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multiBand.py
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1#!/usr/bin/env python
2#
3# LSST Data Management System
4# Copyright 2008-2015 AURA/LSST.
5#
6# This product includes software developed by the
7# LSST Project (http://www.lsst.org/).
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the LSST License Statement and
20# the GNU General Public License along with this program. If not,
21# see <https://www.lsstcorp.org/LegalNotices/>.
22#
23import warnings
24import numpy as np
25
26from lsst.coadd.utils.coaddDataIdContainer import ExistingCoaddDataIdContainer
27from lsst.coadd.utils.getGen3CoaddExposureId import getGen3CoaddExposureId
28from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner,
29 PipelineTask, PipelineTaskConfig, PipelineTaskConnections)
30import lsst.pipe.base.connectionTypes as cT
31from lsst.pex.config import Config, Field, ConfigurableField, ChoiceField
32from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader, ScaleVarianceTask
33from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask
34from lsst.meas.deblender import SourceDeblendTask
35from lsst.meas.extensions.scarlet import ScarletDeblendTask
36from lsst.pipe.tasks.coaddBase import getSkyInfo
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 deprecated=("doInsertFakes is no longer supported. This config will be removed "
121 "after v24."))
122 insertFakes = ConfigurableField(target=BaseFakeSourcesTask,
123 doc="Injection of fake sources for testing "
124 "purposes (must be retargeted)",
125 deprecated=("insertFakes is no longer supported. This config will "
126 "be removed after v24."))
127 hasFakes = Field(
128 dtype=bool,
129 default=False,
130 doc="Should be set to True if fake sources have been inserted into the input data.",
131 )
132
133 def setDefaults(self):
134 super().setDefaults()
135 self.detection.thresholdType = "pixel_stdev"
136 self.detection.isotropicGrow = True
137 # Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic
138 self.detection.reEstimateBackground = False
139 self.detection.background.useApprox = False
140 self.detection.background.binSize = 4096
141 self.detection.background.undersampleStyle = 'REDUCE_INTERP_ORDER'
142 self.detection.doTempWideBackground = True # Suppress large footprints that overwhelm the deblender
143
144
150
151
152class DetectCoaddSourcesTask(PipelineTask, CmdLineTask):
153 r"""!
154 @anchor DetectCoaddSourcesTask_
155
156 @brief Detect sources on a coadd
157
158 @section pipe_tasks_multiBand_Contents Contents
159
160 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose
161 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize
162 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run
163 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config
164 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug
165 - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example
166
167 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
168
169 Command-line task that detects sources on a coadd of exposures obtained with a single filter.
170
171 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise
172 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane
173 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should
174 propagate the full covariance matrix -- but it is simple and works well in practice.
175
176 After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref
177 SourceDetectionTask_ "detection" subtask.
178
179 @par Inputs:
180 deepCoadd{tract,patch,filter}: ExposureF
181 @par Outputs:
182 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
183 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input
184 exposure (ExposureF)
185 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList
186 @par Data Unit:
187 tract, patch, filter
188
189 DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask.
190 You can retarget this subtask if you wish.
191
192 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
193
194 @copydoc \_\_init\_\_
195
196 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
197
198 @copydoc run
199
200 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
201
202 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig"
203
204 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
205
206 The command line task interface supports a
207 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
208 files.
209
210 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to
211 @ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for
212 @ref SourceDetectionTask_ "SourceDetectionTask" for further information.
213
214 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example
215 of using DetectCoaddSourcesTask
216
217 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of
218 the task is to update the background, detect all sources in a single band and generate a set of parent
219 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and,
220 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data
221 reference to the coadd to be processed. A list of the available optional arguments can be obtained by
222 calling detectCoaddSources.py with the `--help` command line argument:
223 @code
224 detectCoaddSources.py --help
225 @endcode
226
227 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
228 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed
229 steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows:
230 @code
231 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
232 @endcode
233 that will process the HSC-I band data. The results are written to
234 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
235
236 It is also necessary to run:
237 @code
238 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
239 @endcode
240 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
241 processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask".
242 """
243 _DefaultName = "detectCoaddSources"
244 ConfigClass = DetectCoaddSourcesConfig
245 getSchemaCatalogs = _makeGetSchemaCatalogs("det")
246 makeIdFactory = _makeMakeIdFactory("CoaddId")
247
248 @classmethod
249 def _makeArgumentParser(cls):
250 parser = ArgumentParser(name=cls._DefaultName)
251 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
252 ContainerClass=ExistingCoaddDataIdContainer)
253 return parser
254
255 def __init__(self, schema=None, **kwargs):
256 """!
257 @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask.
258
259 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
260
261 @param[in] schema: initial schema for the output catalog, modified-in place to include all
262 fields set by this task. If None, the source minimal schema will be used.
263 @param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__
264 """
265 # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree
266 # call structure has been reviewed carefully to be sure super will work as intended.
267 super().__init__(**kwargs)
268 if schema is None:
269 schema = afwTable.SourceTable.makeMinimalSchema()
270 self.schema = schema
271 self.makeSubtask("detection", schema=self.schema)
272 if self.config.doScaleVariance:
273 self.makeSubtask("scaleVariance")
274
275 self.detectionSchema = afwTable.SourceCatalog(self.schema)
276
277 def runDataRef(self, patchRef):
278 """!
279 @brief Run detection on a coadd.
280
281 Invokes @ref run and then uses @ref write to output the
282 results.
283
284 @param[in] patchRef: data reference for patch
285 """
286 if self.config.hasFakes:
287 exposure = patchRef.get("fakes_" + self.config.coaddName + "Coadd", immediate=True)
288 else:
289 exposure = patchRef.get(self.config.coaddName + "Coadd", immediate=True)
290 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, log=self.log)
291 results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId)
292 self.write(results, patchRef)
293 return results
294
295 def runQuantum(self, butlerQC, inputRefs, outputRefs):
296 inputs = butlerQC.get(inputRefs)
297 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch_band")
298 inputs["idFactory"] = exposureIdInfo.makeSourceIdFactory()
299 inputs["expId"] = exposureIdInfo.expId
300 outputs = self.run(**inputs)
301 butlerQC.put(outputs, outputRefs)
302
303 def run(self, exposure, idFactory, expId):
304 """!
305 @brief Run detection on an exposure.
306
307 First scale the variance plane to match the observed variance
308 using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to
309 detect sources.
310
311 @param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled,
312 depending on configuration).
313 @param[in] idFactory: IdFactory to set source identifiers
314 @param[in] expId: Exposure identifier (integer) for RNG seed
315
316 @return a pipe.base.Struct with fields
317 - sources: catalog of detections
318 - backgrounds: list of backgrounds
319 """
320 if self.config.doScaleVariance:
321 varScale = self.scaleVariance.run(exposure.maskedImage)
322 exposure.getMetadata().add("VARIANCE_SCALE", varScale)
323 backgrounds = afwMath.BackgroundList()
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
539 so we can measure in-place.
540 """
541 merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=True)
542 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
543 idFactory = self.makeIdFactory(dataRef)
544 # There may be gaps in the mergeDet catalog, which will cause the
545 # source ids to be inconsistent. So we update the id factory
546 # with the largest id already in the catalog.
547 maxId = np.max(merged["id"])
548 idFactory.notify(maxId)
549 table = afwTable.SourceTable.make(self.schema, idFactory)
550 sources = afwTable.SourceCatalog(table)
551 sources.extend(merged, self.schemaMapper)
552 return sources
553
554 def write(self, dataRef, sources, catalogType):
555 """Write the source catalog(s)
556
557 Parameters
558 ----------
559 dataRef: Data Reference
560 Reference to the output catalog.
561 sources: `SourceCatalog`
562 Flux conserved sources to write to file.
563 If using the single band deblender, this is the catalog
564 generated.
565 template_sources: `SourceCatalog`
566 Source catalog using the multiband template models
567 as footprints.
568 """
569 dataRef.put(sources, self.config.coaddName + f"Coadd_deblended{catalogType}")
570 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)
571
572 def writeMetadata(self, dataRefList):
573 """Write the metadata produced from processing the data.
574 Parameters
575 ----------
576 dataRefList
577 List of Butler data references used to write the metadata.
578 The metadata is written to dataset type `CmdLineTask._getMetadataName`.
579 """
580 for dataRef in dataRefList:
581 try:
582 metadataName = self._getMetadataName()
583 if metadataName is not None:
584 dataRef.put(self.getFullMetadata(), metadataName)
585 except Exception as e:
586 self.log.warning("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
587
588
589class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections,
590 dimensions=("tract", "patch", "band", "skymap"),
591 defaultTemplates={"inputCoaddName": "deep",
592 "outputCoaddName": "deep",
593 "deblendedCatalog": "deblendedFlux"}):
594 warnings.warn("MeasureMergedCoaddSourcesConnections.defaultTemplates is deprecated and no longer used. "
595 "Use MeasureMergedCoaddSourcesConfig.inputCatalog.")
596 inputSchema = cT.InitInput(
597 doc="Input schema for measure merged task produced by a deblender or detection task",
598 name="{inputCoaddName}Coadd_deblendedFlux_schema",
599 storageClass="SourceCatalog"
600 )
601 outputSchema = cT.InitOutput(
602 doc="Output schema after all new fields are added by task",
603 name="{inputCoaddName}Coadd_meas_schema",
604 storageClass="SourceCatalog"
605 )
606 refCat = cT.PrerequisiteInput(
607 doc="Reference catalog used to match measured sources against known sources",
608 name="ref_cat",
609 storageClass="SimpleCatalog",
610 dimensions=("skypix",),
611 deferLoad=True,
612 multiple=True
613 )
614 exposure = cT.Input(
615 doc="Input coadd image",
616 name="{inputCoaddName}Coadd_calexp",
617 storageClass="ExposureF",
618 dimensions=("tract", "patch", "band", "skymap")
619 )
620 skyMap = cT.Input(
621 doc="SkyMap to use in processing",
622 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
623 storageClass="SkyMap",
624 dimensions=("skymap",),
625 )
626 visitCatalogs = cT.Input(
627 doc="Source catalogs for visits which overlap input tract, patch, band. Will be "
628 "further filtered in the task for the purpose of propagating flags from image calibration "
629 "and characterization to coadd objects. Only used in legacy PropagateVisitFlagsTask.",
630 name="src",
631 dimensions=("instrument", "visit", "detector"),
632 storageClass="SourceCatalog",
633 multiple=True
634 )
635 sourceTableHandles = cT.Input(
636 doc=("Source tables that are derived from the ``CalibrateTask`` sources. "
637 "These tables contain astrometry and photometry flags, and optionally "
638 "PSF flags."),
639 name="sourceTable_visit",
640 storageClass="DataFrame",
641 dimensions=("instrument", "visit"),
642 multiple=True,
643 deferLoad=True,
644 )
645 finalizedSourceTableHandles = cT.Input(
646 doc=("Finalized source tables from ``FinalizeCalibrationTask``. These "
647 "tables contain PSF flags from the finalized PSF estimation."),
648 name="finalized_src_table",
649 storageClass="DataFrame",
650 dimensions=("instrument", "visit"),
651 multiple=True,
652 deferLoad=True,
653 )
654 inputCatalog = cT.Input(
655 doc=("Name of the input catalog to use."
656 "If the single band deblender was used this should be 'deblendedFlux."
657 "If the multi-band deblender was used this should be 'deblendedModel, "
658 "or deblendedFlux if the multiband deblender was configured to output "
659 "deblended flux catalogs. If no deblending was performed this should "
660 "be 'mergeDet'"),
661 name="{inputCoaddName}Coadd_{deblendedCatalog}",
662 storageClass="SourceCatalog",
663 dimensions=("tract", "patch", "band", "skymap"),
664 )
665 scarletCatalog = cT.Input(
666 doc="Catalogs produced by multiband deblending",
667 name="{inputCoaddName}Coadd_deblendedCatalog",
668 storageClass="SourceCatalog",
669 dimensions=("tract", "patch", "skymap"),
670 )
671 scarletModels = cT.Input(
672 doc="Multiband scarlet models produced by the deblender",
673 name="{inputCoaddName}Coadd_scarletModelData",
674 storageClass="ScarletModelData",
675 dimensions=("tract", "patch", "skymap"),
676 )
677 outputSources = cT.Output(
678 doc="Source catalog containing all the measurement information generated in this task",
679 name="{outputCoaddName}Coadd_meas",
680 dimensions=("tract", "patch", "band", "skymap"),
681 storageClass="SourceCatalog",
682 )
683 matchResult = cT.Output(
684 doc="Match catalog produced by configured matcher, optional on doMatchSources",
685 name="{outputCoaddName}Coadd_measMatch",
686 dimensions=("tract", "patch", "band", "skymap"),
687 storageClass="Catalog",
688 )
689 denormMatches = cT.Output(
690 doc="Denormalized Match catalog produced by configured matcher, optional on "
691 "doWriteMatchesDenormalized",
692 name="{outputCoaddName}Coadd_measMatchFull",
693 dimensions=("tract", "patch", "band", "skymap"),
694 storageClass="Catalog",
695 )
696
697 def __init__(self, *, config=None):
698 super().__init__(config=config)
699 if config.doPropagateFlags is False:
700 self.inputs -= set(("visitCatalogs",))
701 self.inputs -= set(("sourceTableHandles",))
702 self.inputs -= set(("finalizedSourceTableHandles",))
703 elif config.propagateFlags.target == PropagateSourceFlagsTask:
704 # New PropagateSourceFlagsTask does not use visitCatalogs.
705 self.inputs -= set(("visitCatalogs",))
706 # Check for types of flags required.
707 if not config.propagateFlags.source_flags:
708 self.inputs -= set(("sourceTableHandles",))
709 if not config.propagateFlags.finalized_source_flags:
710 self.inputs -= set(("finalizedSourceTableHandles",))
711 else:
712 # Deprecated PropagateVisitFlagsTask uses visitCatalogs.
713 self.inputs -= set(("sourceTableHandles",))
714 self.inputs -= set(("finalizedSourceTableHandles",))
715
716 if config.inputCatalog == "deblendedCatalog":
717 self.inputs -= set(("inputCatalog",))
718
719 if not config.doAddFootprints:
720 self.inputs -= set(("scarletModels",))
721 else:
722 self.inputs -= set(("deblendedCatalog"))
723 self.inputs -= set(("scarletModels",))
724
725 if config.doMatchSources is False:
726 self.outputs -= set(("matchResult",))
727
728 if config.doWriteMatchesDenormalized is False:
729 self.outputs -= set(("denormMatches",))
730
731
732class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
733 pipelineConnections=MeasureMergedCoaddSourcesConnections):
734 """!
735 @anchor MeasureMergedCoaddSourcesConfig_
736
737 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask
738 """
739 inputCatalog = ChoiceField(
740 dtype=str,
741 default="deblendedCatalog",
742 allowed={
743 "deblendedCatalog": "Output catalog from ScarletDeblendTask",
744 "deblendedFlux": "Output catalog from SourceDeblendTask",
745 "mergeDet": "The merged detections before deblending."
746 },
747 doc="The name of the input catalog.",
748 )
749 doAddFootprints = Field(dtype=bool,
750 default=True,
751 doc="Whether or not to add footprints to the input catalog from scarlet models. "
752 "This should be true whenever using the multi-band deblender, "
753 "otherwise this should be False.")
754 doConserveFlux = Field(dtype=bool, default=True,
755 doc="Whether to use the deblender models as templates to re-distribute the flux "
756 "from the 'exposure' (True), or to perform measurements on the deblender "
757 "model footprints.")
758 doStripFootprints = Field(dtype=bool, default=True,
759 doc="Whether to strip footprints from the output catalog before "
760 "saving to disk. "
761 "This is usually done when using scarlet models to save disk space.")
762 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement")
763 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch")
764 doPropagateFlags = Field(
765 dtype=bool, default=True,
766 doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
767 )
768 propagateFlags = ConfigurableField(target=PropagateSourceFlagsTask, doc="Propagate source flags to coadd")
769 doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?")
770 match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog")
771 doWriteMatchesDenormalized = Field(
772 dtype=bool,
773 default=False,
774 doc=("Write reference matches in denormalized format? "
775 "This format uses more disk space, but is more convenient to read."),
776 )
777 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
778 psfCache = Field(dtype=int, default=100, doc="Size of psfCache")
779 checkUnitsParseStrict = Field(
780 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
781 dtype=str,
782 default="raise",
783 )
784 doApCorr = Field(
785 dtype=bool,
786 default=True,
787 doc="Apply aperture corrections"
788 )
789 applyApCorr = ConfigurableField(
790 target=ApplyApCorrTask,
791 doc="Subtask to apply aperture corrections"
792 )
793 doRunCatalogCalculation = Field(
794 dtype=bool,
795 default=True,
796 doc='Run catalogCalculation task'
797 )
798 catalogCalculation = ConfigurableField(
799 target=CatalogCalculationTask,
800 doc="Subtask to run catalogCalculation plugins on catalog"
801 )
802
803 hasFakes = Field(
804 dtype=bool,
805 default=False,
806 doc="Should be set to True if fake sources have been inserted into the input data."
807 )
808
809 @property
810 def refObjLoader(self):
811 return self.match.refObjLoader
812
813 def setDefaults(self):
814 super().setDefaults()
815 self.measurement.plugins.names |= ['base_InputCount',
816 'base_Variance',
817 'base_LocalPhotoCalib',
818 'base_LocalWcs']
819 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE',
820 'INEXACT_PSF']
821 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE',
822 'INEXACT_PSF']
823
824 def validate(self):
825 super().validate()
826 refCatGen2 = getattr(self.refObjLoader, "ref_dataset_name", None)
827 if refCatGen2 is not None and refCatGen2 != self.connections.refCat:
828 raise ValueError(
829 f"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
830 f"are different. These options must be kept in sync until Gen2 is retired."
831 )
832
833
834
840
841
842class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
843 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
844 @staticmethod
845 def getTargetList(parsedCmd, **kwargs):
846 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
847
848
849class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
850 r"""!
851 @anchor MeasureMergedCoaddSourcesTask_
852
853 @brief Deblend sources from master catalog in each coadd seperately and measure.
854
855 @section pipe_tasks_multiBand_Contents Contents
856
857 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
858 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
859 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
860 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
861 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
862 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
863
864 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
865
866 Command-line task that uses peaks and footprints from a master catalog to perform deblending and
867 measurement in each coadd.
868
869 Given a master input catalog of sources (peaks and footprints) or deblender outputs
870 (including a HeavyFootprint in each band), measure each source on the
871 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a
872 consistent set of child sources.
873
874 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source
875 properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit
876 flags are propagated to the coadd sources.
877
878 Optionally, we can match the coadd sources to an external reference catalog.
879
880 @par Inputs:
881 deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog
882 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
883 @par Outputs:
884 deepCoadd_meas{tract,patch,filter}: SourceCatalog
885 @par Data Unit:
886 tract, patch, filter
887
888 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
889
890 <DL>
891 <DT> @ref SingleFrameMeasurementTask_ "measurement"
892 <DD> Measure source properties of deblended sources.</DD>
893 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags"
894 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are
895 not at the edge of the field and that have either not been deblended or are the children of deblended
896 sources</DD>
897 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags"
898 <DD> Propagate flags set in individual visits to the coadd.</DD>
899 <DT> @ref DirectMatchTask_ "match"
900 <DD> Match input sources to a reference catalog (optional).
901 </DD>
902 </DL>
903 These subtasks may be retargeted as required.
904
905 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
906
907 @copydoc \_\_init\_\_
908
909 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
910
911 @copydoc run
912
913 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
914
915 See @ref MeasureMergedCoaddSourcesConfig_
916
917 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
918
919 The command line task interface supports a
920 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
921 files.
922
923 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
924 the various sub-tasks. See the documetation for individual sub-tasks for more information.
925
926 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
927 MeasureMergedCoaddSourcesTask
928
929 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
930 The next stage in the multi-band processing procedure will merge these measurements into a suitable
931 catalog for driving forced photometry.
932
933 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
934 to be processed.
935 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the
936 `--help` command line argument:
937 @code
938 measureCoaddSources.py --help
939 @endcode
940
941 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
942 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
943 step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band
944 coadd as follows:
945 @code
946 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
947 @endcode
948 This will process the HSC-I band data. The results are written in
949 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
950
951 It is also necessary to run
952 @code
953 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
954 @endcode
955 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
956 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask".
957 """
958 _DefaultName = "measureCoaddSources"
959 ConfigClass = MeasureMergedCoaddSourcesConfig
960 RunnerClass = MeasureMergedCoaddSourcesRunner
961 getSchemaCatalogs = _makeGetSchemaCatalogs("meas")
962 # The IDs we already have are of this type
963 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False)
964
965 @classmethod
966 def _makeArgumentParser(cls):
967 parser = ArgumentParser(name=cls._DefaultName)
968 parser.add_id_argument("--id", "deepCoadd_calexp",
969 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
970 ContainerClass=ExistingCoaddDataIdContainer)
971 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
972 return parser
973
974 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
975 **kwargs):
976 """!
977 @brief Initialize the task.
978
979 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
980 @param[in] schema: the schema of the merged detection catalog used as input to this one
981 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog
982 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
983 catalog. May be None if the loader can be constructed from the butler argument or all steps
984 requiring a reference catalog are disabled.
985 @param[in] butler: a butler used to read the input schemas from disk or construct the reference
986 catalog loader, if schema or peakSchema or refObjLoader is None
987
988 The task will set its own self.schema attribute to the schema of the output measurement catalog.
989 This will include all fields from the input schema, as well as additional fields for all the
990 measurements.
991 """
992 super().__init__(**kwargs)
993 self.deblended = self.config.inputCatalog.startswith("deblended")
994 self.inputCatalog = "Coadd_" + self.config.inputCatalog
995 if initInputs is not None:
996 schema = initInputs['inputSchema'].schema
997 if schema is None:
998 assert butler is not None, "Neither butler nor schema is defined"
999 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema
1000 self.schemaMapper = afwTable.SchemaMapper(schema)
1001 self.schemaMapper.addMinimalSchema(schema)
1002 self.schema = self.schemaMapper.getOutputSchema()
1003 self.algMetadata = PropertyList()
1004 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata)
1005 self.makeSubtask("setPrimaryFlags", schema=self.schema)
1006 if self.config.doMatchSources:
1007 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
1008 if self.config.doPropagateFlags:
1009 self.makeSubtask("propagateFlags", schema=self.schema)
1010 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
1011 if self.config.doApCorr:
1012 self.makeSubtask("applyApCorr", schema=self.schema)
1013 if self.config.doRunCatalogCalculation:
1014 self.makeSubtask("catalogCalculation", schema=self.schema)
1015
1016 self.outputSchema = afwTable.SourceCatalog(self.schema)
1017
1018 def runQuantum(self, butlerQC, inputRefs, outputRefs):
1019 inputs = butlerQC.get(inputRefs)
1020
1021 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat],
1022 inputs.pop('refCat'), config=self.config.refObjLoader,
1023 log=self.log)
1024 self.match.setRefObjLoader(refObjLoader)
1025
1026 # Set psfcache
1027 # move this to run after gen2 deprecation
1028 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
1029
1030 # Get unique integer ID for IdFactory and RNG seeds
1031 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch")
1032 inputs['exposureId'] = exposureIdInfo.expId
1033 idFactory = exposureIdInfo.makeSourceIdFactory()
1034 # Transform inputCatalog
1035 table = afwTable.SourceTable.make(self.schema, idFactory)
1036 sources = afwTable.SourceCatalog(table)
1037 # Load the correct input catalog
1038 if "scarletCatalog" in inputs:
1039 inputCatalog = inputs.pop("scarletCatalog")
1040 catalogRef = inputRefs.scarletCatalog
1041 else:
1042 inputCatalog = inputs.pop("inputCatalog")
1043 catalogRef = inputRefs.inputCatalog
1044 sources.extend(inputCatalog, self.schemaMapper)
1045 del inputCatalog
1046 # Add the HeavyFootprints to the deblended sources
1047 if self.config.doAddFootprints:
1048 modelData = inputs.pop('scarletModels')
1049 if self.config.doConserveFlux:
1050 redistributeImage = inputs['exposure'].image
1051 else:
1052 redistributeImage = None
1053 modelData.updateCatalogFootprints(
1054 catalog=sources,
1055 band=inputRefs.exposure.dataId["band"],
1056 psfModel=inputs['exposure'].getPsf(),
1057 redistributeImage=redistributeImage,
1058 removeScarletData=True,
1059 )
1060 table = sources.getTable()
1061 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1062 inputs['sources'] = sources
1063
1064 skyMap = inputs.pop('skyMap')
1065 tractNumber = catalogRef.dataId['tract']
1066 tractInfo = skyMap[tractNumber]
1067 patchInfo = tractInfo.getPatchInfo(catalogRef.dataId['patch'])
1068 skyInfo = Struct(
1069 skyMap=skyMap,
1070 tractInfo=tractInfo,
1071 patchInfo=patchInfo,
1072 wcs=tractInfo.getWcs(),
1073 bbox=patchInfo.getOuterBBox()
1074 )
1075 inputs['skyInfo'] = skyInfo
1076
1077 if self.config.doPropagateFlags:
1078 if self.config.propagateFlags.target == PropagateSourceFlagsTask:
1079 # New version
1080 ccdInputs = inputs["exposure"].getInfo().getCoaddInputs().ccds
1081 inputs["ccdInputs"] = ccdInputs
1082
1083 if "sourceTableHandles" in inputs:
1084 sourceTableHandles = inputs.pop("sourceTableHandles")
1085 sourceTableHandleDict = {handle.dataId["visit"]: handle
1086 for handle in sourceTableHandles}
1087 inputs["sourceTableHandleDict"] = sourceTableHandleDict
1088 if "finalizedSourceTableHandles" in inputs:
1089 finalizedSourceTableHandles = inputs.pop("finalizedSourceTableHandles")
1090 finalizedSourceTableHandleDict = {handle.dataId["visit"]: handle
1091 for handle in finalizedSourceTableHandles}
1092 inputs["finalizedSourceTableHandleDict"] = finalizedSourceTableHandleDict
1093 else:
1094 # Deprecated legacy version
1095 # Filter out any visit catalog that is not coadd inputs
1096 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds
1097 visitKey = ccdInputs.schema.find("visit").key
1098 ccdKey = ccdInputs.schema.find("ccd").key
1099 inputVisitIds = set()
1100 ccdRecordsWcs = {}
1101 for ccdRecord in ccdInputs:
1102 visit = ccdRecord.get(visitKey)
1103 ccd = ccdRecord.get(ccdKey)
1104 inputVisitIds.add((visit, ccd))
1105 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
1106
1107 inputCatalogsToKeep = []
1108 inputCatalogWcsUpdate = []
1109 for i, dataRef in enumerate(inputRefs.visitCatalogs):
1110 key = (dataRef.dataId['visit'], dataRef.dataId['detector'])
1111 if key in inputVisitIds:
1112 inputCatalogsToKeep.append(inputs['visitCatalogs'][i])
1113 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
1114 inputs['visitCatalogs'] = inputCatalogsToKeep
1115 inputs['wcsUpdates'] = inputCatalogWcsUpdate
1116 inputs['ccdInputs'] = ccdInputs
1117
1118 outputs = self.run(**inputs)
1119 # Strip HeavyFootprints to save space on disk
1120 sources = outputs.outputSources
1121 butlerQC.put(outputs, outputRefs)
1122
1123 def runDataRef(self, patchRef, psfCache=100):
1124 """!
1125 @brief Deblend and measure.
1126
1127 @param[in] patchRef: Patch reference.
1128
1129 Set 'is-primary' and related flags. Propagate flags
1130 from individual visits. Optionally match the sources to a reference catalog and write the matches.
1131 Finally, write the deblended sources and measurements out.
1132 """
1133 if self.config.hasFakes:
1134 coaddType = "fakes_" + self.config.coaddName
1135 else:
1136 coaddType = self.config.coaddName
1137 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
1138 exposure.getPsf().setCacheCapacity(psfCache)
1139 sources = self.readSources(patchRef)
1140 table = sources.getTable()
1141 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1142 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1143
1144 if self.config.doPropagateFlags:
1145 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1146 else:
1147 ccdInputs = None
1148
1149 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=False,
1150 log=self.log)
1151 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId,
1152 ccdInputs=ccdInputs, butler=patchRef.getButler())
1153
1154 if self.config.doMatchSources:
1155 self.writeMatches(patchRef, results)
1156 self.write(patchRef, results.outputSources)
1157
1158 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1159 butler=None, sourceTableHandleDict=None, finalizedSourceTableHandleDict=None):
1160 """Run measurement algorithms on the input exposure, and optionally populate the
1161 resulting catalog with extra information.
1162
1163 Parameters
1164 ----------
1165 exposure : `lsst.afw.exposure.Exposure`
1166 The input exposure on which measurements are to be performed
1168 A catalog built from the results of merged detections, or
1169 deblender outputs.
1170 skyInfo : `lsst.pipe.base.Struct`
1171 A struct containing information about the position of the input exposure within
1172 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box
1173 exposureId : `int` or `bytes`
1174 packed unique number or bytes unique to the input exposure
1175 ccdInputs : `lsst.afw.table.ExposureCatalog`
1176 Catalog containing information on the individual visits which went into making
1177 the coadd.
1178 sourceTableHandleDict : `dict` [`int`: `lsst.daf.butler.DeferredDatasetHandle`]
1179 Dict for sourceTable_visit handles (key is visit) for propagating flags.
1180 These tables are derived from the ``CalibrateTask`` sources, and contain
1181 astrometry and photometry flags, and optionally PSF flags.
1182 finalizedSourceTableHandleDict : `dict` [`int`: `lsst.daf.butler.DeferredDatasetHandle`], optional
1183 Dict for finalized_src_table handles (key is visit) for propagating flags.
1184 These tables are derived from ``FinalizeCalibrationTask`` and contain
1185 PSF flags from the finalized PSF estimation.
1186 visitCatalogs : list of `lsst.afw.table.SourceCatalogs`
1187 A list of source catalogs corresponding to measurements made on the individual
1188 visits which went into the input exposure. If None and butler is `None` then
1189 the task cannot propagate visit flags to the output catalog.
1190 Deprecated, to be removed with PropagateVisitFlagsTask.
1191 wcsUpdates : list of `lsst.afw.geom.SkyWcs`
1192 If visitCatalogs is not `None` this should be a list of wcs objects which correspond
1193 to the input visits. Used to put all coordinates to common system. If `None` and
1194 butler is `None` then the task cannot propagate visit flags to the output catalog.
1195 Deprecated, to be removed with PropagateVisitFlagsTask.
1196 butler : `lsst.daf.persistence.Butler`
1197 A gen2 butler used to load visit catalogs.
1198 Deprecated, to be removed with Gen2.
1199
1200 Returns
1201 -------
1202 results : `lsst.pipe.base.Struct`
1203 Results of running measurement task. Will contain the catalog in the
1204 sources attribute. Optionally will have results of matching to a
1205 reference catalog in the matchResults attribute, and denormalized
1206 matches in the denormMatches attribute.
1207 """
1208 self.measurement.run(sources, exposure, exposureId=exposureId)
1209
1210 if self.config.doApCorr:
1211 self.applyApCorr.run(
1212 catalog=sources,
1213 apCorrMap=exposure.getInfo().getApCorrMap()
1214 )
1215
1216 # TODO DM-11568: this contiguous check-and-copy could go away if we
1217 # reserve enough space during SourceDetection and/or SourceDeblend.
1218 # NOTE: sourceSelectors require contiguous catalogs, so ensure
1219 # contiguity now, so views are preserved from here on.
1220 if not sources.isContiguous():
1221 sources = sources.copy(deep=True)
1222
1223 if self.config.doRunCatalogCalculation:
1224 self.catalogCalculation.run(sources)
1225
1226 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1227 patchInfo=skyInfo.patchInfo)
1228 if self.config.doPropagateFlags:
1229 if self.config.propagateFlags.target == PropagateSourceFlagsTask:
1230 # New version
1231 self.propagateFlags.run(
1232 sources,
1233 ccdInputs,
1234 sourceTableHandleDict,
1235 finalizedSourceTableHandleDict
1236 )
1237 else:
1238 # Legacy deprecated version
1239 self.propagateFlags.run(
1240 butler,
1241 sources,
1242 ccdInputs,
1243 exposure.getWcs(),
1244 visitCatalogs,
1245 wcsUpdates
1246 )
1247
1248 results = Struct()
1249
1250 if self.config.doMatchSources:
1251 matchResult = self.match.run(sources, exposure.getInfo().getFilter().bandLabel)
1252 matches = afwTable.packMatches(matchResult.matches)
1253 matches.table.setMetadata(matchResult.matchMeta)
1254 results.matchResult = matches
1255 if self.config.doWriteMatchesDenormalized:
1256 if matchResult.matches:
1257 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1258 else:
1259 self.log.warning("No matches, so generating dummy denormalized matches file")
1260 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1261 denormMatches.setMetadata(PropertyList())
1262 denormMatches.getMetadata().add("COMMENT",
1263 "This catalog is empty because no matches were found.")
1264 results.denormMatches = denormMatches
1265 results.denormMatches = denormMatches
1266
1267 results.outputSources = sources
1268 return results
1269
1270 def readSources(self, dataRef):
1271 """!
1272 @brief Read input sources.
1273
1274 @param[in] dataRef: Data reference for catalog of merged detections
1275 @return List of sources in merged catalog
1276
1277 We also need to add columns to hold the measurements we're about to make so we can measure in-place.
1278 """
1279 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1280 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
1281 idFactory = self.makeIdFactory(dataRef)
1282 for s in merged:
1283 idFactory.notify(s.getId())
1284 table = afwTable.SourceTable.make(self.schema, idFactory)
1285 sources = afwTable.SourceCatalog(table)
1286 sources.extend(merged, self.schemaMapper)
1287 return sources
1288
1289 def writeMatches(self, dataRef, results):
1290 """!
1291 @brief Write matches of the sources to the astrometric reference catalog.
1292
1293 @param[in] dataRef: data reference
1294 @param[in] results: results struct from run method
1295 """
1296 if hasattr(results, "matchResult"):
1297 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1298 if hasattr(results, "denormMatches"):
1299 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1300
1301 def write(self, dataRef, sources):
1302 """!
1303 @brief Write the source catalog.
1304
1305 @param[in] dataRef: data reference
1306 @param[in] sources: source catalog
1307 """
1308 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1309 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)
1310