lsst.pipe.tasks ge1bc22dbe7+3fe987bc49
multiBand.py
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1#!/usr/bin/env python
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23import numpy as np
24
25from lsst.coadd.utils.coaddDataIdContainer import ExistingCoaddDataIdContainer
26from lsst.coadd.utils.getGen3CoaddExposureId import getGen3CoaddExposureId
27from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner,
28 PipelineTask, PipelineTaskConfig, PipelineTaskConnections)
29import lsst.pipe.base.connectionTypes as cT
30from lsst.pex.config import Config, Field, ConfigurableField
31from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader
32from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask
33from lsst.meas.deblender import SourceDeblendTask
34from lsst.meas.extensions.scarlet import ScarletDeblendTask
35from lsst.pipe.tasks.coaddBase import getSkyInfo
36from lsst.pipe.tasks.scaleVariance import ScaleVarianceTask
37from lsst.meas.astrom import DirectMatchTask, denormalizeMatches
38from lsst.pipe.tasks.fakes import BaseFakeSourcesTask
39from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
40from lsst.pipe.tasks.propagateSourceFlags import PropagateSourceFlagsTask
41import lsst.afw.image as afwImage
42import lsst.afw.table as afwTable
43import lsst.afw.math as afwMath
44from lsst.daf.base import PropertyList
45from lsst.skymap import BaseSkyMap
46from lsst.obs.base import ExposureIdInfo
47
48# NOTE: these imports are a convenience so multiband users only have to import this file.
49from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401
50from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401
51from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401
52from .multiBandUtils import getInputSchema, readCatalog, _makeMakeIdFactory # noqa: F401
53from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401
54from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401
55from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401
56from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401
57
58
59"""
60New set types:
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.
66
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
70"""
71
72
73
74class DetectCoaddSourcesConnections(PipelineTaskConnections,
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",
81 )
82 exposure = cT.Input(
83 doc="Exposure on which detections are to be performed",
84 name="{inputCoaddName}Coadd",
85 storageClass="ExposureF",
86 dimensions=("tract", "patch", "band", "skymap")
87 )
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")
93 )
94 outputSources = cT.Output(
95 doc="Detected sources catalog",
96 name="{outputCoaddName}Coadd_det",
97 storageClass="SourceCatalog",
98 dimensions=("tract", "patch", "band", "skymap")
99 )
100 outputExposure = cT.Output(
101 doc="Exposure post detection",
102 name="{outputCoaddName}Coadd_calexp",
103 storageClass="ExposureF",
104 dimensions=("tract", "patch", "band", "skymap")
105 )
106
107
108class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections):
109 """!
110 @anchor DetectCoaddSourcesConfig_
111
112 @brief Configuration parameters for the DetectCoaddSourcesTask
113 """
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)")
123 hasFakes = Field(
124 dtype=bool,
125 default=False,
126 doc="Should be set to True if fake sources have been inserted into the input data."
127 )
128
129 def setDefaults(self):
130 super().setDefaults()
131 self.detection.thresholdType = "pixel_stdev"
132 self.detection.isotropicGrow = True
133 # Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic
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 # Suppress large footprints that overwhelm the deblender
139
140
146
147
148class DetectCoaddSourcesTask(PipelineTask, CmdLineTask):
149 r"""!
150 @anchor DetectCoaddSourcesTask_
151
152 @brief Detect sources on a coadd
153
154 @section pipe_tasks_multiBand_Contents Contents
155
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
162
163 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
164
165 Command-line task that detects sources on a coadd of exposures obtained with a single filter.
166
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.
171
172 After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref
173 SourceDetectionTask_ "detection" subtask.
174
175 @par Inputs:
176 deepCoadd{tract,patch,filter}: ExposureF
177 @par Outputs:
178 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
179 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input
180 exposure (ExposureF)
181 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList
182 @par Data Unit:
183 tract, patch, filter
184
185 DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask.
186 You can retarget this subtask if you wish.
187
188 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
189
190 @copydoc \_\_init\_\_
191
192 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
193
194 @copydoc run
195
196 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
197
198 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig"
199
200 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
201
202 The command line task 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
204 files.
205
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.
209
210 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example
211 of using DetectCoaddSourcesTask
212
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:
219 @code
220 detectCoaddSources.py --help
221 @endcode
222
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:
226 @code
227 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
228 @endcode
229 that will process the HSC-I band data. The results are written to
230 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
231
232 It is also necessary to run:
233 @code
234 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
235 @endcode
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".
238 """
239 _DefaultName = "detectCoaddSources"
240 ConfigClass = DetectCoaddSourcesConfig
241 getSchemaCatalogs = _makeGetSchemaCatalogs("det")
242 makeIdFactory = _makeMakeIdFactory("CoaddId")
243
244 @classmethod
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)
249 return parser
250
251 def __init__(self, schema=None, **kwargs):
252 """!
253 @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask.
254
255 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
256
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__
260 """
261 # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree
262 # call structure has been reviewed carefully to be sure super will work as intended.
263 super().__init__(**kwargs)
264 if schema is None:
265 schema = afwTable.SourceTable.makeMinimalSchema()
266 if self.config.doInsertFakes:
267 self.makeSubtask("insertFakes")
268 self.schema = schema
269 self.makeSubtask("detection", schema=self.schema)
270 if self.config.doScaleVariance:
271 self.makeSubtask("scaleVariance")
272
273 self.detectionSchema = afwTable.SourceCatalog(self.schema)
274
275 def runDataRef(self, patchRef):
276 """!
277 @brief Run detection on a coadd.
278
279 Invokes @ref run and then uses @ref write to output the
280 results.
281
282 @param[in] patchRef: data reference for patch
283 """
284 if self.config.hasFakes:
285 exposure = patchRef.get("fakes_" + self.config.coaddName + "Coadd", immediate=True)
286 else:
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)
291 return results
292
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)
300
301 def run(self, exposure, idFactory, expId):
302 """!
303 @brief Run detection on an exposure.
304
305 First scale the variance plane to match the observed variance
306 using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to
307 detect sources.
308
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
313
314 @return a pipe.base.Struct with fields
315 - sources: catalog of detections
316 - backgrounds: list of backgrounds
317 """
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)
332
333 def write(self, results, patchRef):
334 """!
335 @brief Write out results from runDetection.
336
337 @param[in] exposure: Exposure to write out
338 @param[in] results: Struct returned from runDetection
339 @param[in] patchRef: data reference for patch
340 """
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")
346 else:
347 patchRef.put(results.outputExposure, coaddName + "_calexp")
348
349
350
351
352class DeblendCoaddSourcesConfig(Config):
353 """DeblendCoaddSourcesConfig
354
355 Configuration parameters for the `DeblendCoaddSourcesTask`.
356 """
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,
362 default=True,
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,
367 default=False,
368 doc="Should be set to True if fake sources have been inserted into the input data.")
369
370 def setDefaults(self):
371 Config.setDefaults(self)
372 self.singleBandDeblend.propagateAllPeaks = True
373
374
375class DeblendCoaddSourcesRunner(MergeSourcesRunner):
376 """Task runner for the `MergeSourcesTask`
377
378 Required because the run method requires a list of
379 dataRefs rather than a single dataRef.
380 """
381 @staticmethod
382 def getTargetList(parsedCmd, **kwargs):
383 """Provide a list of patch references for each patch, tract, filter combo.
384
385 Parameters
386 ----------
387 parsedCmd:
388 The parsed command
389 kwargs:
390 Keyword arguments passed to the task
391
392 Returns
393 -------
394 targetList: list
395 List of tuples, where each tuple is a (dataRef, kwargs) pair.
396 """
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()]
400
401
402class DeblendCoaddSourcesTask(CmdLineTask):
403 """Deblend the sources in a merged catalog
404
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
413 from the deblender.
414
415 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description
416 ---------------------------------------------------------
417 `
418
419 Parameters
420 ----------
421 butler: `Butler`
422 Butler used to read the input schemas from disk or
423 construct the reference catalog loader, if `schema` or `peakSchema` or
424 schema: `Schema`
425 The schema of the merged detection catalog as an input to this task.
426 peakSchema: `Schema`
427 The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog
428 """
429 ConfigClass = DeblendCoaddSourcesConfig
430 RunnerClass = DeblendCoaddSourcesRunner
431 _DefaultName = "deblendCoaddSources"
432 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False)
433
434 @classmethod
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")
441 return parser
442
443 def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs):
444 CmdLineTask.__init__(self, **kwargs)
445 if schema is None:
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
454
455 if self.config.simultaneous:
456 self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema)
457 else:
458 self.makeSubtask("singleBandDeblend", schema=self.schema, peakSchema=peakSchema)
459
460 def getSchemaCatalogs(self):
461 """Return a dict of empty catalogs for each catalog dataset produced by this task.
462
463 Returns
464 -------
465 result: dict
466 Dictionary of empty catalogs, with catalog names as keys.
467 """
468 catalog = afwTable.SourceCatalog(self.schema)
469 return {self.config.coaddName + "Coadd_deblendedFlux": catalog,
470 self.config.coaddName + "Coadd_deblendedModel": catalog}
471
472 def runDataRef(self, patchRefList, psfCache=100):
473 """Deblend the patch
474
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.
480
481 Parameters
482 ----------
483 patchRefList: list
484 List of data references for each filter
485 """
486
487 if self.config.hasFakes:
488 coaddType = "fakes_" + self.config.coaddName
489 else:
490 coaddType = self.config.coaddName
491
492 if self.config.simultaneous:
493 # Use SCARLET to simultaneously deblend across filters
494 filters = []
495 exposures = []
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)
501 # Sort inputs by band to match Gen3 order of inputs
502 exposures = [exposure for _, exposure in sorted(zip(filters, exposures))]
503 patchRefList = [patchRef for _, patchRef in sorted(zip(filters, patchRefList))]
504 filters.sort()
505 # The input sources are the same for all bands, since it is a merged catalog
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")
513 else:
514 # Use the singeband deblender to deblend each band separately
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)
521
522 def readSources(self, dataRef):
523 """Read merged catalog
524
525 Read the catalog of merged detections and create a catalog
526 in a single band.
527
528 Parameters
529 ----------
530 dataRef: data reference
531 Data reference for catalog of merged detections
532
533 Returns
534 -------
535 sources: `SourceCatalog`
536 List of sources in merged catalog
537
538 We also need to add columns to hold the measurements we're about to make so we can measure in-place.
539 """
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)
543 # There may be gaps in the mergeDet catalog, which will cause the
544 # source ids to be inconsistent. So we update the id factory
545 # with the largest id already in the catalog.
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)
551 return sources
552
553 def write(self, dataRef, sources, catalogType):
554 """Write the source catalog(s)
555
556 Parameters
557 ----------
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
563 generated.
564 template_sources: `SourceCatalog`
565 Source catalog using the multiband template models
566 as footprints.
567 """
568 dataRef.put(sources, self.config.coaddName + f"Coadd_deblended{catalogType}")
569 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)
570
571 def writeMetadata(self, dataRefList):
572 """Write the metadata produced from processing the data.
573 Parameters
574 ----------
575 dataRefList
576 List of Butler data references used to write the metadata.
577 The metadata is written to dataset type `CmdLineTask._getMetadataName`.
578 """
579 for dataRef in dataRefList:
580 try:
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)
586
587
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"
597 )
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"
602 )
603 refCat = cT.PrerequisiteInput(
604 doc="Reference catalog used to match measured sources against known sources",
605 name="ref_cat",
606 storageClass="SimpleCatalog",
607 dimensions=("skypix",),
608 deferLoad=True,
609 multiple=True
610 )
611 exposure = cT.Input(
612 doc="Input coadd image",
613 name="{inputCoaddName}Coadd_calexp",
614 storageClass="ExposureF",
615 dimensions=("tract", "patch", "band", "skymap")
616 )
617 skyMap = cT.Input(
618 doc="SkyMap to use in processing",
619 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
620 storageClass="SkyMap",
621 dimensions=("skymap",),
622 )
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 coadd objects. Only used in legacy PropagateVisitFlagsTask.",
627 name="src",
628 dimensions=("instrument", "visit", "detector"),
629 storageClass="SourceCatalog",
630 multiple=True
631 )
632 sourceTableHandles = cT.Input(
633 doc=("Source tables that are derived from the ``CalibrateTask`` sources. "
634 "These tables contain astrometry and photometry flags, and optionally "
635 "PSF flags."),
636 name="sourceTable_visit",
637 storageClass="DataFrame",
638 dimensions=("instrument", "visit"),
639 multiple=True,
640 deferLoad=True,
641 )
642 finalizedSourceTableHandles = cT.Input(
643 doc=("Finalized source tables from ``FinalizeCalibrationTask``. These "
644 "tables contain PSF flags from the finalized PSF estimation."),
645 name="finalized_src_table",
646 storageClass="DataFrame",
647 dimensions=("instrument", "visit"),
648 multiple=True,
649 deferLoad=True,
650 )
651 inputCatalog = cT.Input(
652 doc=("Name of the input catalog to use."
653 "If the single band deblender was used this should be 'deblendedFlux."
654 "If the multi-band deblender was used this should be 'deblendedModel, "
655 "or deblendedFlux if the multiband deblender was configured to output "
656 "deblended flux catalogs. If no deblending was performed this should "
657 "be 'mergeDet'"),
658 name="{inputCoaddName}Coadd_{deblendedCatalog}",
659 storageClass="SourceCatalog",
660 dimensions=("tract", "patch", "band", "skymap"),
661 )
662 outputSources = cT.Output(
663 doc="Source catalog containing all the measurement information generated in this task",
664 name="{outputCoaddName}Coadd_meas",
665 dimensions=("tract", "patch", "band", "skymap"),
666 storageClass="SourceCatalog",
667 )
668 matchResult = cT.Output(
669 doc="Match catalog produced by configured matcher, optional on doMatchSources",
670 name="{outputCoaddName}Coadd_measMatch",
671 dimensions=("tract", "patch", "band", "skymap"),
672 storageClass="Catalog",
673 )
674 denormMatches = cT.Output(
675 doc="Denormalized Match catalog produced by configured matcher, optional on "
676 "doWriteMatchesDenormalized",
677 name="{outputCoaddName}Coadd_measMatchFull",
678 dimensions=("tract", "patch", "band", "skymap"),
679 storageClass="Catalog",
680 )
681
682 def __init__(self, *, config=None):
683 super().__init__(config=config)
684 if config.doPropagateFlags is False:
685 self.inputs -= set(("visitCatalogs",))
686 self.inputs -= set(("sourceTableHandles",))
687 self.inputs -= set(("finalizedSourceTableHandles",))
688 elif config.propagateFlags.target == PropagateSourceFlagsTask:
689 # New PropagateSourceFlagsTask does not use visitCatalogs.
690 self.inputs -= set(("visitCatalogs",))
691 # Check for types of flags required.
692 if not config.propagateFlags.source_flags:
693 self.inputs -= set(("sourceTableHandles",))
694 if not config.propagateFlags.finalized_source_flags:
695 self.inputs -= set(("finalizedSourceTableHandles",))
696 else:
697 # Deprecated PropagateVisitFlagsTask uses visitCatalogs.
698 self.inputs -= set(("sourceTableHandles",))
699 self.inputs -= set(("finalizedSourceTableHandles",))
700
701 if config.doMatchSources is False:
702 self.outputs -= set(("matchResult",))
703
704 if config.doWriteMatchesDenormalized is False:
705 self.outputs -= set(("denormMatches",))
706
707
708class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
709 pipelineConnections=MeasureMergedCoaddSourcesConnections):
710 """!
711 @anchor MeasureMergedCoaddSourcesConfig_
712
713 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask
714 """
715 inputCatalog = Field(dtype=str, default="deblendedFlux",
716 doc=("Name of the input catalog to use."
717 "If the single band deblender was used this should be 'deblendedFlux."
718 "If the multi-band deblender was used this should be 'deblendedModel."
719 "If no deblending was performed this should be 'mergeDet'"))
720 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement")
721 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch")
722 doPropagateFlags = Field(
723 dtype=bool, default=True,
724 doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
725 )
726 propagateFlags = ConfigurableField(target=PropagateSourceFlagsTask, doc="Propagate source flags to coadd")
727 doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?")
728 match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog")
729 doWriteMatchesDenormalized = Field(
730 dtype=bool,
731 default=False,
732 doc=("Write reference matches in denormalized format? "
733 "This format uses more disk space, but is more convenient to read."),
734 )
735 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
736 psfCache = Field(dtype=int, default=100, doc="Size of psfCache")
737 checkUnitsParseStrict = Field(
738 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
739 dtype=str,
740 default="raise",
741 )
742 doApCorr = Field(
743 dtype=bool,
744 default=True,
745 doc="Apply aperture corrections"
746 )
747 applyApCorr = ConfigurableField(
748 target=ApplyApCorrTask,
749 doc="Subtask to apply aperture corrections"
750 )
751 doRunCatalogCalculation = Field(
752 dtype=bool,
753 default=True,
754 doc='Run catalogCalculation task'
755 )
756 catalogCalculation = ConfigurableField(
757 target=CatalogCalculationTask,
758 doc="Subtask to run catalogCalculation plugins on catalog"
759 )
760
761 hasFakes = Field(
762 dtype=bool,
763 default=False,
764 doc="Should be set to True if fake sources have been inserted into the input data."
765 )
766
767 @property
768 def refObjLoader(self):
769 return self.match.refObjLoader
770
771 def setDefaults(self):
772 super().setDefaults()
773 self.measurement.plugins.names |= ['base_InputCount',
774 'base_Variance',
775 'base_LocalPhotoCalib',
776 'base_LocalWcs']
777 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE',
778 'INEXACT_PSF']
779 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE',
780 'INEXACT_PSF']
781
782 def validate(self):
783 super().validate()
784 refCatGen2 = getattr(self.refObjLoader, "ref_dataset_name", None)
785 if refCatGen2 is not None and refCatGen2 != self.connections.refCat:
786 raise ValueError(
787 f"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
788 f"are different. These options must be kept in sync until Gen2 is retired."
789 )
790
791
792
798
799
800class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
801 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
802 @staticmethod
803 def getTargetList(parsedCmd, **kwargs):
804 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
805
806
807class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
808 r"""!
809 @anchor MeasureMergedCoaddSourcesTask_
810
811 @brief Deblend sources from master catalog in each coadd seperately and measure.
812
813 @section pipe_tasks_multiBand_Contents Contents
814
815 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
816 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
817 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
818 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
819 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
820 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
821
822 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
823
824 Command-line task that uses peaks and footprints from a master catalog to perform deblending and
825 measurement in each coadd.
826
827 Given a master input catalog of sources (peaks and footprints) or deblender outputs
828 (including a HeavyFootprint in each band), measure each source on the
829 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a
830 consistent set of child sources.
831
832 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source
833 properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit
834 flags are propagated to the coadd sources.
835
836 Optionally, we can match the coadd sources to an external reference catalog.
837
838 @par Inputs:
839 deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog
840 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
841 @par Outputs:
842 deepCoadd_meas{tract,patch,filter}: SourceCatalog
843 @par Data Unit:
844 tract, patch, filter
845
846 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
847
848 <DL>
849 <DT> @ref SingleFrameMeasurementTask_ "measurement"
850 <DD> Measure source properties of deblended sources.</DD>
851 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags"
852 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are
853 not at the edge of the field and that have either not been deblended or are the children of deblended
854 sources</DD>
855 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags"
856 <DD> Propagate flags set in individual visits to the coadd.</DD>
857 <DT> @ref DirectMatchTask_ "match"
858 <DD> Match input sources to a reference catalog (optional).
859 </DD>
860 </DL>
861 These subtasks may be retargeted as required.
862
863 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
864
865 @copydoc \_\_init\_\_
866
867 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
868
869 @copydoc run
870
871 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
872
873 See @ref MeasureMergedCoaddSourcesConfig_
874
875 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
876
877 The command line task interface supports a
878 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
879 files.
880
881 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
882 the various sub-tasks. See the documetation for individual sub-tasks for more information.
883
884 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
885 MeasureMergedCoaddSourcesTask
886
887 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
888 The next stage in the multi-band processing procedure will merge these measurements into a suitable
889 catalog for driving forced photometry.
890
891 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
892 to be processed.
893 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the
894 `--help` command line argument:
895 @code
896 measureCoaddSources.py --help
897 @endcode
898
899 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
900 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
901 step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band
902 coadd as follows:
903 @code
904 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
905 @endcode
906 This will process the HSC-I band data. The results are written in
907 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
908
909 It is also necessary to run
910 @code
911 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
912 @endcode
913 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
914 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask".
915 """
916 _DefaultName = "measureCoaddSources"
917 ConfigClass = MeasureMergedCoaddSourcesConfig
918 RunnerClass = MeasureMergedCoaddSourcesRunner
919 getSchemaCatalogs = _makeGetSchemaCatalogs("meas")
920 # The IDs we already have are of this type
921 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False)
922
923 @classmethod
924 def _makeArgumentParser(cls):
925 parser = ArgumentParser(name=cls._DefaultName)
926 parser.add_id_argument("--id", "deepCoadd_calexp",
927 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
928 ContainerClass=ExistingCoaddDataIdContainer)
929 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
930 return parser
931
932 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
933 **kwargs):
934 """!
935 @brief Initialize the task.
936
937 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
938 @param[in] schema: the schema of the merged detection catalog used as input to this one
939 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog
940 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
941 catalog. May be None if the loader can be constructed from the butler argument or all steps
942 requiring a reference catalog are disabled.
943 @param[in] butler: a butler used to read the input schemas from disk or construct the reference
944 catalog loader, if schema or peakSchema or refObjLoader is None
945
946 The task will set its own self.schema attribute to the schema of the output measurement catalog.
947 This will include all fields from the input schema, as well as additional fields for all the
948 measurements.
949 """
950 super().__init__(**kwargs)
951 self.deblended = self.config.inputCatalog.startswith("deblended")
952 self.inputCatalog = "Coadd_" + self.config.inputCatalog
953 if initInputs is not None:
954 schema = initInputs['inputSchema'].schema
955 if schema is None:
956 assert butler is not None, "Neither butler nor schema is defined"
957 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema
958 self.schemaMapper = afwTable.SchemaMapper(schema)
959 self.schemaMapper.addMinimalSchema(schema)
960 self.schema = self.schemaMapper.getOutputSchema()
961 self.algMetadata = PropertyList()
962 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata)
963 self.makeSubtask("setPrimaryFlags", schema=self.schema)
964 if self.config.doMatchSources:
965 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
966 if self.config.doPropagateFlags:
967 self.makeSubtask("propagateFlags", schema=self.schema)
968 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
969 if self.config.doApCorr:
970 self.makeSubtask("applyApCorr", schema=self.schema)
971 if self.config.doRunCatalogCalculation:
972 self.makeSubtask("catalogCalculation", schema=self.schema)
973
974 self.outputSchema = afwTable.SourceCatalog(self.schema)
975
976 def runQuantum(self, butlerQC, inputRefs, outputRefs):
977 inputs = butlerQC.get(inputRefs)
978
979 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat],
980 inputs.pop('refCat'), config=self.config.refObjLoader,
981 log=self.log)
982 self.match.setRefObjLoader(refObjLoader)
983
984 # Set psfcache
985 # move this to run after gen2 deprecation
986 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
987
988 # Get unique integer ID for IdFactory and RNG seeds
989 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch")
990 inputs['exposureId'] = exposureIdInfo.expId
991 idFactory = exposureIdInfo.makeSourceIdFactory()
992 # Transform inputCatalog
993 table = afwTable.SourceTable.make(self.schema, idFactory)
994 sources = afwTable.SourceCatalog(table)
995 sources.extend(inputs.pop('inputCatalog'), self.schemaMapper)
996 table = sources.getTable()
997 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
998 inputs['sources'] = sources
999
1000 skyMap = inputs.pop('skyMap')
1001 tractNumber = inputRefs.inputCatalog.dataId['tract']
1002 tractInfo = skyMap[tractNumber]
1003 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId['patch'])
1004 skyInfo = Struct(
1005 skyMap=skyMap,
1006 tractInfo=tractInfo,
1007 patchInfo=patchInfo,
1008 wcs=tractInfo.getWcs(),
1009 bbox=patchInfo.getOuterBBox()
1010 )
1011 inputs['skyInfo'] = skyInfo
1012
1013 if self.config.doPropagateFlags:
1014 if self.config.propagateFlags.target == PropagateSourceFlagsTask:
1015 # New version
1016 ccdInputs = inputs["exposure"].getInfo().getCoaddInputs().ccds
1017 inputs["ccdInputs"] = ccdInputs
1018
1019 if "sourceTableHandles" in inputs:
1020 sourceTableHandles = inputs.pop("sourceTableHandles")
1021 sourceTableHandleDict = {handle.dataId["visit"]: handle
1022 for handle in sourceTableHandles}
1023 inputs["sourceTableHandleDict"] = sourceTableHandleDict
1024 if "finalizedSourceTableHandles" in inputs:
1025 finalizedSourceTableHandles = inputs.pop("finalizedSourceTableHandles")
1026 finalizedSourceTableHandleDict = {handle.dataId["visit"]: handle
1027 for handle in finalizedSourceTableHandles}
1028 inputs["finalizedSourceTableHandleDict"] = finalizedSourceTableHandleDict
1029 else:
1030 # Deprecated legacy version
1031 # Filter out any visit catalog that is not coadd inputs
1032 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds
1033 visitKey = ccdInputs.schema.find("visit").key
1034 ccdKey = ccdInputs.schema.find("ccd").key
1035 inputVisitIds = set()
1036 ccdRecordsWcs = {}
1037 for ccdRecord in ccdInputs:
1038 visit = ccdRecord.get(visitKey)
1039 ccd = ccdRecord.get(ccdKey)
1040 inputVisitIds.add((visit, ccd))
1041 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
1042
1043 inputCatalogsToKeep = []
1044 inputCatalogWcsUpdate = []
1045 for i, dataRef in enumerate(inputRefs.visitCatalogs):
1046 key = (dataRef.dataId['visit'], dataRef.dataId['detector'])
1047 if key in inputVisitIds:
1048 inputCatalogsToKeep.append(inputs['visitCatalogs'][i])
1049 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
1050 inputs['visitCatalogs'] = inputCatalogsToKeep
1051 inputs['wcsUpdates'] = inputCatalogWcsUpdate
1052 inputs['ccdInputs'] = ccdInputs
1053
1054 outputs = self.run(**inputs)
1055 butlerQC.put(outputs, outputRefs)
1056
1057 def runDataRef(self, patchRef, psfCache=100):
1058 """!
1059 @brief Deblend and measure.
1060
1061 @param[in] patchRef: Patch reference.
1062
1063 Set 'is-primary' and related flags. Propagate flags
1064 from individual visits. Optionally match the sources to a reference catalog and write the matches.
1065 Finally, write the deblended sources and measurements out.
1066 """
1067 if self.config.hasFakes:
1068 coaddType = "fakes_" + self.config.coaddName
1069 else:
1070 coaddType = self.config.coaddName
1071 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
1072 exposure.getPsf().setCacheCapacity(psfCache)
1073 sources = self.readSources(patchRef)
1074 table = sources.getTable()
1075 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1076 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1077
1078 if self.config.doPropagateFlags:
1079 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1080 else:
1081 ccdInputs = None
1082
1083 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=False,
1084 log=self.log)
1085 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId,
1086 ccdInputs=ccdInputs, butler=patchRef.getButler())
1087
1088 if self.config.doMatchSources:
1089 self.writeMatches(patchRef, results)
1090 self.write(patchRef, results.outputSources)
1091
1092 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1093 butler=None, sourceTableHandleDict=None, finalizedSourceTableHandleDict=None):
1094 """Run measurement algorithms on the input exposure, and optionally populate the
1095 resulting catalog with extra information.
1096
1097 Parameters
1098 ----------
1099 exposure : `lsst.afw.exposure.Exposure`
1100 The input exposure on which measurements are to be performed
1102 A catalog built from the results of merged detections, or
1103 deblender outputs.
1104 skyInfo : `lsst.pipe.base.Struct`
1105 A struct containing information about the position of the input exposure within
1106 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box
1107 exposureId : `int` or `bytes`
1108 packed unique number or bytes unique to the input exposure
1109 ccdInputs : `lsst.afw.table.ExposureCatalog`
1110 Catalog containing information on the individual visits which went into making
1111 the coadd.
1112 sourceTableHandleDict : `dict` [`int`: `lsst.daf.butler.DeferredDatasetHandle`]
1113 Dict for sourceTable_visit handles (key is visit) for propagating flags.
1114 These tables are derived from the ``CalibrateTask`` sources, and contain
1115 astrometry and photometry flags, and optionally PSF flags.
1116 finalizedSourceTableHandleDict : `dict` [`int`: `lsst.daf.butler.DeferredDatasetHandle`], optional
1117 Dict for finalized_src_table handles (key is visit) for propagating flags.
1118 These tables are derived from ``FinalizeCalibrationTask`` and contain
1119 PSF flags from the finalized PSF estimation.
1120 visitCatalogs : list of `lsst.afw.table.SourceCatalogs`
1121 A list of source catalogs corresponding to measurements made on the individual
1122 visits which went into the input exposure. If None and butler is `None` then
1123 the task cannot propagate visit flags to the output catalog.
1124 Deprecated, to be removed with PropagateVisitFlagsTask.
1125 wcsUpdates : list of `lsst.afw.geom.SkyWcs`
1126 If visitCatalogs is not `None` this should be a list of wcs objects which correspond
1127 to the input visits. Used to put all coordinates to common system. If `None` and
1128 butler is `None` then the task cannot propagate visit flags to the output catalog.
1129 Deprecated, to be removed with PropagateVisitFlagsTask.
1130 butler : `lsst.daf.persistence.Butler`
1131 A gen2 butler used to load visit catalogs.
1132 Deprecated, to be removed with Gen2.
1133
1134 Returns
1135 -------
1136 results : `lsst.pipe.base.Struct`
1137 Results of running measurement task. Will contain the catalog in the
1138 sources attribute. Optionally will have results of matching to a
1139 reference catalog in the matchResults attribute, and denormalized
1140 matches in the denormMatches attribute.
1141 """
1142 self.measurement.run(sources, exposure, exposureId=exposureId)
1143
1144 if self.config.doApCorr:
1145 self.applyApCorr.run(
1146 catalog=sources,
1147 apCorrMap=exposure.getInfo().getApCorrMap()
1148 )
1149
1150 # TODO DM-11568: this contiguous check-and-copy could go away if we
1151 # reserve enough space during SourceDetection and/or SourceDeblend.
1152 # NOTE: sourceSelectors require contiguous catalogs, so ensure
1153 # contiguity now, so views are preserved from here on.
1154 if not sources.isContiguous():
1155 sources = sources.copy(deep=True)
1156
1157 if self.config.doRunCatalogCalculation:
1158 self.catalogCalculation.run(sources)
1159
1160 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1161 patchInfo=skyInfo.patchInfo)
1162 if self.config.doPropagateFlags:
1163 if self.config.propagateFlags.target == PropagateSourceFlagsTask:
1164 # New version
1165 self.propagateFlags.run(
1166 sources,
1167 ccdInputs,
1168 sourceTableHandleDict,
1169 finalizedSourceTableHandleDict
1170 )
1171 else:
1172 # Legacy deprecated version
1173 self.propagateFlags.run(
1174 butler,
1175 sources,
1176 ccdInputs,
1177 exposure.getWcs(),
1178 visitCatalogs,
1179 wcsUpdates
1180 )
1181
1182 results = Struct()
1183
1184 if self.config.doMatchSources:
1185 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel)
1186 matches = afwTable.packMatches(matchResult.matches)
1187 matches.table.setMetadata(matchResult.matchMeta)
1188 results.matchResult = matches
1189 if self.config.doWriteMatchesDenormalized:
1190 if matchResult.matches:
1191 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1192 else:
1193 self.log.warning("No matches, so generating dummy denormalized matches file")
1194 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1195 denormMatches.setMetadata(PropertyList())
1196 denormMatches.getMetadata().add("COMMENT",
1197 "This catalog is empty because no matches were found.")
1198 results.denormMatches = denormMatches
1199 results.denormMatches = denormMatches
1200
1201 results.outputSources = sources
1202 return results
1203
1204 def readSources(self, dataRef):
1205 """!
1206 @brief Read input sources.
1207
1208 @param[in] dataRef: Data reference for catalog of merged detections
1209 @return List of sources in merged catalog
1210
1211 We also need to add columns to hold the measurements we're about to make so we can measure in-place.
1212 """
1213 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1214 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
1215 idFactory = self.makeIdFactory(dataRef)
1216 for s in merged:
1217 idFactory.notify(s.getId())
1218 table = afwTable.SourceTable.make(self.schema, idFactory)
1219 sources = afwTable.SourceCatalog(table)
1220 sources.extend(merged, self.schemaMapper)
1221 return sources
1222
1223 def writeMatches(self, dataRef, results):
1224 """!
1225 @brief Write matches of the sources to the astrometric reference catalog.
1226
1227 @param[in] dataRef: data reference
1228 @param[in] results: results struct from run method
1229 """
1230 if hasattr(results, "matchResult"):
1231 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1232 if hasattr(results, "denormMatches"):
1233 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1234
1235 def write(self, dataRef, sources):
1236 """!
1237 @brief Write the source catalog.
1238
1239 @param[in] dataRef: data reference
1240 @param[in] sources: source catalog
1241 """
1242 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1243 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)