27from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner,
28 PipelineTask, PipelineTaskConfig, PipelineTaskConnections)
29import lsst.pipe.base.connectionTypes
as cT
32from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask
34from lsst.meas.extensions.scarlet
import ScarletDeblendTask
46from lsst.obs.base
import ExposureIdInfo
49from .mergeDetections
import MergeDetectionsConfig, MergeDetectionsTask
50from .mergeMeasurements
import MergeMeasurementsConfig, MergeMeasurementsTask
51from .multiBandUtils
import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs
52from .multiBandUtils
import getInputSchema, readCatalog, _makeMakeIdFactory
53from .deblendCoaddSourcesPipeline
import DeblendCoaddSourcesSingleConfig
54from .deblendCoaddSourcesPipeline
import DeblendCoaddSourcesSingleTask
55from .deblendCoaddSourcesPipeline
import DeblendCoaddSourcesMultiConfig
56from .deblendCoaddSourcesPipeline
import DeblendCoaddSourcesMultiTask
61* deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter)
62* deepCoadd_mergeDet: merged detections (tract, patch)
63* deepCoadd_meas: measurements of merged detections (tract, patch, filter)
64* deepCoadd_ref: reference sources (tract, patch)
65All of these have associated *_schema catalogs that require no data ID and hold no records.
67In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in
68the mergeDet, meas, and ref dataset Footprints:
69* deepCoadd_peak_schema
75 dimensions=(
"tract",
"patch",
"band",
"skymap"),
76 defaultTemplates={
"inputCoaddName":
"deep",
"outputCoaddName":
"deep"}):
77 detectionSchema = cT.InitOutput(
78 doc=
"Schema of the detection catalog",
79 name=
"{outputCoaddName}Coadd_det_schema",
80 storageClass=
"SourceCatalog",
83 doc=
"Exposure on which detections are to be performed",
84 name=
"{inputCoaddName}Coadd",
85 storageClass=
"ExposureF",
86 dimensions=(
"tract",
"patch",
"band",
"skymap")
88 outputBackgrounds = cT.Output(
89 doc=
"Output Backgrounds used in detection",
90 name=
"{outputCoaddName}Coadd_calexp_background",
91 storageClass=
"Background",
92 dimensions=(
"tract",
"patch",
"band",
"skymap")
94 outputSources = cT.Output(
95 doc=
"Detected sources catalog",
96 name=
"{outputCoaddName}Coadd_det",
97 storageClass=
"SourceCatalog",
98 dimensions=(
"tract",
"patch",
"band",
"skymap")
100 outputExposure = cT.Output(
101 doc=
"Exposure post detection",
102 name=
"{outputCoaddName}Coadd_calexp",
103 storageClass=
"ExposureF",
104 dimensions=(
"tract",
"patch",
"band",
"skymap")
108class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections):
110 @anchor DetectCoaddSourcesConfig_
112 @brief Configuration parameters
for the DetectCoaddSourcesTask
114 doScaleVariance = Field(dtype=bool, default=True, doc=
"Scale variance plane using empirical noise?")
115 scaleVariance = ConfigurableField(target=ScaleVarianceTask, doc=
"Variance rescaling")
116 detection = ConfigurableField(target=DynamicDetectionTask, doc=
"Source detection")
117 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
118 doInsertFakes = Field(dtype=bool, default=
False,
119 doc=
"Run fake sources injection task")
120 insertFakes = ConfigurableField(target=BaseFakeSourcesTask,
121 doc=
"Injection of fake sources for testing "
122 "purposes (must be retargeted)")
126 doc=
"Should be set to True if fake sources have been inserted into the input data."
129 def setDefaults(self):
130 super().setDefaults()
131 self.detection.thresholdType =
"pixel_stdev"
132 self.detection.isotropicGrow =
True
134 self.detection.reEstimateBackground =
False
135 self.detection.background.useApprox =
False
136 self.detection.background.binSize = 4096
137 self.detection.background.undersampleStyle =
'REDUCE_INTERP_ORDER'
138 self.detection.doTempWideBackground =
True
148class DetectCoaddSourcesTask(PipelineTask, CmdLineTask):
150 @anchor DetectCoaddSourcesTask_
152 @brief Detect sources on a coadd
154 @section pipe_tasks_multiBand_Contents Contents
156 -
@ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose
157 -
@ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize
158 -
@ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run
159 -
@ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config
160 -
@ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug
161 -
@ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example
163 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
165 Command-line task that detects sources on a coadd of exposures obtained
with a single filter.
167 Coadding individual visits requires each exposure to be warped. This introduces covariance
in the noise
168 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane
169 in the coadd to match the observed variance. This
is an approximate approach -- strictly, we should
170 propagate the full covariance matrix -- but it
is simple
and works well
in practice.
172 After scaling the variance plane, we detect sources
and generate footprints by delegating to the
@ref
173 SourceDetectionTask_
"detection" subtask.
176 deepCoadd{tract,patch,filter}: ExposureF
178 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
179 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input
181 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList
185 DetectCoaddSourcesTask delegates most of its work to the
@ref SourceDetectionTask_
"detection" subtask.
186 You can retarget this subtask
if you wish.
188 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
190 @copydoc \_\_init\_\_
192 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
196 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
198 See
@ref DetectCoaddSourcesConfig_
"DetectSourcesConfig"
200 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
202 The
@link lsst.pipe.base.cmdLineTask.CmdLineTask command line task
@endlink interface supports a
203 flag
@c -d to
import @b debug.py
from your
@c PYTHONPATH; see
@ref baseDebug
for more about
@b debug.py
206 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to
207 @ref SourceDetectionTask_
"SourceDetectionTask"; see the documetation
for
208 @ref SourceDetectionTask_
"SourceDetectionTask" for further information.
210 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example
211 of using DetectCoaddSourcesTask
213 DetectCoaddSourcesTask
is meant to be run after assembling a coadded image
in a given band. The purpose of
214 the task
is to update the background, detect all sources
in a single band
and generate a set of parent
215 footprints. Subsequent tasks
in the multi-band processing procedure will merge sources across bands
and,
216 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data
217 reference to the coadd to be processed. A list of the available optional arguments can be obtained by
218 calling detectCoaddSources.py
with the `--help` command line argument:
220 detectCoaddSources.py --help
223 To demonstrate usage of the DetectCoaddSourcesTask
in the larger context of multi-band processing, we
224 will process HSC data
in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed
225 steps 1 - 4 at
@ref pipeTasks_multiBand, one may detect all the sources
in each coadd
as follows:
227 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
229 that will process the HSC-I band data. The results are written to
230 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
232 It
is also necessary to run:
234 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
236 to generate the sources catalogs
for the HSC-R band required by the next step
in the multi-band
237 processing procedure:
@ref MergeDetectionsTask_
"MergeDetectionsTask".
239 _DefaultName = "detectCoaddSources"
240 ConfigClass = DetectCoaddSourcesConfig
241 getSchemaCatalogs = _makeGetSchemaCatalogs(
"det")
242 makeIdFactory = _makeMakeIdFactory(
"CoaddId")
245 def _makeArgumentParser(cls):
246 parser = ArgumentParser(name=cls._DefaultName)
247 parser.add_id_argument(
"--id",
"deepCoadd", help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=r",
248 ContainerClass=ExistingCoaddDataIdContainer)
251 def __init__(self, schema=None, **kwargs):
253 @brief Initialize the task. Create the
@ref SourceDetectionTask_
"detection" subtask.
255 Keyword arguments (
in addition to those forwarded to CmdLineTask.__init__):
257 @param[
in] schema: initial schema
for the output catalog, modified-
in place to include all
258 fields set by this task. If
None, the source minimal schema will be used.
259 @param[
in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__
263 super().__init__(**kwargs)
265 schema = afwTable.SourceTable.makeMinimalSchema()
266 if self.config.doInsertFakes:
267 self.makeSubtask(
"insertFakes")
269 self.makeSubtask(
"detection", schema=self.schema)
270 if self.config.doScaleVariance:
271 self.makeSubtask(
"scaleVariance")
273 self.detectionSchema = afwTable.SourceCatalog(self.schema)
275 def runDataRef(self, patchRef):
277 @brief Run detection on a coadd.
279 Invokes
@ref run
and then uses
@ref write to output the
282 @param[
in] patchRef: data reference
for patch
284 if self.config.hasFakes:
285 exposure = patchRef.get(
"fakes_" + self.config.coaddName +
"Coadd", immediate=
True)
287 exposure = patchRef.get(self.config.coaddName +
"Coadd", immediate=
True)
288 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, log=self.log)
289 results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId)
290 self.write(results, patchRef)
293 def runQuantum(self, butlerQC, inputRefs, outputRefs):
294 inputs = butlerQC.get(inputRefs)
295 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId,
"tract_patch_band")
296 inputs[
"idFactory"] = exposureIdInfo.makeSourceIdFactory()
297 inputs[
"expId"] = exposureIdInfo.expId
298 outputs = self.run(**inputs)
299 butlerQC.put(outputs, outputRefs)
301 def run(self, exposure, idFactory, expId):
303 @brief Run detection on an exposure.
305 First scale the variance plane to match the observed variance
306 using
@ref ScaleVarianceTask. Then invoke the
@ref SourceDetectionTask_
"detection" subtask to
309 @param[
in,out] exposure: Exposure on which to detect (may be backround-subtracted
and scaled,
310 depending on configuration).
311 @param[
in] idFactory: IdFactory to set source identifiers
312 @param[
in] expId: Exposure identifier (integer)
for RNG seed
314 @return a pipe.base.Struct
with fields
315 - sources: catalog of detections
316 - backgrounds: list of backgrounds
318 if self.config.doScaleVariance:
319 varScale = self.scaleVariance.run(exposure.maskedImage)
320 exposure.getMetadata().add(
"VARIANCE_SCALE", varScale)
321 backgrounds = afwMath.BackgroundList()
322 if self.config.doInsertFakes:
323 self.insertFakes.run(exposure, background=backgrounds)
324 table = afwTable.SourceTable.make(self.schema, idFactory)
325 detections = self.detection.run(table, exposure, expId=expId)
326 sources = detections.sources
327 fpSets = detections.fpSets
328 if hasattr(fpSets,
"background")
and fpSets.background:
329 for bg
in fpSets.background:
330 backgrounds.append(bg)
331 return Struct(outputSources=sources, outputBackgrounds=backgrounds, outputExposure=exposure)
333 def write(self, results, patchRef):
335 @brief Write out results
from runDetection.
337 @param[
in] exposure: Exposure to write out
338 @param[
in] results: Struct returned
from runDetection
339 @param[
in] patchRef: data reference
for patch
341 coaddName = self.config.coaddName + "Coadd"
342 patchRef.put(results.outputBackgrounds, coaddName +
"_calexp_background")
343 patchRef.put(results.outputSources, coaddName +
"_det")
344 if self.config.hasFakes:
345 patchRef.put(results.outputExposure,
"fakes_" + coaddName +
"_calexp")
347 patchRef.put(results.outputExposure, coaddName +
"_calexp")
352class DeblendCoaddSourcesConfig(Config):
353 """DeblendCoaddSourcesConfig
355 Configuration parameters for the `DeblendCoaddSourcesTask`.
357 singleBandDeblend = ConfigurableField(target=SourceDeblendTask,
358 doc="Deblend sources separately in each band")
359 multiBandDeblend = ConfigurableField(target=ScarletDeblendTask,
360 doc=
"Deblend sources simultaneously across bands")
361 simultaneous = Field(dtype=bool,
363 doc=
"Simultaneously deblend all bands? "
364 "True uses `multibandDeblend` while False uses `singleBandDeblend`")
365 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
366 hasFakes = Field(dtype=bool,
368 doc=
"Should be set to True if fake sources have been inserted into the input data.")
370 def setDefaults(self):
371 Config.setDefaults(self)
372 self.singleBandDeblend.propagateAllPeaks =
True
376 """Task runner for the `MergeSourcesTask`
378 Required because the run method requires a list of
379 dataRefs rather than a single dataRef.
382 def getTargetList(parsedCmd, **kwargs):
383 """Provide a list of patch references for each patch, tract, filter combo.
390 Keyword arguments passed to the task
395 List of tuples, where each tuple is a (dataRef, kwargs) pair.
397 refDict = MergeSourcesRunner.buildRefDict(parsedCmd)
398 kwargs["psfCache"] = parsedCmd.psfCache
399 return [(list(p.values()), kwargs)
for t
in refDict.values()
for p
in t.values()]
402class DeblendCoaddSourcesTask(CmdLineTask):
403 """Deblend the sources in a merged catalog
405 Deblend sources from master catalog
in each coadd.
406 This can either be done separately
in each band using the HSC-SDSS deblender
407 (`DeblendCoaddSourcesTask.config.simultaneous==
False`)
408 or use SCARLET to simultaneously fit the blend
in all bands
409 (`DeblendCoaddSourcesTask.config.simultaneous==
True`).
410 The task will set its own `self.schema` atribute to the `Schema` of the
411 output deblended catalog.
412 This will include all fields
from the input `Schema`,
as well
as additional fields
415 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description
416 ---------------------------------------------------------
422 Butler used to read the input schemas
from disk
or
423 construct the reference catalog loader,
if `schema`
or `peakSchema`
or
425 The schema of the merged detection catalog
as an input to this task.
427 The schema of the `PeakRecord`s
in the `Footprint`s
in the merged detection catalog
429 ConfigClass = DeblendCoaddSourcesConfig
430 RunnerClass = DeblendCoaddSourcesRunner
431 _DefaultName = "deblendCoaddSources"
432 makeIdFactory = _makeMakeIdFactory(
"MergedCoaddId", includeBand=
False)
435 def _makeArgumentParser(cls):
436 parser = ArgumentParser(name=cls._DefaultName)
437 parser.add_id_argument(
"--id",
"deepCoadd_calexp",
438 help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i",
439 ContainerClass=ExistingCoaddDataIdContainer)
440 parser.add_argument(
"--psfCache", type=int, default=100, help=
"Size of CoaddPsf cache")
443 def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs):
444 CmdLineTask.__init__(self, **kwargs)
446 assert butler
is not None,
"Neither butler nor schema is defined"
447 schema = butler.get(self.config.coaddName +
"Coadd_mergeDet_schema", immediate=
True).schema
448 self.schemaMapper = afwTable.SchemaMapper(schema)
449 self.schemaMapper.addMinimalSchema(schema)
450 self.schema = self.schemaMapper.getOutputSchema()
451 if peakSchema
is None:
452 assert butler
is not None,
"Neither butler nor peakSchema is defined"
453 peakSchema = butler.get(self.config.coaddName +
"Coadd_peak_schema", immediate=
True).schema
455 if self.config.simultaneous:
456 self.makeSubtask(
"multiBandDeblend", schema=self.schema, peakSchema=peakSchema)
458 self.makeSubtask(
"singleBandDeblend", schema=self.schema, peakSchema=peakSchema)
460 def getSchemaCatalogs(self):
461 """Return a dict of empty catalogs for each catalog dataset produced by this task.
466 Dictionary of empty catalogs, with catalog names
as keys.
468 catalog = afwTable.SourceCatalog(self.schema)
469 return {self.config.coaddName +
"Coadd_deblendedFlux": catalog,
470 self.config.coaddName +
"Coadd_deblendedModel": catalog}
472 def runDataRef(self, patchRefList, psfCache=100):
475 Deblend each source simultaneously or separately
476 (depending on `DeblendCoaddSourcesTask.config.simultaneous`).
477 Set `
is-primary`
and related flags.
478 Propagate flags
from individual visits.
479 Write the deblended sources out.
484 List of data references
for each filter
487 if self.config.hasFakes:
488 coaddType =
"fakes_" + self.config.coaddName
490 coaddType = self.config.coaddName
492 if self.config.simultaneous:
496 for patchRef
in patchRefList:
497 exposure = patchRef.get(coaddType +
"Coadd_calexp", immediate=
True)
498 filter = patchRef.get(coaddType +
"Coadd_filterLabel", immediate=
True)
499 filters.append(filter.bandLabel)
500 exposures.append(exposure)
502 exposures = [exposure
for _, exposure
in sorted(zip(filters, exposures))]
503 patchRefList = [patchRef
for _, patchRef
in sorted(zip(filters, patchRefList))]
506 sources = self.readSources(patchRef)
507 exposure = afwImage.MultibandExposure.fromExposures(filters, exposures)
508 templateCatalogs, fluxCatalogs = self.multiBandDeblend.run(exposure, sources)
509 for n
in range(len(patchRefList)):
510 self.write(patchRefList[n], templateCatalogs[filters[n]],
"Model")
511 if filters[n]
in fluxCatalogs:
512 self.write(patchRefList[n], fluxCatalogs[filters[n]],
"Flux")
515 for patchRef
in patchRefList:
516 exposure = patchRef.get(coaddType +
"Coadd_calexp", immediate=
True)
517 exposure.getPsf().setCacheCapacity(psfCache)
518 sources = self.readSources(patchRef)
519 self.singleBandDeblend.run(exposure, sources)
520 self.write(patchRef, sources)
522 def readSources(self, dataRef):
523 """Read merged catalog
525 Read the catalog of merged detections and create a catalog
530 dataRef: data reference
531 Data reference
for catalog of merged detections
535 sources: `SourceCatalog`
536 List of sources
in merged catalog
538 We also need to add columns to hold the measurements we
're about to make so we can measure in-place.
540 merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=
True)
541 self.log.info(
"Read %d detections: %s", len(merged), dataRef.dataId)
542 idFactory = self.makeIdFactory(dataRef)
546 maxId = np.max(merged[
"id"])
547 idFactory.notify(maxId)
548 table = afwTable.SourceTable.make(self.schema, idFactory)
549 sources = afwTable.SourceCatalog(table)
550 sources.extend(merged, self.schemaMapper)
553 def write(self, dataRef, sources, catalogType):
554 """Write the source catalog(s)
558 dataRef: Data Reference
559 Reference to the output catalog.
560 sources: `SourceCatalog`
561 Flux conserved sources to write to file.
562 If using the single band deblender, this is the catalog
564 template_sources: `SourceCatalog`
565 Source catalog using the multiband template models
568 dataRef.put(sources, self.config.coaddName + f"Coadd_deblended{catalogType}")
569 self.log.info(
"Wrote %d sources: %s", len(sources), dataRef.dataId)
572 """Write the metadata produced from processing the data.
576 List of Butler data references used to write the metadata.
577 The metadata is written to dataset type `CmdLineTask._getMetadataName`.
579 for dataRef
in dataRefList:
581 metadataName = self._getMetadataName()
582 if metadataName
is not None:
583 dataRef.put(self.getFullMetadata(), metadataName)
584 except Exception
as e:
585 self.log.warning(
"Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
588class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections,
589 dimensions=(
"tract",
"patch",
"band",
"skymap"),
590 defaultTemplates={
"inputCoaddName":
"deep",
591 "outputCoaddName":
"deep"}):
592 inputSchema = cT.InitInput(
593 doc=
"Input schema for measure merged task produced by a deblender or detection task",
594 name=
"{inputCoaddName}Coadd_deblendedFlux_schema",
595 storageClass=
"SourceCatalog"
597 outputSchema = cT.InitOutput(
598 doc=
"Output schema after all new fields are added by task",
599 name=
"{inputCoaddName}Coadd_meas_schema",
600 storageClass=
"SourceCatalog"
602 refCat = cT.PrerequisiteInput(
603 doc=
"Reference catalog used to match measured sources against known sources",
605 storageClass=
"SimpleCatalog",
606 dimensions=(
"skypix",),
611 doc=
"Input coadd image",
612 name=
"{inputCoaddName}Coadd_calexp",
613 storageClass=
"ExposureF",
614 dimensions=(
"tract",
"patch",
"band",
"skymap")
617 doc=
"SkyMap to use in processing",
618 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
619 storageClass=
"SkyMap",
620 dimensions=(
"skymap",),
622 visitCatalogs = cT.Input(
623 doc=
"Source catalogs for visits which overlap input tract, patch, band. Will be "
624 "further filtered in the task for the purpose of propagating flags from image calibration "
625 "and characterization to codd objects",
627 dimensions=(
"instrument",
"visit",
"detector"),
628 storageClass=
"SourceCatalog",
631 inputCatalog = cT.Input(
632 doc=(
"Name of the input catalog to use."
633 "If the single band deblender was used this should be 'deblendedFlux."
634 "If the multi-band deblender was used this should be 'deblendedModel, "
635 "or deblendedFlux if the multiband deblender was configured to output "
636 "deblended flux catalogs. If no deblending was performed this should "
638 name=
"{inputCoaddName}Coadd_deblendedFlux",
639 storageClass=
"SourceCatalog",
640 dimensions=(
"tract",
"patch",
"band",
"skymap"),
642 outputSources = cT.Output(
643 doc=
"Source catalog containing all the measurement information generated in this task",
644 name=
"{outputCoaddName}Coadd_meas",
645 dimensions=(
"tract",
"patch",
"band",
"skymap"),
646 storageClass=
"SourceCatalog",
648 matchResult = cT.Output(
649 doc=
"Match catalog produced by configured matcher, optional on doMatchSources",
650 name=
"{outputCoaddName}Coadd_measMatch",
651 dimensions=(
"tract",
"patch",
"band",
"skymap"),
652 storageClass=
"Catalog",
654 denormMatches = cT.Output(
655 doc=
"Denormalized Match catalog produced by configured matcher, optional on "
656 "doWriteMatchesDenormalized",
657 name=
"{outputCoaddName}Coadd_measMatchFull",
658 dimensions=(
"tract",
"patch",
"band",
"skymap"),
659 storageClass=
"Catalog",
662 def __init__(self, *, config=None):
663 super().__init__(config=config)
664 if config.doPropagateFlags
is False:
665 self.inputs -= set((
"visitCatalogs",))
667 if config.doMatchSources
is False:
668 self.outputs -= set((
"matchResult",))
670 if config.doWriteMatchesDenormalized
is False:
671 self.outputs -= set((
"denormMatches",))
674class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
675 pipelineConnections=MeasureMergedCoaddSourcesConnections):
677 @anchor MeasureMergedCoaddSourcesConfig_
679 @brief Configuration parameters
for the MeasureMergedCoaddSourcesTask
681 inputCatalog = Field(dtype=str, default="deblendedFlux",
682 doc=(
"Name of the input catalog to use."
683 "If the single band deblender was used this should be 'deblendedFlux."
684 "If the multi-band deblender was used this should be 'deblendedModel."
685 "If no deblending was performed this should be 'mergeDet'"))
686 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc=
"Source measurement")
687 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc=
"Set flags for primary tract/patch")
688 doPropagateFlags = Field(
689 dtype=bool, default=
True,
690 doc=
"Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
692 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc=
"Propagate visit flags to coadd")
693 doMatchSources = Field(dtype=bool, default=
True, doc=
"Match sources to reference catalog?")
694 match = ConfigurableField(target=DirectMatchTask, doc=
"Matching to reference catalog")
695 doWriteMatchesDenormalized = Field(
698 doc=(
"Write reference matches in denormalized format? "
699 "This format uses more disk space, but is more convenient to read."),
701 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
702 psfCache = Field(dtype=int, default=100, doc=
"Size of psfCache")
703 checkUnitsParseStrict = Field(
704 doc=
"Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
711 doc=
"Apply aperture corrections"
713 applyApCorr = ConfigurableField(
714 target=ApplyApCorrTask,
715 doc=
"Subtask to apply aperture corrections"
717 doRunCatalogCalculation = Field(
720 doc=
'Run catalogCalculation task'
722 catalogCalculation = ConfigurableField(
723 target=CatalogCalculationTask,
724 doc=
"Subtask to run catalogCalculation plugins on catalog"
730 doc=
"Should be set to True if fake sources have been inserted into the input data."
734 def refObjLoader(self):
735 return self.match.refObjLoader
737 def setDefaults(self):
738 super().setDefaults()
739 self.measurement.plugins.names |= [
'base_InputCount',
741 'base_LocalPhotoCalib',
743 self.measurement.plugins[
'base_PixelFlags'].masksFpAnywhere = [
'CLIPPED',
'SENSOR_EDGE',
745 self.measurement.plugins[
'base_PixelFlags'].masksFpCenter = [
'CLIPPED',
'SENSOR_EDGE',
750 refCatGen2 = getattr(self.refObjLoader,
"ref_dataset_name",
None)
751 if refCatGen2
is not None and refCatGen2 != self.connections.refCat:
753 f
"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
754 f
"are different. These options must be kept in sync until Gen2 is retired."
766class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
767 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
769 def getTargetList(parsedCmd, **kwargs):
770 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
773class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
775 @anchor MeasureMergedCoaddSourcesTask_
777 @brief Deblend sources
from master catalog
in each coadd seperately
and measure.
779 @section pipe_tasks_multiBand_Contents Contents
781 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
782 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
783 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
784 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
785 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
786 -
@ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
788 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
790 Command-line task that uses peaks
and footprints
from a master catalog to perform deblending
and
791 measurement
in each coadd.
793 Given a master input catalog of sources (peaks
and footprints)
or deblender outputs
794 (including a HeavyFootprint
in each band), measure each source on the
795 coadd. Repeating this procedure
with the same master catalog across multiple coadds will generate a
796 consistent set of child sources.
798 The deblender retains all peaks
and deblends any missing peaks (dropouts
in that band)
as PSFs. Source
799 properties are measured
and the
@c is-primary flag (indicating sources
with no children)
is set. Visit
800 flags are propagated to the coadd sources.
802 Optionally, we can match the coadd sources to an external reference catalog.
805 deepCoadd_mergeDet{tract,patch}
or deepCoadd_deblend{tract,patch}: SourceCatalog
806 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
808 deepCoadd_meas{tract,patch,filter}: SourceCatalog
812 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
815 <DT>
@ref SingleFrameMeasurementTask_
"measurement"
816 <DD> Measure source properties of deblended sources.</DD>
817 <DT>
@ref SetPrimaryFlagsTask_
"setPrimaryFlags"
818 <DD> Set flag
'is-primary' as well
as related flags on sources.
'is-primary' is set
for sources that are
819 not at the edge of the field
and that have either
not been deblended
or are the children of deblended
821 <DT>
@ref PropagateVisitFlagsTask_
"propagateFlags"
822 <DD> Propagate flags set
in individual visits to the coadd.</DD>
823 <DT>
@ref DirectMatchTask_
"match"
824 <DD> Match input sources to a reference catalog (optional).
827 These subtasks may be retargeted
as required.
829 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
831 @copydoc \_\_init\_\_
833 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
837 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
839 See
@ref MeasureMergedCoaddSourcesConfig_
841 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
843 The
@link lsst.pipe.base.cmdLineTask.CmdLineTask command line task
@endlink interface supports a
844 flag
@c -d to
import @b debug.py
from your
@c PYTHONPATH; see
@ref baseDebug
for more about
@b debug.py
847 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
848 the various sub-tasks. See the documetation
for individual sub-tasks
for more information.
850 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
851 MeasureMergedCoaddSourcesTask
853 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
854 The next stage
in the multi-band processing procedure will merge these measurements into a suitable
855 catalog
for driving forced photometry.
857 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
859 A list of the available optional arguments can be obtained by calling measureCoaddSources.py
with the
860 `--help` command line argument:
862 measureCoaddSources.py --help
865 To demonstrate usage of the DetectCoaddSourcesTask
in the larger context of multi-band processing, we
866 will process HSC data
in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
867 step 6 at
@ref pipeTasks_multiBand, one may perform deblending
and measure sources
in the HSC-I band
870 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
872 This will process the HSC-I band data. The results are written
in
873 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
875 It
is also necessary to run
877 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
879 to generate the sources catalogs
for the HSC-R band required by the next step
in the multi-band
880 procedure:
@ref MergeMeasurementsTask_
"MergeMeasurementsTask".
882 _DefaultName = "measureCoaddSources"
883 ConfigClass = MeasureMergedCoaddSourcesConfig
884 RunnerClass = MeasureMergedCoaddSourcesRunner
885 getSchemaCatalogs = _makeGetSchemaCatalogs(
"meas")
887 makeIdFactory = _makeMakeIdFactory(
"MergedCoaddId", includeBand=
False)
890 def _makeArgumentParser(cls):
891 parser = ArgumentParser(name=cls._DefaultName)
892 parser.add_id_argument(
"--id",
"deepCoadd_calexp",
893 help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=r",
894 ContainerClass=ExistingCoaddDataIdContainer)
895 parser.add_argument(
"--psfCache", type=int, default=100, help=
"Size of CoaddPsf cache")
898 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
901 @brief Initialize the task.
903 Keyword arguments (
in addition to those forwarded to CmdLineTask.__init__):
904 @param[
in] schema: the schema of the merged detection catalog used
as input to this one
905 @param[
in] peakSchema: the schema of the PeakRecords
in the Footprints
in the merged detection catalog
906 @param[
in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
907 catalog. May be
None if the loader can be constructed
from the butler argument
or all steps
908 requiring a reference catalog are disabled.
909 @param[
in] butler: a butler used to read the input schemas
from disk
or construct the reference
910 catalog loader,
if schema
or peakSchema
or refObjLoader
is None
912 The task will set its own self.schema attribute to the schema of the output measurement catalog.
913 This will include all fields
from the input schema,
as well
as additional fields
for all the
916 super().__init__(**kwargs)
917 self.deblended = self.config.inputCatalog.startswith("deblended")
918 self.inputCatalog =
"Coadd_" + self.config.inputCatalog
919 if initInputs
is not None:
920 schema = initInputs[
'inputSchema'].schema
922 assert butler
is not None,
"Neither butler nor schema is defined"
923 schema = butler.get(self.config.coaddName + self.inputCatalog +
"_schema", immediate=
True).schema
924 self.schemaMapper = afwTable.SchemaMapper(schema)
925 self.schemaMapper.addMinimalSchema(schema)
926 self.schema = self.schemaMapper.getOutputSchema()
928 self.makeSubtask(
"measurement", schema=self.schema, algMetadata=self.algMetadata)
929 self.makeSubtask(
"setPrimaryFlags", schema=self.schema)
930 if self.config.doMatchSources:
931 self.makeSubtask(
"match", butler=butler, refObjLoader=refObjLoader)
932 if self.config.doPropagateFlags:
933 self.makeSubtask(
"propagateFlags", schema=self.schema)
934 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
935 if self.config.doApCorr:
936 self.makeSubtask(
"applyApCorr", schema=self.schema)
937 if self.config.doRunCatalogCalculation:
938 self.makeSubtask(
"catalogCalculation", schema=self.schema)
940 self.outputSchema = afwTable.SourceCatalog(self.schema)
942 def runQuantum(self, butlerQC, inputRefs, outputRefs):
943 inputs = butlerQC.get(inputRefs)
945 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId
for ref
in inputRefs.refCat],
946 inputs.pop(
'refCat'), config=self.config.refObjLoader,
948 self.match.setRefObjLoader(refObjLoader)
952 inputs[
'exposure'].getPsf().setCacheCapacity(self.config.psfCache)
955 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId,
"tract_patch")
956 inputs[
'exposureId'] = exposureIdInfo.expId
957 idFactory = exposureIdInfo.makeSourceIdFactory()
959 table = afwTable.SourceTable.make(self.schema, idFactory)
960 sources = afwTable.SourceCatalog(table)
961 sources.extend(inputs.pop(
'inputCatalog'), self.schemaMapper)
962 table = sources.getTable()
963 table.setMetadata(self.algMetadata)
964 inputs[
'sources'] = sources
966 skyMap = inputs.pop(
'skyMap')
967 tractNumber = inputRefs.inputCatalog.dataId[
'tract']
968 tractInfo = skyMap[tractNumber]
969 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId[
'patch'])
974 wcs=tractInfo.getWcs(),
975 bbox=patchInfo.getOuterBBox()
977 inputs[
'skyInfo'] = skyInfo
979 if self.config.doPropagateFlags:
981 ccdInputs = inputs[
'exposure'].getInfo().getCoaddInputs().ccds
982 visitKey = ccdInputs.schema.find(
"visit").key
983 ccdKey = ccdInputs.schema.find(
"ccd").key
984 inputVisitIds = set()
986 for ccdRecord
in ccdInputs:
987 visit = ccdRecord.get(visitKey)
988 ccd = ccdRecord.get(ccdKey)
989 inputVisitIds.add((visit, ccd))
990 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
992 inputCatalogsToKeep = []
993 inputCatalogWcsUpdate = []
994 for i, dataRef
in enumerate(inputRefs.visitCatalogs):
995 key = (dataRef.dataId[
'visit'], dataRef.dataId[
'detector'])
996 if key
in inputVisitIds:
997 inputCatalogsToKeep.append(inputs[
'visitCatalogs'][i])
998 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
999 inputs[
'visitCatalogs'] = inputCatalogsToKeep
1000 inputs[
'wcsUpdates'] = inputCatalogWcsUpdate
1001 inputs[
'ccdInputs'] = ccdInputs
1003 outputs = self.run(**inputs)
1004 butlerQC.put(outputs, outputRefs)
1006 def runDataRef(self, patchRef, psfCache=100):
1008 @brief Deblend
and measure.
1010 @param[
in] patchRef: Patch reference.
1012 Set
'is-primary' and related flags. Propagate flags
1013 from individual visits. Optionally match the sources to a reference catalog
and write the matches.
1014 Finally, write the deblended sources
and measurements out.
1016 if self.config.hasFakes:
1017 coaddType =
"fakes_" + self.config.coaddName
1019 coaddType = self.config.coaddName
1020 exposure = patchRef.get(coaddType +
"Coadd_calexp", immediate=
True)
1021 exposure.getPsf().setCacheCapacity(psfCache)
1022 sources = self.readSources(patchRef)
1023 table = sources.getTable()
1024 table.setMetadata(self.algMetadata)
1025 skyInfo =
getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1027 if self.config.doPropagateFlags:
1028 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1032 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=
False,
1034 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId,
1035 ccdInputs=ccdInputs, butler=patchRef.getButler())
1037 if self.config.doMatchSources:
1038 self.writeMatches(patchRef, results)
1039 self.write(patchRef, results.outputSources)
1041 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1043 """Run measurement algorithms on the input exposure, and optionally populate the
1044 resulting catalog with extra information.
1048 exposure : `lsst.afw.exposure.Exposure`
1049 The input exposure on which measurements are to be performed
1051 A catalog built
from the results of merged detections,
or
1053 skyInfo : `lsst.pipe.base.Struct`
1054 A struct containing information about the position of the input exposure within
1055 a `SkyMap`, the `SkyMap`, its `Wcs`,
and its bounding box
1056 exposureId : `int`
or `bytes`
1057 packed unique number
or bytes unique to the input exposure
1059 Catalog containing information on the individual visits which went into making
1061 visitCatalogs : list of `lsst.afw.table.SourceCatalogs`
or `
None`
1062 A list of source catalogs corresponding to measurements made on the individual
1063 visits which went into the input exposure. If
None and butler
is `
None` then
1064 the task cannot propagate visit flags to the output catalog.
1066 If visitCatalogs
is not `
None` this should be a list of wcs objects which correspond
1067 to the input visits. Used to put all coordinates to common system. If `
None`
and
1068 butler
is `
None` then the task cannot propagate visit flags to the output catalog.
1069 butler : `lsst.daf.butler.Butler`
or `lsst.daf.persistence.Butler`
1070 Either a gen2
or gen3 butler used to load visit catalogs
1074 results : `lsst.pipe.base.Struct`
1075 Results of running measurement task. Will contain the catalog
in the
1076 sources attribute. Optionally will have results of matching to a
1077 reference catalog
in the matchResults attribute,
and denormalized
1078 matches
in the denormMatches attribute.
1080 self.measurement.run(sources, exposure, exposureId=exposureId)
1082 if self.config.doApCorr:
1083 self.applyApCorr.run(
1085 apCorrMap=exposure.getInfo().getApCorrMap()
1092 if not sources.isContiguous():
1093 sources = sources.copy(deep=
True)
1095 if self.config.doRunCatalogCalculation:
1096 self.catalogCalculation.run(sources)
1098 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1099 patchInfo=skyInfo.patchInfo)
1100 if self.config.doPropagateFlags:
1101 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates)
1105 if self.config.doMatchSources:
1106 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel)
1107 matches = afwTable.packMatches(matchResult.matches)
1108 matches.table.setMetadata(matchResult.matchMeta)
1109 results.matchResult = matches
1110 if self.config.doWriteMatchesDenormalized:
1111 if matchResult.matches:
1112 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1114 self.log.warning(
"No matches, so generating dummy denormalized matches file")
1115 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1117 denormMatches.getMetadata().add(
"COMMENT",
1118 "This catalog is empty because no matches were found.")
1119 results.denormMatches = denormMatches
1120 results.denormMatches = denormMatches
1122 results.outputSources = sources
1125 def readSources(self, dataRef):
1127 @brief Read input sources.
1129 @param[
in] dataRef: Data reference
for catalog of merged detections
1130 @return List of sources
in merged catalog
1132 We also need to add columns to hold the measurements we
're about to make so we can measure in-place.
1134 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1135 self.log.info(
"Read %d detections: %s", len(merged), dataRef.dataId)
1136 idFactory = self.makeIdFactory(dataRef)
1138 idFactory.notify(s.getId())
1139 table = afwTable.SourceTable.make(self.schema, idFactory)
1140 sources = afwTable.SourceCatalog(table)
1141 sources.extend(merged, self.schemaMapper)
1144 def writeMatches(self, dataRef, results):
1146 @brief Write matches of the sources to the astrometric reference catalog.
1148 @param[
in] dataRef: data reference
1149 @param[
in] results: results struct
from run method
1151 if hasattr(results,
"matchResult"):
1152 dataRef.put(results.matchResult, self.config.coaddName +
"Coadd_measMatch")
1153 if hasattr(results,
"denormMatches"):
1154 dataRef.put(results.denormMatches, self.config.coaddName +
"Coadd_measMatchFull")
1156 def write(self, dataRef, sources):
1158 @brief Write the source catalog.
1160 @param[
in] dataRef: data reference
1161 @param[
in] sources: source catalog
1163 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1164 self.log.info(
"Wrote %d sources: %s", len(sources), dataRef.dataId)
1165
def getSkyInfo(coaddName, patchRef)
Return the SkyMap, tract and patch information, wcs, and outer bbox of the patch to be coadded.
def writeMetadata(self, dataRefList)
No metadata to write, and not sure how to write it for a list of dataRefs.