lsst.pipe.tasks 21.0.0-178-g80f1dd77+d3f2e76fa8
multiBand.py
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1#!/usr/bin/env python
2#
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4# Copyright 2008-2015 AURA/LSST.
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23from lsst.coadd.utils.coaddDataIdContainer import ExistingCoaddDataIdContainer
24from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner,
25 PipelineTask, PipelineTaskConfig, PipelineTaskConnections)
26import lsst.pipe.base.connectionTypes as cT
27from lsst.pex.config import Config, Field, ConfigurableField
28from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader
29from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask
30from lsst.meas.deblender import SourceDeblendTask
31from lsst.meas.extensions.scarlet import ScarletDeblendTask
32from lsst.pipe.tasks.coaddBase import getSkyInfo
33from lsst.pipe.tasks.scaleVariance import ScaleVarianceTask
34from lsst.meas.astrom import DirectMatchTask, denormalizeMatches
35from lsst.pipe.tasks.fakes import BaseFakeSourcesTask
36from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
37from lsst.pipe.tasks.propagateVisitFlags import PropagateVisitFlagsTask
38import lsst.afw.image as afwImage
39import lsst.afw.table as afwTable
40import lsst.afw.math as afwMath
41from lsst.daf.base import PropertyList
42from lsst.skymap import BaseSkyMap
43from lsst.obs.base import ExposureIdInfo
44
45# NOTE: these imports are a convenience so multiband users only have to import this file.
46from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401
47from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401
48from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401
49from .multiBandUtils import getInputSchema, readCatalog, _makeMakeIdFactory # noqa: F401
50from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401
51from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401
52from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401
53from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401
54
55
56"""
57New set types:
58* deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter)
59* deepCoadd_mergeDet: merged detections (tract, patch)
60* deepCoadd_meas: measurements of merged detections (tract, patch, filter)
61* deepCoadd_ref: reference sources (tract, patch)
62All of these have associated *_schema catalogs that require no data ID and hold no records.
63
64In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in
65the mergeDet, meas, and ref dataset Footprints:
66* deepCoadd_peak_schema
67"""
68
69
70
71class DetectCoaddSourcesConnections(PipelineTaskConnections,
72 dimensions=("tract", "patch", "band", "skymap"),
73 defaultTemplates={"inputCoaddName": "deep", "outputCoaddName": "deep"}):
74 detectionSchema = cT.InitOutput(
75 doc="Schema of the detection catalog",
76 name="{outputCoaddName}Coadd_det_schema",
77 storageClass="SourceCatalog",
78 )
79 exposure = cT.Input(
80 doc="Exposure on which detections are to be performed",
81 name="{inputCoaddName}Coadd",
82 storageClass="ExposureF",
83 dimensions=("tract", "patch", "band", "skymap")
84 )
85 outputBackgrounds = cT.Output(
86 doc="Output Backgrounds used in detection",
87 name="{outputCoaddName}Coadd_calexp_background",
88 storageClass="Background",
89 dimensions=("tract", "patch", "band", "skymap")
90 )
91 outputSources = cT.Output(
92 doc="Detected sources catalog",
93 name="{outputCoaddName}Coadd_det",
94 storageClass="SourceCatalog",
95 dimensions=("tract", "patch", "band", "skymap")
96 )
97 outputExposure = cT.Output(
98 doc="Exposure post detection",
99 name="{outputCoaddName}Coadd_calexp",
100 storageClass="ExposureF",
101 dimensions=("tract", "patch", "band", "skymap")
102 )
103
104
105class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections):
106 """!
107 @anchor DetectCoaddSourcesConfig_
108
109 @brief Configuration parameters for the DetectCoaddSourcesTask
110 """
111 doScaleVariance = Field(dtype=bool, default=True, doc="Scale variance plane using empirical noise?")
112 scaleVariance = ConfigurableField(target=ScaleVarianceTask, doc="Variance rescaling")
113 detection = ConfigurableField(target=DynamicDetectionTask, doc="Source detection")
114 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
115 doInsertFakes = Field(dtype=bool, default=False,
116 doc="Run fake sources injection task")
117 insertFakes = ConfigurableField(target=BaseFakeSourcesTask,
118 doc="Injection of fake sources for testing "
119 "purposes (must be retargeted)")
120 hasFakes = Field(
121 dtype=bool,
122 default=False,
123 doc="Should be set to True if fake sources have been inserted into the input data."
124 )
125
126 def setDefaults(self):
127 super().setDefaults()
128 self.detection.thresholdType = "pixel_stdev"
129 self.detection.isotropicGrow = True
130 # Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic
131 self.detection.reEstimateBackground = False
132 self.detection.background.useApprox = False
133 self.detection.background.binSize = 4096
134 self.detection.background.undersampleStyle = 'REDUCE_INTERP_ORDER'
135 self.detection.doTempWideBackground = True # Suppress large footprints that overwhelm the deblender
136
137
143
144
145class DetectCoaddSourcesTask(PipelineTask, CmdLineTask):
146 r"""!
147 @anchor DetectCoaddSourcesTask_
148
149 @brief Detect sources on a coadd
150
151 @section pipe_tasks_multiBand_Contents Contents
152
153 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose
154 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize
155 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run
156 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config
157 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug
158 - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example
159
160 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
161
162 Command-line task that detects sources on a coadd of exposures obtained with a single filter.
163
164 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise
165 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane
166 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should
167 propagate the full covariance matrix -- but it is simple and works well in practice.
168
169 After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref
170 SourceDetectionTask_ "detection" subtask.
171
172 @par Inputs:
173 deepCoadd{tract,patch,filter}: ExposureF
174 @par Outputs:
175 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
176 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input
177 exposure (ExposureF)
178 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList
179 @par Data Unit:
180 tract, patch, filter
181
182 DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask.
183 You can retarget this subtask if you wish.
184
185 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
186
187 @copydoc \_\_init\_\_
188
189 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
190
191 @copydoc run
192
193 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
194
195 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig"
196
197 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
198
199 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
200 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
201 files.
202
203 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to
204 @ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for
205 @ref SourceDetectionTask_ "SourceDetectionTask" for further information.
206
207 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example
208 of using DetectCoaddSourcesTask
209
210 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of
211 the task is to update the background, detect all sources in a single band and generate a set of parent
212 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and,
213 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data
214 reference to the coadd to be processed. A list of the available optional arguments can be obtained by
215 calling detectCoaddSources.py with the `--help` command line argument:
216 @code
217 detectCoaddSources.py --help
218 @endcode
219
220 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
221 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed
222 steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows:
223 @code
224 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
225 @endcode
226 that will process the HSC-I band data. The results are written to
227 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
228
229 It is also necessary to run:
230 @code
231 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
232 @endcode
233 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
234 processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask".
235 """
236 _DefaultName = "detectCoaddSources"
237 ConfigClass = DetectCoaddSourcesConfig
238 getSchemaCatalogs = _makeGetSchemaCatalogs("det")
239 makeIdFactory = _makeMakeIdFactory("CoaddId")
240
241 @classmethod
242 def _makeArgumentParser(cls):
243 parser = ArgumentParser(name=cls._DefaultName)
244 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
245 ContainerClass=ExistingCoaddDataIdContainer)
246 return parser
247
248 def __init__(self, schema=None, **kwargs):
249 """!
250 @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask.
251
252 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
253
254 @param[in] schema: initial schema for the output catalog, modified-in place to include all
255 fields set by this task. If None, the source minimal schema will be used.
256 @param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__
257 """
258 # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree
259 # call structure has been reviewed carefully to be sure super will work as intended.
260 super().__init__(**kwargs)
261 if schema is None:
262 schema = afwTable.SourceTable.makeMinimalSchema()
263 if self.config.doInsertFakes:
264 self.makeSubtask("insertFakes")
265 self.schema = schema
266 self.makeSubtask("detection", schema=self.schema)
267 if self.config.doScaleVariance:
268 self.makeSubtask("scaleVariance")
269
270 self.detectionSchema = afwTable.SourceCatalog(self.schema)
271
272 def runDataRef(self, patchRef):
273 """!
274 @brief Run detection on a coadd.
275
276 Invokes @ref run and then uses @ref write to output the
277 results.
278
279 @param[in] patchRef: data reference for patch
280 """
281 if self.config.hasFakes:
282 exposure = patchRef.get("fakes_" + self.config.coaddName + "Coadd", immediate=True)
283 else:
284 exposure = patchRef.get(self.config.coaddName + "Coadd", immediate=True)
285 expId = int(patchRef.get(self.config.coaddName + "CoaddId"))
286 results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId)
287 self.write(results, patchRef)
288 return results
289
290 def runQuantum(self, butlerQC, inputRefs, outputRefs):
291 inputs = butlerQC.get(inputRefs)
292 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch_band")
293 inputs["idFactory"] = exposureIdInfo.makeSourceIdFactory()
294 inputs["expId"] = exposureIdInfo.expId
295 outputs = self.run(**inputs)
296 butlerQC.put(outputs, outputRefs)
297
298 def run(self, exposure, idFactory, expId):
299 """!
300 @brief Run detection on an exposure.
301
302 First scale the variance plane to match the observed variance
303 using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to
304 detect sources.
305
306 @param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled,
307 depending on configuration).
308 @param[in] idFactory: IdFactory to set source identifiers
309 @param[in] expId: Exposure identifier (integer) for RNG seed
310
311 @return a pipe.base.Struct with fields
312 - sources: catalog of detections
313 - backgrounds: list of backgrounds
314 """
315 if self.config.doScaleVariance:
316 varScale = self.scaleVariance.run(exposure.maskedImage)
317 exposure.getMetadata().add("VARIANCE_SCALE", varScale)
318 backgrounds = afwMath.BackgroundList()
319 if self.config.doInsertFakes:
320 self.insertFakes.run(exposure, background=backgrounds)
321 table = afwTable.SourceTable.make(self.schema, idFactory)
322 detections = self.detection.run(table, exposure, expId=expId)
323 sources = detections.sources
324 fpSets = detections.fpSets
325 if hasattr(fpSets, "background") and fpSets.background:
326 for bg in fpSets.background:
327 backgrounds.append(bg)
328 return Struct(outputSources=sources, outputBackgrounds=backgrounds, outputExposure=exposure)
329
330 def write(self, results, patchRef):
331 """!
332 @brief Write out results from runDetection.
333
334 @param[in] exposure: Exposure to write out
335 @param[in] results: Struct returned from runDetection
336 @param[in] patchRef: data reference for patch
337 """
338 coaddName = self.config.coaddName + "Coadd"
339 patchRef.put(results.outputBackgrounds, coaddName + "_calexp_background")
340 patchRef.put(results.outputSources, coaddName + "_det")
341 if self.config.hasFakes:
342 patchRef.put(results.outputExposure, "fakes_" + coaddName + "_calexp")
343 else:
344 patchRef.put(results.outputExposure, coaddName + "_calexp")
345
346
347
348
349class DeblendCoaddSourcesConfig(Config):
350 """DeblendCoaddSourcesConfig
351
352 Configuration parameters for the `DeblendCoaddSourcesTask`.
353 """
354 singleBandDeblend = ConfigurableField(target=SourceDeblendTask,
355 doc="Deblend sources separately in each band")
356 multiBandDeblend = ConfigurableField(target=ScarletDeblendTask,
357 doc="Deblend sources simultaneously across bands")
358 simultaneous = Field(dtype=bool,
359 default=True,
360 doc="Simultaneously deblend all bands? "
361 "True uses `multibandDeblend` while False uses `singleBandDeblend`")
362 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
363 hasFakes = Field(dtype=bool,
364 default=False,
365 doc="Should be set to True if fake sources have been inserted into the input data.")
366
367 def setDefaults(self):
368 Config.setDefaults(self)
369 self.singleBandDeblend.propagateAllPeaks = True
370
371
372class DeblendCoaddSourcesRunner(MergeSourcesRunner):
373 """Task runner for the `MergeSourcesTask`
374
375 Required because the run method requires a list of
376 dataRefs rather than a single dataRef.
377 """
378 @staticmethod
379 def getTargetList(parsedCmd, **kwargs):
380 """Provide a list of patch references for each patch, tract, filter combo.
381
382 Parameters
383 ----------
384 parsedCmd:
385 The parsed command
386 kwargs:
387 Keyword arguments passed to the task
388
389 Returns
390 -------
391 targetList: list
392 List of tuples, where each tuple is a (dataRef, kwargs) pair.
393 """
394 refDict = MergeSourcesRunner.buildRefDict(parsedCmd)
395 kwargs["psfCache"] = parsedCmd.psfCache
396 return [(list(p.values()), kwargs) for t in refDict.values() for p in t.values()]
397
398
399class DeblendCoaddSourcesTask(CmdLineTask):
400 """Deblend the sources in a merged catalog
401
402 Deblend sources from master catalog in each coadd.
403 This can either be done separately in each band using the HSC-SDSS deblender
404 (`DeblendCoaddSourcesTask.config.simultaneous==False`)
405 or use SCARLET to simultaneously fit the blend in all bands
406 (`DeblendCoaddSourcesTask.config.simultaneous==True`).
407 The task will set its own `self.schema` atribute to the `Schema` of the
408 output deblended catalog.
409 This will include all fields from the input `Schema`, as well as additional fields
410 from the deblender.
411
412 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description
413 ---------------------------------------------------------
414 `
415
416 Parameters
417 ----------
418 butler: `Butler`
419 Butler used to read the input schemas from disk or
420 construct the reference catalog loader, if `schema` or `peakSchema` or
421 schema: `Schema`
422 The schema of the merged detection catalog as an input to this task.
423 peakSchema: `Schema`
424 The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog
425 """
426 ConfigClass = DeblendCoaddSourcesConfig
427 RunnerClass = DeblendCoaddSourcesRunner
428 _DefaultName = "deblendCoaddSources"
429 makeIdFactory = _makeMakeIdFactory("MergedCoaddId")
430
431 @classmethod
432 def _makeArgumentParser(cls):
433 parser = ArgumentParser(name=cls._DefaultName)
434 parser.add_id_argument("--id", "deepCoadd_calexp",
435 help="data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i",
436 ContainerClass=ExistingCoaddDataIdContainer)
437 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
438 return parser
439
440 def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs):
441 CmdLineTask.__init__(self, **kwargs)
442 if schema is None:
443 assert butler is not None, "Neither butler nor schema is defined"
444 schema = butler.get(self.config.coaddName + "Coadd_mergeDet_schema", immediate=True).schema
445 self.schemaMapper = afwTable.SchemaMapper(schema)
446 self.schemaMapper.addMinimalSchema(schema)
447 self.schema = self.schemaMapper.getOutputSchema()
448 if peakSchema is None:
449 assert butler is not None, "Neither butler nor peakSchema is defined"
450 peakSchema = butler.get(self.config.coaddName + "Coadd_peak_schema", immediate=True).schema
451
452 if self.config.simultaneous:
453 self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema)
454 else:
455 self.makeSubtask("singleBandDeblend", schema=self.schema, peakSchema=peakSchema)
456
457 def getSchemaCatalogs(self):
458 """Return a dict of empty catalogs for each catalog dataset produced by this task.
459
460 Returns
461 -------
462 result: dict
463 Dictionary of empty catalogs, with catalog names as keys.
464 """
465 catalog = afwTable.SourceCatalog(self.schema)
466 return {self.config.coaddName + "Coadd_deblendedFlux": catalog,
467 self.config.coaddName + "Coadd_deblendedModel": catalog}
468
469 def runDataRef(self, patchRefList, psfCache=100):
470 """Deblend the patch
471
472 Deblend each source simultaneously or separately
473 (depending on `DeblendCoaddSourcesTask.config.simultaneous`).
474 Set `is-primary` and related flags.
475 Propagate flags from individual visits.
476 Write the deblended sources out.
477
478 Parameters
479 ----------
480 patchRefList: list
481 List of data references for each filter
482 """
483
484 if self.config.hasFakes:
485 coaddType = "fakes_" + self.config.coaddName
486 else:
487 coaddType = self.config.coaddName
488
489 if self.config.simultaneous:
490 # Use SCARLET to simultaneously deblend across filters
491 filters = []
492 exposures = []
493 for patchRef in patchRefList:
494 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
495 filter = patchRef.get(coaddType + "Coadd_filterLabel", immediate=True)
496 filters.append(filter.bandLabel)
497 exposures.append(exposure)
498 # The input sources are the same for all bands, since it is a merged catalog
499 sources = self.readSources(patchRef)
500 exposure = afwImage.MultibandExposure.fromExposures(filters, exposures)
501 templateCatalogs = self.multiBandDeblend.run(exposure, sources)
502 for n in range(len(patchRefList)):
503 self.write(patchRefList[n], templateCatalogs[filters[n]])
504 else:
505 # Use the singeband deblender to deblend each band separately
506 for patchRef in patchRefList:
507 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
508 exposure.getPsf().setCacheCapacity(psfCache)
509 sources = self.readSources(patchRef)
510 self.singleBandDeblend.run(exposure, sources)
511 self.write(patchRef, sources)
512
513 def readSources(self, dataRef):
514 """Read merged catalog
515
516 Read the catalog of merged detections and create a catalog
517 in a single band.
518
519 Parameters
520 ----------
521 dataRef: data reference
522 Data reference for catalog of merged detections
523
524 Returns
525 -------
526 sources: `SourceCatalog`
527 List of sources in merged catalog
528
529 We also need to add columns to hold the measurements we're about to make so we can measure in-place.
530 """
531 merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=True)
532 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
533 idFactory = self.makeIdFactory(dataRef)
534 for s in merged:
535 idFactory.notify(s.getId())
536 table = afwTable.SourceTable.make(self.schema, idFactory)
537 sources = afwTable.SourceCatalog(table)
538 sources.extend(merged, self.schemaMapper)
539 return sources
540
541 def write(self, dataRef, sources):
542 """Write the source catalog(s)
543
544 Parameters
545 ----------
546 dataRef: Data Reference
547 Reference to the output catalog.
548 sources: `SourceCatalog`
549 Flux conserved sources to write to file.
550 If using the single band deblender, this is the catalog
551 generated.
552 template_sources: `SourceCatalog`
553 Source catalog using the multiband template models
554 as footprints.
555 """
556 dataRef.put(sources, self.config.coaddName + "Coadd_deblendedFlux")
557 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)
558
559 def writeMetadata(self, dataRefList):
560 """Write the metadata produced from processing the data.
561 Parameters
562 ----------
563 dataRefList
564 List of Butler data references used to write the metadata.
565 The metadata is written to dataset type `CmdLineTask._getMetadataName`.
566 """
567 for dataRef in dataRefList:
568 try:
569 metadataName = self._getMetadataName()
570 if metadataName is not None:
571 dataRef.put(self.getFullMetadata(), metadataName)
572 except Exception as e:
573 self.log.warning("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
574
575 def getExposureId(self, dataRef):
576 """Get the ExposureId from a data reference
577 """
578 return int(dataRef.get(self.config.coaddName + "CoaddId"))
579
580
581class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections,
582 dimensions=("tract", "patch", "band", "skymap"),
583 defaultTemplates={"inputCoaddName": "deep",
584 "outputCoaddName": "deep"}):
585 inputSchema = cT.InitInput(
586 doc="Input schema for measure merged task produced by a deblender or detection task",
587 name="{inputCoaddName}Coadd_deblendedFlux_schema",
588 storageClass="SourceCatalog"
589 )
590 outputSchema = cT.InitOutput(
591 doc="Output schema after all new fields are added by task",
592 name="{inputCoaddName}Coadd_meas_schema",
593 storageClass="SourceCatalog"
594 )
595 refCat = cT.PrerequisiteInput(
596 doc="Reference catalog used to match measured sources against known sources",
597 name="ref_cat",
598 storageClass="SimpleCatalog",
599 dimensions=("skypix",),
600 deferLoad=True,
601 multiple=True
602 )
603 exposure = cT.Input(
604 doc="Input coadd image",
605 name="{inputCoaddName}Coadd_calexp",
606 storageClass="ExposureF",
607 dimensions=("tract", "patch", "band", "skymap")
608 )
609 skyMap = cT.Input(
610 doc="SkyMap to use in processing",
611 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
612 storageClass="SkyMap",
613 dimensions=("skymap",),
614 )
615 visitCatalogs = cT.Input(
616 doc="Source catalogs for visits which overlap input tract, patch, band. Will be "
617 "further filtered in the task for the purpose of propagating flags from image calibration "
618 "and characterization to codd objects",
619 name="src",
620 dimensions=("instrument", "visit", "detector"),
621 storageClass="SourceCatalog",
622 multiple=True
623 )
624 inputCatalog = cT.Input(
625 doc=("Name of the input catalog to use."
626 "If the single band deblender was used this should be 'deblendedFlux."
627 "If the multi-band deblender was used this should be 'deblendedModel, "
628 "or deblendedFlux if the multiband deblender was configured to output "
629 "deblended flux catalogs. If no deblending was performed this should "
630 "be 'mergeDet'"),
631 name="{inputCoaddName}Coadd_deblendedFlux",
632 storageClass="SourceCatalog",
633 dimensions=("tract", "patch", "band", "skymap"),
634 )
635 outputSources = cT.Output(
636 doc="Source catalog containing all the measurement information generated in this task",
637 name="{outputCoaddName}Coadd_meas",
638 dimensions=("tract", "patch", "band", "skymap"),
639 storageClass="SourceCatalog",
640 )
641 matchResult = cT.Output(
642 doc="Match catalog produced by configured matcher, optional on doMatchSources",
643 name="{outputCoaddName}Coadd_measMatch",
644 dimensions=("tract", "patch", "band", "skymap"),
645 storageClass="Catalog",
646 )
647 denormMatches = cT.Output(
648 doc="Denormalized Match catalog produced by configured matcher, optional on "
649 "doWriteMatchesDenormalized",
650 name="{outputCoaddName}Coadd_measMatchFull",
651 dimensions=("tract", "patch", "band", "skymap"),
652 storageClass="Catalog",
653 )
654
655 def __init__(self, *, config=None):
656 super().__init__(config=config)
657 if config.doPropagateFlags is False:
658 self.inputs -= set(("visitCatalogs",))
659
660 if config.doMatchSources is False:
661 self.outputs -= set(("matchResult",))
662
663 if config.doWriteMatchesDenormalized is False:
664 self.outputs -= set(("denormMatches",))
665
666
667class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
668 pipelineConnections=MeasureMergedCoaddSourcesConnections):
669 """!
670 @anchor MeasureMergedCoaddSourcesConfig_
671
672 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask
673 """
674 inputCatalog = Field(dtype=str, default="deblendedFlux",
675 doc=("Name of the input catalog to use."
676 "If the single band deblender was used this should be 'deblendedFlux."
677 "If the multi-band deblender was used this should be 'deblendedModel."
678 "If no deblending was performed this should be 'mergeDet'"))
679 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement")
680 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch")
681 doPropagateFlags = Field(
682 dtype=bool, default=True,
683 doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
684 )
685 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc="Propagate visit flags to coadd")
686 doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?")
687 match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog")
688 doWriteMatchesDenormalized = Field(
689 dtype=bool,
690 default=False,
691 doc=("Write reference matches in denormalized format? "
692 "This format uses more disk space, but is more convenient to read."),
693 )
694 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
695 psfCache = Field(dtype=int, default=100, doc="Size of psfCache")
696 checkUnitsParseStrict = Field(
697 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
698 dtype=str,
699 default="raise",
700 )
701 doApCorr = Field(
702 dtype=bool,
703 default=True,
704 doc="Apply aperture corrections"
705 )
706 applyApCorr = ConfigurableField(
707 target=ApplyApCorrTask,
708 doc="Subtask to apply aperture corrections"
709 )
710 doRunCatalogCalculation = Field(
711 dtype=bool,
712 default=True,
713 doc='Run catalogCalculation task'
714 )
715 catalogCalculation = ConfigurableField(
716 target=CatalogCalculationTask,
717 doc="Subtask to run catalogCalculation plugins on catalog"
718 )
719
720 hasFakes = Field(
721 dtype=bool,
722 default=False,
723 doc="Should be set to True if fake sources have been inserted into the input data."
724 )
725
726 @property
727 def refObjLoader(self):
728 return self.match.refObjLoader
729
730 def setDefaults(self):
731 super().setDefaults()
732 self.measurement.plugins.names |= ['base_InputCount',
733 'base_Variance',
734 'base_LocalPhotoCalib',
735 'base_LocalWcs']
736 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE',
737 'INEXACT_PSF']
738 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE',
739 'INEXACT_PSF']
740
741 def validate(self):
742 super().validate()
743 refCatGen2 = getattr(self.refObjLoader, "ref_dataset_name", None)
744 if refCatGen2 is not None and refCatGen2 != self.connections.refCat:
745 raise ValueError(
746 f"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
747 f"are different. These options must be kept in sync until Gen2 is retired."
748 )
749
750
751
757
758
759class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
760 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
761 @staticmethod
762 def getTargetList(parsedCmd, **kwargs):
763 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
764
765
766class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
767 r"""!
768 @anchor MeasureMergedCoaddSourcesTask_
769
770 @brief Deblend sources from master catalog in each coadd seperately and measure.
771
772 @section pipe_tasks_multiBand_Contents Contents
773
774 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
775 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
776 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
777 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
778 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
779 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
780
781 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
782
783 Command-line task that uses peaks and footprints from a master catalog to perform deblending and
784 measurement in each coadd.
785
786 Given a master input catalog of sources (peaks and footprints) or deblender outputs
787 (including a HeavyFootprint in each band), measure each source on the
788 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a
789 consistent set of child sources.
790
791 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source
792 properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit
793 flags are propagated to the coadd sources.
794
795 Optionally, we can match the coadd sources to an external reference catalog.
796
797 @par Inputs:
798 deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog
799 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
800 @par Outputs:
801 deepCoadd_meas{tract,patch,filter}: SourceCatalog
802 @par Data Unit:
803 tract, patch, filter
804
805 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
806
807 <DL>
808 <DT> @ref SingleFrameMeasurementTask_ "measurement"
809 <DD> Measure source properties of deblended sources.</DD>
810 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags"
811 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are
812 not at the edge of the field and that have either not been deblended or are the children of deblended
813 sources</DD>
814 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags"
815 <DD> Propagate flags set in individual visits to the coadd.</DD>
816 <DT> @ref DirectMatchTask_ "match"
817 <DD> Match input sources to a reference catalog (optional).
818 </DD>
819 </DL>
820 These subtasks may be retargeted as required.
821
822 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
823
824 @copydoc \_\_init\_\_
825
826 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
827
828 @copydoc run
829
830 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
831
832 See @ref MeasureMergedCoaddSourcesConfig_
833
834 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
835
836 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
837 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
838 files.
839
840 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
841 the various sub-tasks. See the documetation for individual sub-tasks for more information.
842
843 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
844 MeasureMergedCoaddSourcesTask
845
846 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
847 The next stage in the multi-band processing procedure will merge these measurements into a suitable
848 catalog for driving forced photometry.
849
850 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
851 to be processed.
852 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the
853 `--help` command line argument:
854 @code
855 measureCoaddSources.py --help
856 @endcode
857
858 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
859 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
860 step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band
861 coadd as follows:
862 @code
863 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
864 @endcode
865 This will process the HSC-I band data. The results are written in
866 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
867
868 It is also necessary to run
869 @code
870 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
871 @endcode
872 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
873 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask".
874 """
875 _DefaultName = "measureCoaddSources"
876 ConfigClass = MeasureMergedCoaddSourcesConfig
877 RunnerClass = MeasureMergedCoaddSourcesRunner
878 getSchemaCatalogs = _makeGetSchemaCatalogs("meas")
879 makeIdFactory = _makeMakeIdFactory("MergedCoaddId") # The IDs we already have are of this type
880
881 @classmethod
882 def _makeArgumentParser(cls):
883 parser = ArgumentParser(name=cls._DefaultName)
884 parser.add_id_argument("--id", "deepCoadd_calexp",
885 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
886 ContainerClass=ExistingCoaddDataIdContainer)
887 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
888 return parser
889
890 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
891 **kwargs):
892 """!
893 @brief Initialize the task.
894
895 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
896 @param[in] schema: the schema of the merged detection catalog used as input to this one
897 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog
898 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
899 catalog. May be None if the loader can be constructed from the butler argument or all steps
900 requiring a reference catalog are disabled.
901 @param[in] butler: a butler used to read the input schemas from disk or construct the reference
902 catalog loader, if schema or peakSchema or refObjLoader is None
903
904 The task will set its own self.schema attribute to the schema of the output measurement catalog.
905 This will include all fields from the input schema, as well as additional fields for all the
906 measurements.
907 """
908 super().__init__(**kwargs)
909 self.deblended = self.config.inputCatalog.startswith("deblended")
910 self.inputCatalog = "Coadd_" + self.config.inputCatalog
911 if initInputs is not None:
912 schema = initInputs['inputSchema'].schema
913 if schema is None:
914 assert butler is not None, "Neither butler nor schema is defined"
915 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema
916 self.schemaMapper = afwTable.SchemaMapper(schema)
917 self.schemaMapper.addMinimalSchema(schema)
918 self.schema = self.schemaMapper.getOutputSchema()
919 self.algMetadata = PropertyList()
920 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata)
921 self.makeSubtask("setPrimaryFlags", schema=self.schema)
922 if self.config.doMatchSources:
923 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
924 if self.config.doPropagateFlags:
925 self.makeSubtask("propagateFlags", schema=self.schema)
926 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
927 if self.config.doApCorr:
928 self.makeSubtask("applyApCorr", schema=self.schema)
929 if self.config.doRunCatalogCalculation:
930 self.makeSubtask("catalogCalculation", schema=self.schema)
931
932 self.outputSchema = afwTable.SourceCatalog(self.schema)
933
934 def runQuantum(self, butlerQC, inputRefs, outputRefs):
935 inputs = butlerQC.get(inputRefs)
936
937 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat],
938 inputs.pop('refCat'), config=self.config.refObjLoader,
939 log=self.log)
940 self.match.setRefObjLoader(refObjLoader)
941
942 # Set psfcache
943 # move this to run after gen2 deprecation
944 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
945
946 # Get unique integer ID for IdFactory and RNG seeds
947 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch")
948 inputs['exposureId'] = exposureIdInfo.expId
949 idFactory = exposureIdInfo.makeSourceIdFactory()
950 # Transform inputCatalog
951 table = afwTable.SourceTable.make(self.schema, idFactory)
952 sources = afwTable.SourceCatalog(table)
953 sources.extend(inputs.pop('inputCatalog'), self.schemaMapper)
954 table = sources.getTable()
955 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
956 inputs['sources'] = sources
957
958 skyMap = inputs.pop('skyMap')
959 tractNumber = inputRefs.inputCatalog.dataId['tract']
960 tractInfo = skyMap[tractNumber]
961 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId['patch'])
962 skyInfo = Struct(
963 skyMap=skyMap,
964 tractInfo=tractInfo,
965 patchInfo=patchInfo,
966 wcs=tractInfo.getWcs(),
967 bbox=patchInfo.getOuterBBox()
968 )
969 inputs['skyInfo'] = skyInfo
970
971 if self.config.doPropagateFlags:
972 # Filter out any visit catalog that is not coadd inputs
973 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds
974 visitKey = ccdInputs.schema.find("visit").key
975 ccdKey = ccdInputs.schema.find("ccd").key
976 inputVisitIds = set()
977 ccdRecordsWcs = {}
978 for ccdRecord in ccdInputs:
979 visit = ccdRecord.get(visitKey)
980 ccd = ccdRecord.get(ccdKey)
981 inputVisitIds.add((visit, ccd))
982 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
983
984 inputCatalogsToKeep = []
985 inputCatalogWcsUpdate = []
986 for i, dataRef in enumerate(inputRefs.visitCatalogs):
987 key = (dataRef.dataId['visit'], dataRef.dataId['detector'])
988 if key in inputVisitIds:
989 inputCatalogsToKeep.append(inputs['visitCatalogs'][i])
990 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
991 inputs['visitCatalogs'] = inputCatalogsToKeep
992 inputs['wcsUpdates'] = inputCatalogWcsUpdate
993 inputs['ccdInputs'] = ccdInputs
994
995 outputs = self.run(**inputs)
996 butlerQC.put(outputs, outputRefs)
997
998 def runDataRef(self, patchRef, psfCache=100):
999 """!
1000 @brief Deblend and measure.
1001
1002 @param[in] patchRef: Patch reference.
1003
1004 Set 'is-primary' and related flags. Propagate flags
1005 from individual visits. Optionally match the sources to a reference catalog and write the matches.
1006 Finally, write the deblended sources and measurements out.
1007 """
1008 if self.config.hasFakes:
1009 coaddType = "fakes_" + self.config.coaddName
1010 else:
1011 coaddType = self.config.coaddName
1012 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
1013 exposure.getPsf().setCacheCapacity(psfCache)
1014 sources = self.readSources(patchRef)
1015 table = sources.getTable()
1016 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1017 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1018
1019 if self.config.doPropagateFlags:
1020 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1021 else:
1022 ccdInputs = None
1023
1024 results = self.run(exposure=exposure, sources=sources,
1025 ccdInputs=ccdInputs,
1026 skyInfo=skyInfo, butler=patchRef.getButler(),
1027 exposureId=self.getExposureId(patchRef))
1028
1029 if self.config.doMatchSources:
1030 self.writeMatches(patchRef, results)
1031 self.write(patchRef, results.outputSources)
1032
1033 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1034 butler=None):
1035 """Run measurement algorithms on the input exposure, and optionally populate the
1036 resulting catalog with extra information.
1037
1038 Parameters
1039 ----------
1040 exposure : `lsst.afw.exposure.Exposure`
1041 The input exposure on which measurements are to be performed
1043 A catalog built from the results of merged detections, or
1044 deblender outputs.
1045 skyInfo : `lsst.pipe.base.Struct`
1046 A struct containing information about the position of the input exposure within
1047 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box
1048 exposureId : `int` or `bytes`
1049 packed unique number or bytes unique to the input exposure
1050 ccdInputs : `lsst.afw.table.ExposureCatalog`
1051 Catalog containing information on the individual visits which went into making
1052 the exposure
1053 visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None`
1054 A list of source catalogs corresponding to measurements made on the individual
1055 visits which went into the input exposure. If None and butler is `None` then
1056 the task cannot propagate visit flags to the output catalog.
1057 wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None`
1058 If visitCatalogs is not `None` this should be a list of wcs objects which correspond
1059 to the input visits. Used to put all coordinates to common system. If `None` and
1060 butler is `None` then the task cannot propagate visit flags to the output catalog.
1061 butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler`
1062 Either a gen2 or gen3 butler used to load visit catalogs
1063
1064 Returns
1065 -------
1066 results : `lsst.pipe.base.Struct`
1067 Results of running measurement task. Will contain the catalog in the
1068 sources attribute. Optionally will have results of matching to a
1069 reference catalog in the matchResults attribute, and denormalized
1070 matches in the denormMatches attribute.
1071 """
1072 self.measurement.run(sources, exposure, exposureId=exposureId)
1073
1074 if self.config.doApCorr:
1075 self.applyApCorr.run(
1076 catalog=sources,
1077 apCorrMap=exposure.getInfo().getApCorrMap()
1078 )
1079
1080 # TODO DM-11568: this contiguous check-and-copy could go away if we
1081 # reserve enough space during SourceDetection and/or SourceDeblend.
1082 # NOTE: sourceSelectors require contiguous catalogs, so ensure
1083 # contiguity now, so views are preserved from here on.
1084 if not sources.isContiguous():
1085 sources = sources.copy(deep=True)
1086
1087 if self.config.doRunCatalogCalculation:
1088 self.catalogCalculation.run(sources)
1089
1090 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1091 patchInfo=skyInfo.patchInfo)
1092 if self.config.doPropagateFlags:
1093 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates)
1094
1095 results = Struct()
1096
1097 if self.config.doMatchSources:
1098 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel)
1099 matches = afwTable.packMatches(matchResult.matches)
1100 matches.table.setMetadata(matchResult.matchMeta)
1101 results.matchResult = matches
1102 if self.config.doWriteMatchesDenormalized:
1103 if matchResult.matches:
1104 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1105 else:
1106 self.log.warning("No matches, so generating dummy denormalized matches file")
1107 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1108 denormMatches.setMetadata(PropertyList())
1109 denormMatches.getMetadata().add("COMMENT",
1110 "This catalog is empty because no matches were found.")
1111 results.denormMatches = denormMatches
1112 results.denormMatches = denormMatches
1113
1114 results.outputSources = sources
1115 return results
1116
1117 def readSources(self, dataRef):
1118 """!
1119 @brief Read input sources.
1120
1121 @param[in] dataRef: Data reference for catalog of merged detections
1122 @return List of sources in merged catalog
1123
1124 We also need to add columns to hold the measurements we're about to make so we can measure in-place.
1125 """
1126 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1127 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
1128 idFactory = self.makeIdFactory(dataRef)
1129 for s in merged:
1130 idFactory.notify(s.getId())
1131 table = afwTable.SourceTable.make(self.schema, idFactory)
1132 sources = afwTable.SourceCatalog(table)
1133 sources.extend(merged, self.schemaMapper)
1134 return sources
1135
1136 def writeMatches(self, dataRef, results):
1137 """!
1138 @brief Write matches of the sources to the astrometric reference catalog.
1139
1140 @param[in] dataRef: data reference
1141 @param[in] results: results struct from run method
1142 """
1143 if hasattr(results, "matchResult"):
1144 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1145 if hasattr(results, "denormMatches"):
1146 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1147
1148 def write(self, dataRef, sources):
1149 """!
1150 @brief Write the source catalog.
1151
1152 @param[in] dataRef: data reference
1153 @param[in] sources: source catalog
1154 """
1155 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1156 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)
1157
1158 def getExposureId(self, dataRef):
1159 return int(dataRef.get(self.config.coaddName + "CoaddId"))