, patch) All of these have associated *_schema catalogs that require no data ID and hold no records.
In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in the mergeDet, meas, and ref dataset Footprints: * deepCoadd_peak_schema """
##############################################################################################################
"""! @anchor DetectCoaddSourcesConfig_
@brief Configuration parameters for the DetectCoaddSourcesTask """ doc="Run fake sources injection task") doc="Injection of fake sources for testing " "purposes (must be retargeted)") doc="Schema of the detection catalog", nameTemplate="{outputCoaddName}Coadd_det_schema", storageClass="SourceCatalog", ) doc="Exposure on which detections are to be performed", nameTemplate="{inputCoaddName}Coadd", scalar=True, storageClass="ExposureF", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") ) doc="Output Backgrounds used in detection", nameTemplate="{outputCoaddName}Coadd_calexp_background", scalar=True, storageClass="Background", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") ) doc="Detected sources catalog", nameTemplate="{outputCoaddName}Coadd_det", scalar=True, storageClass="SourceCatalog", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") ) doc="Exposure post detection", nameTemplate="{outputCoaddName}Coadd_calexp", scalar=True, storageClass="ExposureF", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") )
# Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic
## @addtogroup LSST_task_documentation ## @{ ## @page DetectCoaddSourcesTask ## @ref DetectCoaddSourcesTask_ "DetectCoaddSourcesTask" ## @copybrief DetectCoaddSourcesTask ## @}
r"""! @anchor DetectCoaddSourcesTask_
@brief Detect sources on a coadd
@section pipe_tasks_multiBand_Contents Contents
- @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example
@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
Command-line task that detects sources on a coadd of exposures obtained with a single filter.
Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane in the coadd to match the observed variance. This is an approximate approach -- strictly, we should propagate the full covariance matrix -- but it is simple and works well in practice.
After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref SourceDetectionTask_ "detection" subtask.
@par Inputs: deepCoadd{tract,patch,filter}: ExposureF @par Outputs: deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints) @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input exposure (ExposureF) @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList @par Data Unit: tract, patch, filter
DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask. You can retarget this subtask if you wish.
@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
@copydoc \_\_init\_\_
@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
@copydoc run
@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig"
@section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py files.
DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to @ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for @ref SourceDetectionTask_ "SourceDetectionTask" for further information.
@section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example of using DetectCoaddSourcesTask
DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of the task is to update the background, detect all sources in a single band and generate a set of parent footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and, eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data reference to the coadd to be processed. A list of the available optional arguments can be obtained by calling detectCoaddSources.py with the `--help` command line argument: @code detectCoaddSources.py --help @endcode
To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows: @code detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I @endcode that will process the HSC-I band data. The results are written to `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
It is also necessary to run: @code detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R @endcode to generate the sources catalogs for the HSC-R band required by the next step in the multi-band processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask". """
def _makeArgumentParser(cls): parser = ArgumentParser(name=cls._DefaultName) parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r", ContainerClass=ExistingCoaddDataIdContainer) return parser
"""! @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask.
Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
@param[in] schema: initial schema for the output catalog, modified-in place to include all fields set by this task. If None, the source minimal schema will be used. @param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__ """ # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree # call structure has been reviewed carefully to be sure super will work as intended. self.makeSubtask("insertFakes")
return {"detectionSchema": afwTable.SourceCatalog(self.schema)}
"""! @brief Run detection on a coadd.
Invokes @ref run and then uses @ref write to output the results.
@param[in] patchRef: data reference for patch """
packedId, maxBits = butler.registry.packDataId("TractPatchAbstractFilter", inputDataIds["exposure"], returnMaxBits=True) inputData["idFactory"] = afwTable.IdFactory.makeSource(packedId, 64 - maxBits) inputData["expId"] = packedId return self.run(**inputData)
"""! @brief Run detection on an exposure.
First scale the variance plane to match the observed variance using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to detect sources.
@param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled, depending on configuration). @param[in] idFactory: IdFactory to set source identifiers @param[in] expId: Exposure identifier (integer) for RNG seed
@return a pipe.base.Struct with fields - sources: catalog of detections - backgrounds: list of backgrounds """ self.insertFakes.run(exposure, background=backgrounds)
"""! @brief Write out results from runDetection.
@param[in] exposure: Exposure to write out @param[in] results: Struct returned from runDetection @param[in] patchRef: data reference for patch """
##############################################################################################################
"""DeblendCoaddSourcesConfig
Configuration parameters for the `DeblendCoaddSourcesTask`. """ doc="Deblend sources separately in each band") doc="Deblend sources simultaneously across bands")
"""Task runner for the `MergeSourcesTask`
Required because the run method requires a list of dataRefs rather than a single dataRef. """ def getTargetList(parsedCmd, **kwargs): """Provide a list of patch references for each patch, tract, filter combo.
Parameters ---------- parsedCmd: The parsed command kwargs: Keyword arguments passed to the task
Returns ------- targetList: list List of tuples, where each tuple is a (dataRef, kwargs) pair. """ refDict = MergeSourcesRunner.buildRefDict(parsedCmd) kwargs["psfCache"] = parsedCmd.psfCache return [(list(p.values()), kwargs) for t in refDict.values() for p in t.values()]
"""Deblend the sources in a merged catalog
Deblend sources from master catalog in each coadd. This can either be done separately in each band using the HSC-SDSS deblender (`DeblendCoaddSourcesTask.config.simultaneous==False`) or use SCARLET to simultaneously fit the blend in all bands (`DeblendCoaddSourcesTask.config.simultaneous==True`). The task will set its own `self.schema` atribute to the `Schema` of the output deblended catalog. This will include all fields from the input `Schema`, as well as additional fields from the deblender.
`pipe.tasks.multiband.DeblendCoaddSourcesTask Description --------------------------------------------------------- `
Parameters ---------- butler: `Butler` Butler used to read the input schemas from disk or construct the reference catalog loader, if `schema` or `peakSchema` or schema: `Schema` The schema of the merged detection catalog as an input to this task. peakSchema: `Schema` The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog """
def _makeArgumentParser(cls): parser = ArgumentParser(name=cls._DefaultName) parser.add_id_argument("--id", "deepCoadd_calexp", help="data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i", ContainerClass=ExistingCoaddDataIdContainer) parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache") return parser
self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema) else:
"""Return a dict of empty catalogs for each catalog dataset produced by this task.
Returns ------- result: dict Dictionary of empty catalogs, with catalog names as keys. """ self.config.coaddName + "Coadd_deblendedModel": catalog}
"""Deblend the patch
Deblend each source simultaneously or separately (depending on `DeblendCoaddSourcesTask.config.simultaneous`). Set `is-primary` and related flags. Propagate flags from individual visits. Write the deblended sources out.
Parameters ---------- patchRefList: list List of data references for each filter """ # Use SCARLET to simultaneously deblend across filters filters = [] exposures = [] for patchRef in patchRefList: exposure = patchRef.get(self.config.coaddName + "Coadd_calexp", immediate=True) filters.append(patchRef.dataId["filter"]) exposures.append(exposure) # The input sources are the same for all bands, since it is a merged catalog sources = self.readSources(patchRef) exposure = afwImage.MultibandExposure.fromExposures(filters, exposures) fluxCatalogs, templateCatalogs = self.multiBandDeblend.run(exposure, sources) for n in range(len(patchRefList)): self.write(patchRefList[n], fluxCatalogs[filters[n]], templateCatalogs[filters[n]]) else: # Use the singeband deblender to deblend each band separately
"""Read merged catalog
Read the catalog of merged detections and create a catalog in a single band.
Parameters ---------- dataRef: data reference Data reference for catalog of merged detections
Returns ------- sources: `SourceCatalog` List of sources in merged catalog
We also need to add columns to hold the measurements we're about to make so we can measure in-place. """
"""Write the source catalog(s)
Parameters ---------- dataRef: Data Reference Reference to the output catalog. flux_sources: `SourceCatalog` Flux conserved sources to write to file. If using the single band deblender, this is the catalog generated. template_sources: `SourceCatalog` Source catalog using the multiband template models as footprints. """ # The multiband deblender does not have to conserve flux, # so only write the flux conserved catalog if it exists # Only the multiband deblender has the option to output the # template model catalog, which can optionally be used # in MeasureMergedCoaddSources assert self.config.multiBandDeblend.saveTemplates dataRef.put(template_sources, self.config.coaddName + "Coadd_deblendedModel")
"""Write the metadata produced from processing the data. Parameters ---------- dataRefList List of Butler data references used to write the metadata. The metadata is written to dataset type `CmdLineTask._getMetadataName`. """ for dataRef in dataRefList: try: metadataName = self._getMetadataName() if metadataName is not None: dataRef.put(self.getFullMetadata(), metadataName) except Exception as e: self.log.warn("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
"""Get the ExposureId from a data reference """ return int(dataRef.get(self.config.coaddName + "CoaddId"))
"""! @anchor MeasureMergedCoaddSourcesConfig_
@brief Configuration parameters for the MeasureMergedCoaddSourcesTask """ doc=("Name of the input catalog to use." "If the single band deblender was used this should be 'deblendedFlux." "If the multi-band deblender was used this should be 'deblendedModel." "If no deblending was performed this should be 'mergeDet'")) dtype=bool, default=True, doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)" ) dtype=bool, default=False, doc=("Write reference matches in denormalized format? " "This format uses more disk space, but is more convenient to read."), ) doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'", dtype=str, default="raise", ) dtype=bool, default=True, doc="Apply aperture corrections" ) target=ApplyApCorrTask, doc="Subtask to apply aperture corrections" ) dtype=bool, default=True, doc='Run catalogCalculation task' ) target=CatalogCalculationTask, doc="Subtask to run catalogCalculation plugins on catalog" ) doc="Input schema for measure merged task produced by a deblender or detection task", nameTemplate="{inputCoaddName}Coadd_deblendedFlux_schema", storageClass="SourceCatalog" ) doc="Output schema after all new fields are added by task", nameTemplate="{inputCoaddName}Coadd_meas_schema", storageClass="SourceCatalog" ) doc="Reference catalog used to match measured sources against known sources", name="ref_cat", storageClass="SimpleCatalog", dimensions=("SkyPix",), manualLoad=True ) doc="Input coadd image", nameTemplate="{inputCoaddName}Coadd_calexp", scalar=True, storageClass="ExposureF", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap") ) doc="SkyMap to use in processing", nameTemplate="{inputCoaddName}Coadd_skyMap", storageClass="SkyMap", dimensions=("SkyMap",), scalar=True ) doc="Source catalogs for visits which overlap input tract, patch, abstract_filter. Will be " "further filtered in the task for the purpose of propagating flags from image calibration " "and characterization to codd objects", name="src", dimensions=("Instrument", "Visit", "Detector"), storageClass="SourceCatalog" ) doc=("Name of the input catalog to use." "If the single band deblender was used this should be 'deblendedFlux." "If the multi-band deblender was used this should be 'deblendedModel, " "or deblendedFlux if the multiband deblender was configured to output " "deblended flux catalogs. If no deblending was performed this should " "be 'mergeDet'"), nameTemplate="{inputCoaddName}Coadd_deblendedFlux", storageClass="SourceCatalog", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap"), scalar=True ) doc="Source catalog containing all the measurement information generated in this task", nameTemplate="{outputCoaddName}Coadd_meas", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap"), storageClass="SourceCatalog", scalar=True ) doc="Match catalog produced by configured matcher, optional on doMatchSources", nameTemplate="{outputCoaddName}Coadd_measMatch", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap"), storageClass="Catalog", scalar=True ) doc="Denormalized Match catalog produced by configured matcher, optional on " "doWriteMatchesDenormalized", nameTemplate="{outputCoaddName}Coadd_measMatchFull", dimensions=("Tract", "Patch", "AbstractFilter", "SkyMap"), storageClass="Catalog", scalar=True )
def refObjLoader(self): return self.match.refObjLoader
'INEXACT_PSF'] 'INEXACT_PSF']
## @addtogroup LSST_task_documentation ## @{ ## @page MeasureMergedCoaddSourcesTask ## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask" ## @copybrief MeasureMergedCoaddSourcesTask ## @}
"""Get the psfCache setting into MeasureMergedCoaddSourcesTask""" def getTargetList(parsedCmd, **kwargs): return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
r"""! @anchor MeasureMergedCoaddSourcesTask_
@brief Deblend sources from master catalog in each coadd seperately and measure.
@section pipe_tasks_multiBand_Contents Contents
- @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
Command-line task that uses peaks and footprints from a master catalog to perform deblending and measurement in each coadd.
Given a master input catalog of sources (peaks and footprints) or deblender outputs (including a HeavyFootprint in each band), measure each source on the coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a consistent set of child sources.
The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit flags are propagated to the coadd sources.
Optionally, we can match the coadd sources to an external reference catalog.
@par Inputs: deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog @n deepCoadd_calexp{tract,patch,filter}: ExposureF @par Outputs: deepCoadd_meas{tract,patch,filter}: SourceCatalog @par Data Unit: tract, patch, filter
MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
<DL> <DT> @ref SingleFrameMeasurementTask_ "measurement" <DD> Measure source properties of deblended sources.</DD> <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags" <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are not at the edge of the field and that have either not been deblended or are the children of deblended sources</DD> <DT> @ref PropagateVisitFlagsTask_ "propagateFlags" <DD> Propagate flags set in individual visits to the coadd.</DD> <DT> @ref DirectMatchTask_ "match" <DD> Match input sources to a reference catalog (optional). </DD> </DL> These subtasks may be retargeted as required.
@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
@copydoc \_\_init\_\_
@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
@copydoc run
@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
See @ref MeasureMergedCoaddSourcesConfig_
@section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py files.
MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to the various sub-tasks. See the documetation for individual sub-tasks for more information.
@section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using MeasureMergedCoaddSourcesTask
After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs. The next stage in the multi-band processing procedure will merge these measurements into a suitable catalog for driving forced photometry.
Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds to be processed. A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the `--help` command line argument: @code measureCoaddSources.py --help @endcode
To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band coadd as follows: @code measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I @endcode This will process the HSC-I band data. The results are written in `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
It is also necessary to run @code measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R @endcode to generate the sources catalogs for the HSC-R band required by the next step in the multi-band procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask". """
def _makeArgumentParser(cls): parser = ArgumentParser(name=cls._DefaultName) parser.add_id_argument("--id", "deepCoadd_calexp", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r", ContainerClass=ExistingCoaddDataIdContainer) parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache") return parser
**kwargs): """! @brief Initialize the task.
Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): @param[in] schema: the schema of the merged detection catalog used as input to this one @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference catalog. May be None if the loader can be constructed from the butler argument or all steps requiring a reference catalog are disabled. @param[in] butler: a butler used to read the input schemas from disk or construct the reference catalog loader, if schema or peakSchema or refObjLoader is None
The task will set its own self.schema attribute to the schema of the output measurement catalog. This will include all fields from the input schema, as well as additional fields for all the measurements. """ schema = initInputs['inputSchema'].schema self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
def getInputDatasetTypes(cls, config): inputDatasetTypes = super().getInputDatasetTypes(config) if not config.doPropagateFlags: inputDatasetTypes.pop("visitCatalogs") return inputDatasetTypes
def getOutputDatasetTypes(cls, config): outputDatasetTypes = super().getOutputDatasetTypes(config) if config.doMatchSources is False: outputDatasetTypes.pop("matchResult") if config.doWriteMatchesDenormalized is False: outputDatasetTypes.pop("denormMatches") return outputDatasetTypes
def getPrerequisiteDatasetTypes(cls, config): return frozenset(["refCat"])
return {"outputSchema": afwTable.SourceCatalog(self.schema)}
refObjLoader = ReferenceObjectLoader(inputDataIds['refCat'], butler, config=self.config.refObjLoader, log=self.log) self.match.setRefObjLoader(refObjLoader)
# Set psfcache # move this to run after gen2 deprecation inputData['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
# Get unique integer ID for IdFactory and RNG seeds packedId, maxBits = butler.registry.packDataId("TractPatch", outputDataIds["outputSources"], returnMaxBits=True) inputData['exposureId'] = packedId idFactory = afwTable.IdFactory.makeSource(packedId, 64 - maxBits) # Transform inputCatalog table = afwTable.SourceTable.make(self.schema, idFactory) sources = afwTable.SourceCatalog(table) sources.extend(inputData.pop('intakeCatalog'), self.schemaMapper) table = sources.getTable() table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog. inputData['sources'] = sources
skyMap = inputData.pop('skyMap') tractNumber = inputDataIds['intakeCatalog']['tract'] tractInfo = skyMap[tractNumber] patchInfo = tractInfo.getPatchInfo(inputDataIds['intakeCatalog']['patch']) skyInfo = Struct( skyMap=skyMap, tractInfo=tractInfo, patchInfo=patchInfo, wcs=tractInfo.getWcs(), bbox=patchInfo.getOuterBBox() ) inputData['skyInfo'] = skyInfo
if self.config.doPropagateFlags: # Filter out any visit catalog that is not coadd inputs ccdInputs = inputData['exposure'].getInfo().getCoaddInputs().ccds visitKey = ccdInputs.schema.find("visit").key ccdKey = ccdInputs.schema.find("ccd").key inputVisitIds = set() ccdRecordsWcs = {} for ccdRecord in ccdInputs: visit = ccdRecord.get(visitKey) ccd = ccdRecord.get(ccdKey) inputVisitIds.add((visit, ccd)) ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
inputCatalogsToKeep = [] inputCatalogWcsUpdate = [] for i, dataId in enumerate(inputDataIds['visitCatalogs']): key = (dataId['visit'], dataId['detector']) if key in inputVisitIds: inputCatalogsToKeep.append(inputData['visitCatalogs'][i]) inputCatalogWcsUpdate.append(ccdRecordsWcs[key]) inputData['visitCatalogs'] = inputCatalogsToKeep inputData['wcsUpdates'] = inputCatalogWcsUpdate inputData['ccdInputs'] = ccdInputs
return self.run(**inputData)
"""! @brief Deblend and measure.
@param[in] patchRef: Patch reference.
Set 'is-primary' and related flags. Propagate flags from individual visits. Optionally match the sources to a reference catalog and write the matches. Finally, write the deblended sources and measurements out. """
else: ccdInputs = None
ccdInputs=ccdInputs, skyInfo=skyInfo, butler=patchRef.getButler(), exposureId=self.getExposureId(patchRef))
self.writeMatches(patchRef, results)
butler=None): """Run measurement algorithms on the input exposure, and optionally populate the resulting catalog with extra information.
Parameters ---------- exposure : `lsst.afw.exposure.Exposure` The input exposure on which measurements are to be performed sources : `lsst.afw.table.SourceCatalog` A catalog built from the results of merged detections, or deblender outputs. skyInfo : `lsst.pipe.base.Struct` A struct containing information about the position of the input exposure within a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box exposureId : `int` or `bytes` packed unique number or bytes unique to the input exposure ccdInputs : `lsst.afw.table.ExposureCatalog` Catalog containing information on the individual visits which went into making the exposure visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None` A list of source catalogs corresponding to measurements made on the individual visits which went into the input exposure. If None and butler is `None` then the task cannot propagate visit flags to the output catalog. wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None` If visitCatalogs is not `None` this should be a list of wcs objects which correspond to the input visits. Used to put all coordinates to common system. If `None` and butler is `None` then the task cannot propagate visit flags to the output catalog. butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler` Either a gen2 or gen3 butler used to load visit catalogs
Returns ------- results : `lsst.pipe.base.Struct` Results of running measurement task. Will contain the catalog in the sources attribute. Optionally will have results of matching to a reference catalog in the matchResults attribute, and denormalized matches in the denormMatches attribute. """
catalog=sources, apCorrMap=exposure.getInfo().getApCorrMap() )
# TODO DM-11568: this contiguous check-and-copy could go away if we # reserve enough space during SourceDetection and/or SourceDeblend. # NOTE: sourceSelectors require contiguous catalogs, so ensure # contiguity now, so views are preserved from here on. sources = sources.copy(deep=True)
includeDeblend=self.deblended)
matchResult = self.match.run(sources, exposure.getInfo().getFilter().getName()) matches = afwTable.packMatches(matchResult.matches) matches.table.setMetadata(matchResult.matchMeta) results.matchResult = matches if self.config.doWriteMatchesDenormalized: results.denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
"""! @brief Read input sources.
@param[in] dataRef: Data reference for catalog of merged detections @return List of sources in merged catalog
We also need to add columns to hold the measurements we're about to make so we can measure in-place. """
"""! @brief Write matches of the sources to the astrometric reference catalog.
@param[in] dataRef: data reference @param[in] results: results struct from run method """ if hasattr(results, "matchResult"): dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch") if hasattr(results, "denormMatches"): dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
"""! @brief Write the source catalog.
@param[in] dataRef: data reference @param[in] sources: source catalog """
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