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 "deblendedCatalog":
"deblendedFlux"}):
593 inputSchema = cT.InitInput(
594 doc=
"Input schema for measure merged task produced by a deblender or detection task",
595 name=
"{inputCoaddName}Coadd_deblendedFlux_schema",
596 storageClass=
"SourceCatalog"
598 outputSchema = cT.InitOutput(
599 doc=
"Output schema after all new fields are added by task",
600 name=
"{inputCoaddName}Coadd_meas_schema",
601 storageClass=
"SourceCatalog"
603 refCat = cT.PrerequisiteInput(
604 doc=
"Reference catalog used to match measured sources against known sources",
606 storageClass=
"SimpleCatalog",
607 dimensions=(
"skypix",),
612 doc=
"Input coadd image",
613 name=
"{inputCoaddName}Coadd_calexp",
614 storageClass=
"ExposureF",
615 dimensions=(
"tract",
"patch",
"band",
"skymap")
618 doc=
"SkyMap to use in processing",
619 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
620 storageClass=
"SkyMap",
621 dimensions=(
"skymap",),
623 visitCatalogs = cT.Input(
624 doc=
"Source catalogs for visits which overlap input tract, patch, band. Will be "
625 "further filtered in the task for the purpose of propagating flags from image calibration "
626 "and characterization to codd objects",
628 dimensions=(
"instrument",
"visit",
"detector"),
629 storageClass=
"SourceCatalog",
632 inputCatalog = cT.Input(
633 doc=(
"Name of the input catalog to use."
634 "If the single band deblender was used this should be 'deblendedFlux."
635 "If the multi-band deblender was used this should be 'deblendedModel, "
636 "or deblendedFlux if the multiband deblender was configured to output "
637 "deblended flux catalogs. If no deblending was performed this should "
639 name=
"{inputCoaddName}Coadd_{deblendedCatalog}",
640 storageClass=
"SourceCatalog",
641 dimensions=(
"tract",
"patch",
"band",
"skymap"),
643 outputSources = cT.Output(
644 doc=
"Source catalog containing all the measurement information generated in this task",
645 name=
"{outputCoaddName}Coadd_meas",
646 dimensions=(
"tract",
"patch",
"band",
"skymap"),
647 storageClass=
"SourceCatalog",
649 matchResult = cT.Output(
650 doc=
"Match catalog produced by configured matcher, optional on doMatchSources",
651 name=
"{outputCoaddName}Coadd_measMatch",
652 dimensions=(
"tract",
"patch",
"band",
"skymap"),
653 storageClass=
"Catalog",
655 denormMatches = cT.Output(
656 doc=
"Denormalized Match catalog produced by configured matcher, optional on "
657 "doWriteMatchesDenormalized",
658 name=
"{outputCoaddName}Coadd_measMatchFull",
659 dimensions=(
"tract",
"patch",
"band",
"skymap"),
660 storageClass=
"Catalog",
663 def __init__(self, *, config=None):
664 super().__init__(config=config)
665 if config.doPropagateFlags
is False:
666 self.inputs -= set((
"visitCatalogs",))
668 if config.doMatchSources
is False:
669 self.outputs -= set((
"matchResult",))
671 if config.doWriteMatchesDenormalized
is False:
672 self.outputs -= set((
"denormMatches",))
675class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
676 pipelineConnections=MeasureMergedCoaddSourcesConnections):
678 @anchor MeasureMergedCoaddSourcesConfig_
680 @brief Configuration parameters
for the MeasureMergedCoaddSourcesTask
682 inputCatalog = Field(dtype=str, default="deblendedFlux",
683 doc=(
"Name of the input catalog to use."
684 "If the single band deblender was used this should be 'deblendedFlux."
685 "If the multi-band deblender was used this should be 'deblendedModel."
686 "If no deblending was performed this should be 'mergeDet'"))
687 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc=
"Source measurement")
688 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc=
"Set flags for primary tract/patch")
689 doPropagateFlags = Field(
690 dtype=bool, default=
True,
691 doc=
"Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
693 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc=
"Propagate visit flags to coadd")
694 doMatchSources = Field(dtype=bool, default=
True, doc=
"Match sources to reference catalog?")
695 match = ConfigurableField(target=DirectMatchTask, doc=
"Matching to reference catalog")
696 doWriteMatchesDenormalized = Field(
699 doc=(
"Write reference matches in denormalized format? "
700 "This format uses more disk space, but is more convenient to read."),
702 coaddName = Field(dtype=str, default=
"deep", doc=
"Name of coadd")
703 psfCache = Field(dtype=int, default=100, doc=
"Size of psfCache")
704 checkUnitsParseStrict = Field(
705 doc=
"Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
712 doc=
"Apply aperture corrections"
714 applyApCorr = ConfigurableField(
715 target=ApplyApCorrTask,
716 doc=
"Subtask to apply aperture corrections"
718 doRunCatalogCalculation = Field(
721 doc=
'Run catalogCalculation task'
723 catalogCalculation = ConfigurableField(
724 target=CatalogCalculationTask,
725 doc=
"Subtask to run catalogCalculation plugins on catalog"
731 doc=
"Should be set to True if fake sources have been inserted into the input data."
735 def refObjLoader(self):
736 return self.match.refObjLoader
738 def setDefaults(self):
739 super().setDefaults()
740 self.measurement.plugins.names |= [
'base_InputCount',
742 'base_LocalPhotoCalib',
744 self.measurement.plugins[
'base_PixelFlags'].masksFpAnywhere = [
'CLIPPED',
'SENSOR_EDGE',
746 self.measurement.plugins[
'base_PixelFlags'].masksFpCenter = [
'CLIPPED',
'SENSOR_EDGE',
751 refCatGen2 = getattr(self.refObjLoader,
"ref_dataset_name",
None)
752 if refCatGen2
is not None and refCatGen2 != self.connections.refCat:
754 f
"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
755 f
"are different. These options must be kept in sync until Gen2 is retired."
767class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
768 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
770 def getTargetList(parsedCmd, **kwargs):
771 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
774class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
776 @anchor MeasureMergedCoaddSourcesTask_
778 @brief Deblend sources
from master catalog
in each coadd seperately
and measure.
780 @section pipe_tasks_multiBand_Contents Contents
782 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
783 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
784 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
785 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
786 -
@ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
787 -
@ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
789 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
791 Command-line task that uses peaks
and footprints
from a master catalog to perform deblending
and
792 measurement
in each coadd.
794 Given a master input catalog of sources (peaks
and footprints)
or deblender outputs
795 (including a HeavyFootprint
in each band), measure each source on the
796 coadd. Repeating this procedure
with the same master catalog across multiple coadds will generate a
797 consistent set of child sources.
799 The deblender retains all peaks
and deblends any missing peaks (dropouts
in that band)
as PSFs. Source
800 properties are measured
and the
@c is-primary flag (indicating sources
with no children)
is set. Visit
801 flags are propagated to the coadd sources.
803 Optionally, we can match the coadd sources to an external reference catalog.
806 deepCoadd_mergeDet{tract,patch}
or deepCoadd_deblend{tract,patch}: SourceCatalog
807 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
809 deepCoadd_meas{tract,patch,filter}: SourceCatalog
813 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
816 <DT>
@ref SingleFrameMeasurementTask_
"measurement"
817 <DD> Measure source properties of deblended sources.</DD>
818 <DT>
@ref SetPrimaryFlagsTask_
"setPrimaryFlags"
819 <DD> Set flag
'is-primary' as well
as related flags on sources.
'is-primary' is set
for sources that are
820 not at the edge of the field
and that have either
not been deblended
or are the children of deblended
822 <DT>
@ref PropagateVisitFlagsTask_
"propagateFlags"
823 <DD> Propagate flags set
in individual visits to the coadd.</DD>
824 <DT>
@ref DirectMatchTask_
"match"
825 <DD> Match input sources to a reference catalog (optional).
828 These subtasks may be retargeted
as required.
830 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
832 @copydoc \_\_init\_\_
834 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
838 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
840 See
@ref MeasureMergedCoaddSourcesConfig_
842 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
844 The
@link lsst.pipe.base.cmdLineTask.CmdLineTask command line task
@endlink interface supports a
845 flag
@c -d to
import @b debug.py
from your
@c PYTHONPATH; see
@ref baseDebug
for more about
@b debug.py
848 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
849 the various sub-tasks. See the documetation
for individual sub-tasks
for more information.
851 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
852 MeasureMergedCoaddSourcesTask
854 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
855 The next stage
in the multi-band processing procedure will merge these measurements into a suitable
856 catalog
for driving forced photometry.
858 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
860 A list of the available optional arguments can be obtained by calling measureCoaddSources.py
with the
861 `--help` command line argument:
863 measureCoaddSources.py --help
866 To demonstrate usage of the DetectCoaddSourcesTask
in the larger context of multi-band processing, we
867 will process HSC data
in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
868 step 6 at
@ref pipeTasks_multiBand, one may perform deblending
and measure sources
in the HSC-I band
871 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
873 This will process the HSC-I band data. The results are written
in
874 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
876 It
is also necessary to run
878 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
880 to generate the sources catalogs
for the HSC-R band required by the next step
in the multi-band
881 procedure:
@ref MergeMeasurementsTask_
"MergeMeasurementsTask".
883 _DefaultName = "measureCoaddSources"
884 ConfigClass = MeasureMergedCoaddSourcesConfig
885 RunnerClass = MeasureMergedCoaddSourcesRunner
886 getSchemaCatalogs = _makeGetSchemaCatalogs(
"meas")
888 makeIdFactory = _makeMakeIdFactory(
"MergedCoaddId", includeBand=
False)
891 def _makeArgumentParser(cls):
892 parser = ArgumentParser(name=cls._DefaultName)
893 parser.add_id_argument(
"--id",
"deepCoadd_calexp",
894 help=
"data ID, e.g. --id tract=12345 patch=1,2 filter=r",
895 ContainerClass=ExistingCoaddDataIdContainer)
896 parser.add_argument(
"--psfCache", type=int, default=100, help=
"Size of CoaddPsf cache")
899 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
902 @brief Initialize the task.
904 Keyword arguments (
in addition to those forwarded to CmdLineTask.__init__):
905 @param[
in] schema: the schema of the merged detection catalog used
as input to this one
906 @param[
in] peakSchema: the schema of the PeakRecords
in the Footprints
in the merged detection catalog
907 @param[
in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
908 catalog. May be
None if the loader can be constructed
from the butler argument
or all steps
909 requiring a reference catalog are disabled.
910 @param[
in] butler: a butler used to read the input schemas
from disk
or construct the reference
911 catalog loader,
if schema
or peakSchema
or refObjLoader
is None
913 The task will set its own self.schema attribute to the schema of the output measurement catalog.
914 This will include all fields
from the input schema,
as well
as additional fields
for all the
917 super().__init__(**kwargs)
918 self.deblended = self.config.inputCatalog.startswith("deblended")
919 self.inputCatalog =
"Coadd_" + self.config.inputCatalog
920 if initInputs
is not None:
921 schema = initInputs[
'inputSchema'].schema
923 assert butler
is not None,
"Neither butler nor schema is defined"
924 schema = butler.get(self.config.coaddName + self.inputCatalog +
"_schema", immediate=
True).schema
925 self.schemaMapper = afwTable.SchemaMapper(schema)
926 self.schemaMapper.addMinimalSchema(schema)
927 self.schema = self.schemaMapper.getOutputSchema()
929 self.makeSubtask(
"measurement", schema=self.schema, algMetadata=self.algMetadata)
930 self.makeSubtask(
"setPrimaryFlags", schema=self.schema)
931 if self.config.doMatchSources:
932 self.makeSubtask(
"match", butler=butler, refObjLoader=refObjLoader)
933 if self.config.doPropagateFlags:
934 self.makeSubtask(
"propagateFlags", schema=self.schema)
935 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
936 if self.config.doApCorr:
937 self.makeSubtask(
"applyApCorr", schema=self.schema)
938 if self.config.doRunCatalogCalculation:
939 self.makeSubtask(
"catalogCalculation", schema=self.schema)
941 self.outputSchema = afwTable.SourceCatalog(self.schema)
943 def runQuantum(self, butlerQC, inputRefs, outputRefs):
944 inputs = butlerQC.get(inputRefs)
946 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId
for ref
in inputRefs.refCat],
947 inputs.pop(
'refCat'), config=self.config.refObjLoader,
949 self.match.setRefObjLoader(refObjLoader)
953 inputs[
'exposure'].getPsf().setCacheCapacity(self.config.psfCache)
956 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId,
"tract_patch")
957 inputs[
'exposureId'] = exposureIdInfo.expId
958 idFactory = exposureIdInfo.makeSourceIdFactory()
960 table = afwTable.SourceTable.make(self.schema, idFactory)
961 sources = afwTable.SourceCatalog(table)
962 sources.extend(inputs.pop(
'inputCatalog'), self.schemaMapper)
963 table = sources.getTable()
964 table.setMetadata(self.algMetadata)
965 inputs[
'sources'] = sources
967 skyMap = inputs.pop(
'skyMap')
968 tractNumber = inputRefs.inputCatalog.dataId[
'tract']
969 tractInfo = skyMap[tractNumber]
970 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId[
'patch'])
975 wcs=tractInfo.getWcs(),
976 bbox=patchInfo.getOuterBBox()
978 inputs[
'skyInfo'] = skyInfo
980 if self.config.doPropagateFlags:
982 ccdInputs = inputs[
'exposure'].getInfo().getCoaddInputs().ccds
983 visitKey = ccdInputs.schema.find(
"visit").key
984 ccdKey = ccdInputs.schema.find(
"ccd").key
985 inputVisitIds = set()
987 for ccdRecord
in ccdInputs:
988 visit = ccdRecord.get(visitKey)
989 ccd = ccdRecord.get(ccdKey)
990 inputVisitIds.add((visit, ccd))
991 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
993 inputCatalogsToKeep = []
994 inputCatalogWcsUpdate = []
995 for i, dataRef
in enumerate(inputRefs.visitCatalogs):
996 key = (dataRef.dataId[
'visit'], dataRef.dataId[
'detector'])
997 if key
in inputVisitIds:
998 inputCatalogsToKeep.append(inputs[
'visitCatalogs'][i])
999 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
1000 inputs[
'visitCatalogs'] = inputCatalogsToKeep
1001 inputs[
'wcsUpdates'] = inputCatalogWcsUpdate
1002 inputs[
'ccdInputs'] = ccdInputs
1004 outputs = self.run(**inputs)
1005 butlerQC.put(outputs, outputRefs)
1007 def runDataRef(self, patchRef, psfCache=100):
1009 @brief Deblend
and measure.
1011 @param[
in] patchRef: Patch reference.
1013 Set
'is-primary' and related flags. Propagate flags
1014 from individual visits. Optionally match the sources to a reference catalog
and write the matches.
1015 Finally, write the deblended sources
and measurements out.
1017 if self.config.hasFakes:
1018 coaddType =
"fakes_" + self.config.coaddName
1020 coaddType = self.config.coaddName
1021 exposure = patchRef.get(coaddType +
"Coadd_calexp", immediate=
True)
1022 exposure.getPsf().setCacheCapacity(psfCache)
1023 sources = self.readSources(patchRef)
1024 table = sources.getTable()
1025 table.setMetadata(self.algMetadata)
1026 skyInfo =
getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1028 if self.config.doPropagateFlags:
1029 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1033 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=
False,
1035 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId,
1036 ccdInputs=ccdInputs, butler=patchRef.getButler())
1038 if self.config.doMatchSources:
1039 self.writeMatches(patchRef, results)
1040 self.write(patchRef, results.outputSources)
1042 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1044 """Run measurement algorithms on the input exposure, and optionally populate the
1045 resulting catalog with extra information.
1049 exposure : `lsst.afw.exposure.Exposure`
1050 The input exposure on which measurements are to be performed
1052 A catalog built
from the results of merged detections,
or
1054 skyInfo : `lsst.pipe.base.Struct`
1055 A struct containing information about the position of the input exposure within
1056 a `SkyMap`, the `SkyMap`, its `Wcs`,
and its bounding box
1057 exposureId : `int`
or `bytes`
1058 packed unique number
or bytes unique to the input exposure
1060 Catalog containing information on the individual visits which went into making
1062 visitCatalogs : list of `lsst.afw.table.SourceCatalogs`
or `
None`
1063 A list of source catalogs corresponding to measurements made on the individual
1064 visits which went into the input exposure. If
None and butler
is `
None` then
1065 the task cannot propagate visit flags to the output catalog.
1067 If visitCatalogs
is not `
None` this should be a list of wcs objects which correspond
1068 to the input visits. Used to put all coordinates to common system. If `
None`
and
1069 butler
is `
None` then the task cannot propagate visit flags to the output catalog.
1070 butler : `lsst.daf.butler.Butler`
or `lsst.daf.persistence.Butler`
1071 Either a gen2
or gen3 butler used to load visit catalogs
1075 results : `lsst.pipe.base.Struct`
1076 Results of running measurement task. Will contain the catalog
in the
1077 sources attribute. Optionally will have results of matching to a
1078 reference catalog
in the matchResults attribute,
and denormalized
1079 matches
in the denormMatches attribute.
1081 self.measurement.run(sources, exposure, exposureId=exposureId)
1083 if self.config.doApCorr:
1084 self.applyApCorr.run(
1086 apCorrMap=exposure.getInfo().getApCorrMap()
1093 if not sources.isContiguous():
1094 sources = sources.copy(deep=
True)
1096 if self.config.doRunCatalogCalculation:
1097 self.catalogCalculation.run(sources)
1099 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1100 patchInfo=skyInfo.patchInfo)
1101 if self.config.doPropagateFlags:
1102 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates)
1106 if self.config.doMatchSources:
1107 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel)
1108 matches = afwTable.packMatches(matchResult.matches)
1109 matches.table.setMetadata(matchResult.matchMeta)
1110 results.matchResult = matches
1111 if self.config.doWriteMatchesDenormalized:
1112 if matchResult.matches:
1113 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1115 self.log.warning(
"No matches, so generating dummy denormalized matches file")
1116 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1118 denormMatches.getMetadata().add(
"COMMENT",
1119 "This catalog is empty because no matches were found.")
1120 results.denormMatches = denormMatches
1121 results.denormMatches = denormMatches
1123 results.outputSources = sources
1126 def readSources(self, dataRef):
1128 @brief Read input sources.
1130 @param[
in] dataRef: Data reference
for catalog of merged detections
1131 @return List of sources
in merged catalog
1133 We also need to add columns to hold the measurements we
're about to make so we can measure in-place.
1135 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1136 self.log.info(
"Read %d detections: %s", len(merged), dataRef.dataId)
1137 idFactory = self.makeIdFactory(dataRef)
1139 idFactory.notify(s.getId())
1140 table = afwTable.SourceTable.make(self.schema, idFactory)
1141 sources = afwTable.SourceCatalog(table)
1142 sources.extend(merged, self.schemaMapper)
1145 def writeMatches(self, dataRef, results):
1147 @brief Write matches of the sources to the astrometric reference catalog.
1149 @param[
in] dataRef: data reference
1150 @param[
in] results: results struct
from run method
1152 if hasattr(results,
"matchResult"):
1153 dataRef.put(results.matchResult, self.config.coaddName +
"Coadd_measMatch")
1154 if hasattr(results,
"denormMatches"):
1155 dataRef.put(results.denormMatches, self.config.coaddName +
"Coadd_measMatchFull")
1157 def write(self, dataRef, sources):
1159 @brief Write the source catalog.
1161 @param[
in] dataRef: data reference
1162 @param[
in] sources: source catalog
1164 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1165 self.log.info(
"Wrote %d sources: %s", len(sources), dataRef.dataId)
1166
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.