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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#
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
44from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401
45from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401
46from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401
47from .multiBandUtils import getInputSchema, getShortFilterName, readCatalog, _makeMakeIdFactory # noqa: F401
48from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401
49from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401
50from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401
51from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401
54"""
55New set types:
56* deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter)
57* deepCoadd_mergeDet: merged detections (tract, patch)
58* deepCoadd_meas: measurements of merged detections (tract, patch, filter)
59* deepCoadd_ref: reference sources (tract, patch)
60All of these have associated *_schema catalogs that require no data ID and hold no records.
62In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in
63the mergeDet, meas, and ref dataset Footprints:
64* deepCoadd_peak_schema
65"""
68##############################################################################################################
69class DetectCoaddSourcesConnections(PipelineTaskConnections,
70 dimensions=("tract", "patch", "band", "skymap"),
71 defaultTemplates={"inputCoaddName": "deep", "outputCoaddName": "deep"}):
72 detectionSchema = cT.InitOutput(
73 doc="Schema of the detection catalog",
74 name="{outputCoaddName}Coadd_det_schema",
75 storageClass="SourceCatalog",
76 )
77 exposure = cT.Input(
78 doc="Exposure on which detections are to be performed",
79 name="{inputCoaddName}Coadd",
80 storageClass="ExposureF",
81 dimensions=("tract", "patch", "band", "skymap")
82 )
83 outputBackgrounds = cT.Output(
84 doc="Output Backgrounds used in detection",
85 name="{outputCoaddName}Coadd_calexp_background",
86 storageClass="Background",
87 dimensions=("tract", "patch", "band", "skymap")
88 )
89 outputSources = cT.Output(
90 doc="Detected sources catalog",
91 name="{outputCoaddName}Coadd_det",
92 storageClass="SourceCatalog",
93 dimensions=("tract", "patch", "band", "skymap")
94 )
95 outputExposure = cT.Output(
96 doc="Exposure post detection",
97 name="{outputCoaddName}Coadd_calexp",
98 storageClass="ExposureF",
99 dimensions=("tract", "patch", "band", "skymap")
100 )
103class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections):
104 """!
105 @anchor DetectCoaddSourcesConfig_
107 @brief Configuration parameters for the DetectCoaddSourcesTask
108 """
109 doScaleVariance = Field(dtype=bool, default=True, doc="Scale variance plane using empirical noise?")
110 scaleVariance = ConfigurableField(target=ScaleVarianceTask, doc="Variance rescaling")
111 detection = ConfigurableField(target=DynamicDetectionTask, doc="Source detection")
112 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
113 doInsertFakes = Field(dtype=bool, default=False,
114 doc="Run fake sources injection task")
115 insertFakes = ConfigurableField(target=BaseFakeSourcesTask,
116 doc="Injection of fake sources for testing "
117 "purposes (must be retargeted)")
118 hasFakes = Field(
119 dtype=bool,
120 default=False,
121 doc="Should be set to True if fake sources have been inserted into the input data."
122 )
124 def setDefaults(self):
125 super().setDefaults()
126 self.detection.thresholdType = "pixel_stdev"
127 self.detection.isotropicGrow = True
128 # Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic
129 self.detection.reEstimateBackground = False
130 self.detection.background.useApprox = False
131 self.detection.background.binSize = 4096
132 self.detection.background.undersampleStyle = 'REDUCE_INTERP_ORDER'
133 self.detection.doTempWideBackground = True # Suppress large footprints that overwhelm the deblender
135## @addtogroup LSST_task_documentation
136## @{
137## @page DetectCoaddSourcesTask
138## @ref DetectCoaddSourcesTask_ "DetectCoaddSourcesTask"
139## @copybrief DetectCoaddSourcesTask
140## @}
143class DetectCoaddSourcesTask(PipelineTask, CmdLineTask):
144 r"""!
145 @anchor DetectCoaddSourcesTask_
147 @brief Detect sources on a coadd
149 @section pipe_tasks_multiBand_Contents Contents
151 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose
152 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize
153 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run
154 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config
155 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug
156 - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example
158 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
160 Command-line task that detects sources on a coadd of exposures obtained with a single filter.
162 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise
163 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane
164 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should
165 propagate the full covariance matrix -- but it is simple and works well in practice.
167 After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref
168 SourceDetectionTask_ "detection" subtask.
170 @par Inputs:
171 deepCoadd{tract,patch,filter}: ExposureF
172 @par Outputs:
173 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
174 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input
175 exposure (ExposureF)
176 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList
177 @par Data Unit:
178 tract, patch, filter
180 DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask.
181 You can retarget this subtask if you wish.
183 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
185 @copydoc \_\_init\_\_
187 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
189 @copydoc run
191 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
193 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig"
195 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
197 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
198 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
199 files.
201 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to
202 @ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for
203 @ref SourceDetectionTask_ "SourceDetectionTask" for further information.
205 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example
206 of using DetectCoaddSourcesTask
208 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of
209 the task is to update the background, detect all sources in a single band and generate a set of parent
210 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and,
211 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data
212 reference to the coadd to be processed. A list of the available optional arguments can be obtained by
213 calling detectCoaddSources.py with the `--help` command line argument:
214 @code
215 detectCoaddSources.py --help
216 @endcode
218 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
219 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed
220 steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows:
221 @code
222 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
223 @endcode
224 that will process the HSC-I band data. The results are written to
225 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
227 It is also necessary to run:
228 @code
229 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
230 @endcode
231 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
232 processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask".
233 """
234 _DefaultName = "detectCoaddSources"
235 ConfigClass = DetectCoaddSourcesConfig
236 getSchemaCatalogs = _makeGetSchemaCatalogs("det")
237 makeIdFactory = _makeMakeIdFactory("CoaddId")
239 @classmethod
240 def _makeArgumentParser(cls):
241 parser = ArgumentParser(name=cls._DefaultName)
242 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
243 ContainerClass=ExistingCoaddDataIdContainer)
244 return parser
246 def __init__(self, schema=None, **kwargs):
247 """!
248 @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask.
250 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
252 @param[in] schema: initial schema for the output catalog, modified-in place to include all
253 fields set by this task. If None, the source minimal schema will be used.
254 @param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__
255 """
256 # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree
257 # call structure has been reviewed carefully to be sure super will work as intended.
258 super().__init__(**kwargs)
259 if schema is None: 259 ↛ 261line 259 didn't jump to line 261, because the condition on line 259 was never false
260 schema = afwTable.SourceTable.makeMinimalSchema()
261 if self.config.doInsertFakes: 261 ↛ 262line 261 didn't jump to line 262, because the condition on line 261 was never true
262 self.makeSubtask("insertFakes")
263 self.schema = schema
264 self.makeSubtask("detection", schema=self.schema)
265 if self.config.doScaleVariance: 265 ↛ 268line 265 didn't jump to line 268, because the condition on line 265 was never false
266 self.makeSubtask("scaleVariance")
268 self.detectionSchema = afwTable.SourceCatalog(self.schema)
270 def runDataRef(self, patchRef):
271 """!
272 @brief Run detection on a coadd.
274 Invokes @ref run and then uses @ref write to output the
275 results.
277 @param[in] patchRef: data reference for patch
278 """
279 if self.config.hasFakes: 279 ↛ 280line 279 didn't jump to line 280, because the condition on line 279 was never true
280 exposure = patchRef.get("fakes_" + self.config.coaddName + "Coadd", immediate=True)
281 else:
282 exposure = patchRef.get(self.config.coaddName + "Coadd", immediate=True)
283 expId = int(patchRef.get(self.config.coaddName + "CoaddId"))
284 results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId)
285 self.write(results, patchRef)
286 return results
288 def runQuantum(self, butlerQC, inputRefs, outputRefs):
289 inputs = butlerQC.get(inputRefs)
290 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch_band", returnMaxBits=True)
291 inputs["idFactory"] = afwTable.IdFactory.makeSource(packedId, 64 - maxBits)
292 inputs["expId"] = packedId
293 outputs = self.run(**inputs)
294 butlerQC.put(outputs, outputRefs)
296 def run(self, exposure, idFactory, expId):
297 """!
298 @brief Run detection on an exposure.
300 First scale the variance plane to match the observed variance
301 using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to
302 detect sources.
304 @param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled,
305 depending on configuration).
306 @param[in] idFactory: IdFactory to set source identifiers
307 @param[in] expId: Exposure identifier (integer) for RNG seed
309 @return a pipe.base.Struct with fields
310 - sources: catalog of detections
311 - backgrounds: list of backgrounds
312 """
313 if self.config.doScaleVariance: 313 ↛ 316line 313 didn't jump to line 316, because the condition on line 313 was never false
314 varScale = self.scaleVariance.run(exposure.maskedImage)
315 exposure.getMetadata().add("VARIANCE_SCALE", varScale)
316 backgrounds = afwMath.BackgroundList()
317 if self.config.doInsertFakes: 317 ↛ 318line 317 didn't jump to line 318, because the condition on line 317 was never true
318 self.insertFakes.run(exposure, background=backgrounds)
319 table = afwTable.SourceTable.make(self.schema, idFactory)
320 detections = self.detection.run(table, exposure, expId=expId)
321 sources = detections.sources
322 fpSets = detections.fpSets
323 if hasattr(fpSets, "background") and fpSets.background: 323 ↛ 326line 323 didn't jump to line 326, because the condition on line 323 was never false
324 for bg in fpSets.background:
325 backgrounds.append(bg)
326 return Struct(outputSources=sources, outputBackgrounds=backgrounds, outputExposure=exposure)
328 def write(self, results, patchRef):
329 """!
330 @brief Write out results from runDetection.
332 @param[in] exposure: Exposure to write out
333 @param[in] results: Struct returned from runDetection
334 @param[in] patchRef: data reference for patch
335 """
336 coaddName = self.config.coaddName + "Coadd"
337 patchRef.put(results.outputBackgrounds, coaddName + "_calexp_background")
338 patchRef.put(results.outputSources, coaddName + "_det")
339 if self.config.hasFakes: 339 ↛ 340line 339 didn't jump to line 340, because the condition on line 339 was never true
340 patchRef.put(results.outputExposure, "fakes_" + coaddName + "_calexp")
341 else:
342 patchRef.put(results.outputExposure, coaddName + "_calexp")
344##############################################################################################################
347class DeblendCoaddSourcesConfig(Config):
348 """DeblendCoaddSourcesConfig
350 Configuration parameters for the `DeblendCoaddSourcesTask`.
351 """
352 singleBandDeblend = ConfigurableField(target=SourceDeblendTask,
353 doc="Deblend sources separately in each band")
354 multiBandDeblend = ConfigurableField(target=ScarletDeblendTask,
355 doc="Deblend sources simultaneously across bands")
356 simultaneous = Field(dtype=bool,
357 default=True,
358 doc="Simultaneously deblend all bands? "
359 "True uses 'singleBandDeblend' while False uses 'multibandDeblend'")
360 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
361 hasFakes = Field(dtype=bool,
362 default=False,
363 doc="Should be set to True if fake sources have been inserted into the input data.")
365 def setDefaults(self):
366 Config.setDefaults(self)
367 self.singleBandDeblend.propagateAllPeaks = True
370class DeblendCoaddSourcesRunner(MergeSourcesRunner):
371 """Task runner for the `MergeSourcesTask`
373 Required because the run method requires a list of
374 dataRefs rather than a single dataRef.
375 """
376 @staticmethod
377 def getTargetList(parsedCmd, **kwargs):
378 """Provide a list of patch references for each patch, tract, filter combo.
380 Parameters
381 ----------
382 parsedCmd:
383 The parsed command
384 kwargs:
385 Keyword arguments passed to the task
387 Returns
388 -------
389 targetList: list
390 List of tuples, where each tuple is a (dataRef, kwargs) pair.
391 """
392 refDict = MergeSourcesRunner.buildRefDict(parsedCmd)
393 kwargs["psfCache"] = parsedCmd.psfCache
394 return [(list(p.values()), kwargs) for t in refDict.values() for p in t.values()]
397class DeblendCoaddSourcesTask(CmdLineTask):
398 """Deblend the sources in a merged catalog
400 Deblend sources from master catalog in each coadd.
401 This can either be done separately in each band using the HSC-SDSS deblender
402 (`DeblendCoaddSourcesTask.config.simultaneous==False`)
403 or use SCARLET to simultaneously fit the blend in all bands
404 (`DeblendCoaddSourcesTask.config.simultaneous==True`).
405 The task will set its own `self.schema` atribute to the `Schema` of the
406 output deblended catalog.
407 This will include all fields from the input `Schema`, as well as additional fields
408 from the deblender.
410 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description
411 ---------------------------------------------------------
412 `
414 Parameters
415 ----------
416 butler: `Butler`
417 Butler used to read the input schemas from disk or
418 construct the reference catalog loader, if `schema` or `peakSchema` or
419 schema: `Schema`
420 The schema of the merged detection catalog as an input to this task.
421 peakSchema: `Schema`
422 The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog
423 """
424 ConfigClass = DeblendCoaddSourcesConfig
425 RunnerClass = DeblendCoaddSourcesRunner
426 _DefaultName = "deblendCoaddSources"
427 makeIdFactory = _makeMakeIdFactory("MergedCoaddId")
429 @classmethod
430 def _makeArgumentParser(cls):
431 parser = ArgumentParser(name=cls._DefaultName)
432 parser.add_id_argument("--id", "deepCoadd_calexp",
433 help="data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i",
434 ContainerClass=ExistingCoaddDataIdContainer)
435 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
436 return parser
438 def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs):
439 CmdLineTask.__init__(self, **kwargs)
440 if schema is None: 440 ↛ 443line 440 didn't jump to line 443, because the condition on line 440 was never false
441 assert butler is not None, "Neither butler nor schema is defined"
442 schema = butler.get(self.config.coaddName + "Coadd_mergeDet_schema", immediate=True).schema
443 self.schemaMapper = afwTable.SchemaMapper(schema)
444 self.schemaMapper.addMinimalSchema(schema)
445 self.schema = self.schemaMapper.getOutputSchema()
446 if peakSchema is None: 446 ↛ 450line 446 didn't jump to line 450, because the condition on line 446 was never false
447 assert butler is not None, "Neither butler nor peakSchema is defined"
448 peakSchema = butler.get(self.config.coaddName + "Coadd_peak_schema", immediate=True).schema
450 if self.config.simultaneous: 450 ↛ 453line 450 didn't jump to line 453, because the condition on line 450 was never false
451 self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema)
452 else:
453 self.makeSubtask("singleBandDeblend", schema=self.schema, peakSchema=peakSchema)
455 def getSchemaCatalogs(self):
456 """Return a dict of empty catalogs for each catalog dataset produced by this task.
458 Returns
459 -------
460 result: dict
461 Dictionary of empty catalogs, with catalog names as keys.
462 """
463 catalog = afwTable.SourceCatalog(self.schema)
464 return {self.config.coaddName + "Coadd_deblendedFlux": catalog,
465 self.config.coaddName + "Coadd_deblendedModel": catalog}
467 def runDataRef(self, patchRefList, psfCache=100):
468 """Deblend the patch
470 Deblend each source simultaneously or separately
471 (depending on `DeblendCoaddSourcesTask.config.simultaneous`).
472 Set `is-primary` and related flags.
473 Propagate flags from individual visits.
474 Write the deblended sources out.
476 Parameters
477 ----------
478 patchRefList: list
479 List of data references for each filter
480 """
482 if self.config.hasFakes: 482 ↛ 483line 482 didn't jump to line 483, because the condition on line 482 was never true
483 coaddType = "fakes_" + self.config.coaddName
484 else:
485 coaddType = self.config.coaddName
487 if self.config.simultaneous: 487 ↛ 503line 487 didn't jump to line 503, because the condition on line 487 was never false
488 # Use SCARLET to simultaneously deblend across filters
489 filters = []
490 exposures = []
491 for patchRef in patchRefList:
492 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
493 filters.append(patchRef.dataId["filter"])
494 exposures.append(exposure)
495 # The input sources are the same for all bands, since it is a merged catalog
496 sources = self.readSources(patchRef)
497 exposure = afwImage.MultibandExposure.fromExposures(filters, exposures)
498 templateCatalogs = self.multiBandDeblend.run(exposure, sources)
499 for n in range(len(patchRefList)):
500 self.write(patchRefList[n], templateCatalogs[filters[n]])
501 else:
502 # Use the singeband deblender to deblend each band separately
503 for patchRef in patchRefList:
504 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
505 exposure.getPsf().setCacheCapacity(psfCache)
506 sources = self.readSources(patchRef)
507 self.singleBandDeblend.run(exposure, sources)
508 self.write(patchRef, sources)
510 def readSources(self, dataRef):
511 """Read merged catalog
513 Read the catalog of merged detections and create a catalog
514 in a single band.
516 Parameters
517 ----------
518 dataRef: data reference
519 Data reference for catalog of merged detections
521 Returns
522 -------
523 sources: `SourceCatalog`
524 List of sources in merged catalog
526 We also need to add columns to hold the measurements we're about to make
527 so we can measure in-place.
528 """
529 merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=True)
530 self.log.info("Read %d detections: %s" % (len(merged), dataRef.dataId))
531 idFactory = self.makeIdFactory(dataRef)
532 for s in merged:
533 idFactory.notify(s.getId())
534 table = afwTable.SourceTable.make(self.schema, idFactory)
535 sources = afwTable.SourceCatalog(table)
536 sources.extend(merged, self.schemaMapper)
537 return sources
539 def write(self, dataRef, sources):
540 """Write the source catalog(s)
542 Parameters
543 ----------
544 dataRef: Data Reference
545 Reference to the output catalog.
546 sources: `SourceCatalog`
547 Flux conserved sources to write to file.
548 If using the single band deblender, this is the catalog
549 generated.
550 template_sources: `SourceCatalog`
551 Source catalog using the multiband template models
552 as footprints.
553 """
554 dataRef.put(sources, self.config.coaddName + "Coadd_deblendedFlux")
555 self.log.info("Wrote %d sources: %s" % (len(sources), dataRef.dataId))
557 def writeMetadata(self, dataRefList):
558 """Write the metadata produced from processing the data.
559 Parameters
560 ----------
561 dataRefList
562 List of Butler data references used to write the metadata.
563 The metadata is written to dataset type `CmdLineTask._getMetadataName`.
564 """
565 for dataRef in dataRefList:
566 try:
567 metadataName = self._getMetadataName()
568 if metadataName is not None:
569 dataRef.put(self.getFullMetadata(), metadataName)
570 except Exception as e:
571 self.log.warn("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
573 def getExposureId(self, dataRef):
574 """Get the ExposureId from a data reference
575 """
576 return int(dataRef.get(self.config.coaddName + "CoaddId"))
579class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections,
580 dimensions=("tract", "patch", "band", "skymap"),
581 defaultTemplates={"inputCoaddName": "deep",
582 "outputCoaddName": "deep"}):
583 inputSchema = cT.InitInput(
584 doc="Input schema for measure merged task produced by a deblender or detection task",
585 name="{inputCoaddName}Coadd_deblendedFlux_schema",
586 storageClass="SourceCatalog"
587 )
588 outputSchema = cT.InitOutput(
589 doc="Output schema after all new fields are added by task",
590 name="{inputCoaddName}Coadd_meas_schema",
591 storageClass="SourceCatalog"
592 )
593 refCat = cT.PrerequisiteInput(
594 doc="Reference catalog used to match measured sources against known sources",
595 name="ref_cat",
596 storageClass="SimpleCatalog",
597 dimensions=("skypix",),
598 deferLoad=True,
599 multiple=True
600 )
601 exposure = cT.Input(
602 doc="Input coadd image",
603 name="{inputCoaddName}Coadd_calexp",
604 storageClass="ExposureF",
605 dimensions=("tract", "patch", "band", "skymap")
606 )
607 skyMap = cT.Input(
608 doc="SkyMap to use in processing",
609 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
610 storageClass="SkyMap",
611 dimensions=("skymap",),
612 )
613 visitCatalogs = cT.Input(
614 doc="Source catalogs for visits which overlap input tract, patch, band. Will be "
615 "further filtered in the task for the purpose of propagating flags from image calibration "
616 "and characterization to codd objects",
617 name="src",
618 dimensions=("instrument", "visit", "detector"),
619 storageClass="SourceCatalog",
620 multiple=True
621 )
622 inputCatalog = cT.Input(
623 doc=("Name of the input catalog to use."
624 "If the single band deblender was used this should be 'deblendedFlux."
625 "If the multi-band deblender was used this should be 'deblendedModel, "
626 "or deblendedFlux if the multiband deblender was configured to output "
627 "deblended flux catalogs. If no deblending was performed this should "
628 "be 'mergeDet'"),
629 name="{inputCoaddName}Coadd_deblendedFlux",
630 storageClass="SourceCatalog",
631 dimensions=("tract", "patch", "band", "skymap"),
632 )
633 outputSources = cT.Output(
634 doc="Source catalog containing all the measurement information generated in this task",
635 name="{outputCoaddName}Coadd_meas",
636 dimensions=("tract", "patch", "band", "skymap"),
637 storageClass="SourceCatalog",
638 )
639 matchResult = cT.Output(
640 doc="Match catalog produced by configured matcher, optional on doMatchSources",
641 name="{outputCoaddName}Coadd_measMatch",
642 dimensions=("tract", "patch", "band", "skymap"),
643 storageClass="Catalog",
644 )
645 denormMatches = cT.Output(
646 doc="Denormalized Match catalog produced by configured matcher, optional on "
647 "doWriteMatchesDenormalized",
648 name="{outputCoaddName}Coadd_measMatchFull",
649 dimensions=("tract", "patch", "band", "skymap"),
650 storageClass="Catalog",
651 )
653 def __init__(self, *, config=None):
654 super().__init__(config=config)
655 if config.doPropagateFlags is False:
656 self.inputs -= set(("visitCatalogs",))
658 if config.doMatchSources is False:
659 self.outputs -= set(("matchResult",))
661 if config.doWriteMatchesDenormalized is False:
662 self.outputs -= set(("denormMatches",))
665class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
666 pipelineConnections=MeasureMergedCoaddSourcesConnections):
667 """!
668 @anchor MeasureMergedCoaddSourcesConfig_
670 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask
671 """
672 inputCatalog = Field(dtype=str, default="deblendedFlux",
673 doc=("Name of the input catalog to use."
674 "If the single band deblender was used this should be 'deblendedFlux."
675 "If the multi-band deblender was used this should be 'deblendedModel."
676 "If no deblending was performed this should be 'mergeDet'"))
677 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement")
678 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch")
679 doPropagateFlags = Field(
680 dtype=bool, default=True,
681 doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
682 )
683 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc="Propagate visit flags to coadd")
684 doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?")
685 match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog")
686 doWriteMatchesDenormalized = Field(
687 dtype=bool,
688 default=False,
689 doc=("Write reference matches in denormalized format? "
690 "This format uses more disk space, but is more convenient to read."),
691 )
692 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
693 psfCache = Field(dtype=int, default=100, doc="Size of psfCache")
694 checkUnitsParseStrict = Field(
695 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
696 dtype=str,
697 default="raise",
698 )
699 doApCorr = Field(
700 dtype=bool,
701 default=True,
702 doc="Apply aperture corrections"
703 )
704 applyApCorr = ConfigurableField(
705 target=ApplyApCorrTask,
706 doc="Subtask to apply aperture corrections"
707 )
708 doRunCatalogCalculation = Field(
709 dtype=bool,
710 default=True,
711 doc='Run catalogCalculation task'
712 )
713 catalogCalculation = ConfigurableField(
714 target=CatalogCalculationTask,
715 doc="Subtask to run catalogCalculation plugins on catalog"
716 )
718 hasFakes = Field(
719 dtype=bool,
720 default=False,
721 doc="Should be set to True if fake sources have been inserted into the input data."
722 )
724 @property
725 def refObjLoader(self):
726 return self.match.refObjLoader
728 def setDefaults(self):
729 super().setDefaults()
730 self.measurement.plugins.names |= ['base_InputCount',
731 'base_Variance',
732 'base_LocalPhotoCalib',
733 'base_LocalWcs']
734 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE',
735 'INEXACT_PSF']
736 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE',
737 'INEXACT_PSF']
739 def validate(self):
740 super().validate()
741 refCatGen2 = getattr(self.refObjLoader, "ref_dataset_name", None)
742 if refCatGen2 is not None and refCatGen2 != self.connections.refCat:
743 raise ValueError(
744 f"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
745 f"are different. These options must be kept in sync until Gen2 is retired."
746 )
749## @addtogroup LSST_task_documentation
750## @{
751## @page MeasureMergedCoaddSourcesTask
752## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask"
753## @copybrief MeasureMergedCoaddSourcesTask
754## @}
757class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
758 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
759 @staticmethod
760 def getTargetList(parsedCmd, **kwargs):
761 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
764class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
765 r"""!
766 @anchor MeasureMergedCoaddSourcesTask_
768 @brief Deblend sources from master catalog in each coadd seperately and measure.
770 @section pipe_tasks_multiBand_Contents Contents
772 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
773 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
774 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
775 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
776 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
777 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
779 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
781 Command-line task that uses peaks and footprints from a master catalog to perform deblending and
782 measurement in each coadd.
784 Given a master input catalog of sources (peaks and footprints) or deblender outputs
785 (including a HeavyFootprint in each band), measure each source on the
786 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a
787 consistent set of child sources.
789 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source
790 properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit
791 flags are propagated to the coadd sources.
793 Optionally, we can match the coadd sources to an external reference catalog.
795 @par Inputs:
796 deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog
797 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
798 @par Outputs:
799 deepCoadd_meas{tract,patch,filter}: SourceCatalog
800 @par Data Unit:
801 tract, patch, filter
803 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
805 <DL>
806 <DT> @ref SingleFrameMeasurementTask_ "measurement"
807 <DD> Measure source properties of deblended sources.</DD>
808 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags"
809 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are
810 not at the edge of the field and that have either not been deblended or are the children of deblended
811 sources</DD>
812 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags"
813 <DD> Propagate flags set in individual visits to the coadd.</DD>
814 <DT> @ref DirectMatchTask_ "match"
815 <DD> Match input sources to a reference catalog (optional).
816 </DD>
817 </DL>
818 These subtasks may be retargeted as required.
820 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
822 @copydoc \_\_init\_\_
824 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
826 @copydoc run
828 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
830 See @ref MeasureMergedCoaddSourcesConfig_
832 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
834 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
835 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
836 files.
838 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
839 the various sub-tasks. See the documetation for individual sub-tasks for more information.
841 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
842 MeasureMergedCoaddSourcesTask
844 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
845 The next stage in the multi-band processing procedure will merge these measurements into a suitable
846 catalog for driving forced photometry.
848 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
849 to be processed.
850 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the
851 `--help` command line argument:
852 @code
853 measureCoaddSources.py --help
854 @endcode
856 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
857 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
858 step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band
859 coadd as follows:
860 @code
861 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
862 @endcode
863 This will process the HSC-I band data. The results are written in
864 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
866 It is also necessary to run
867 @code
868 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
869 @endcode
870 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
871 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask".
872 """
873 _DefaultName = "measureCoaddSources"
874 ConfigClass = MeasureMergedCoaddSourcesConfig
875 RunnerClass = MeasureMergedCoaddSourcesRunner
876 getSchemaCatalogs = _makeGetSchemaCatalogs("meas")
877 makeIdFactory = _makeMakeIdFactory("MergedCoaddId") # The IDs we already have are of this type
879 @classmethod
880 def _makeArgumentParser(cls):
881 parser = ArgumentParser(name=cls._DefaultName)
882 parser.add_id_argument("--id", "deepCoadd_calexp",
883 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
884 ContainerClass=ExistingCoaddDataIdContainer)
885 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
886 return parser
888 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
889 **kwargs):
890 """!
891 @brief Initialize the task.
893 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
894 @param[in] schema: the schema of the merged detection catalog used as input to this one
895 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog
896 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
897 catalog. May be None if the loader can be constructed from the butler argument or all steps
898 requiring a reference catalog are disabled.
899 @param[in] butler: a butler used to read the input schemas from disk or construct the reference
900 catalog loader, if schema or peakSchema or refObjLoader is None
902 The task will set its own self.schema attribute to the schema of the output measurement catalog.
903 This will include all fields from the input schema, as well as additional fields for all the
904 measurements.
905 """
906 super().__init__(**kwargs)
907 self.deblended = self.config.inputCatalog.startswith("deblended")
908 self.inputCatalog = "Coadd_" + self.config.inputCatalog
909 if initInputs is not None: 909 ↛ 910line 909 didn't jump to line 910, because the condition on line 909 was never true
910 schema = initInputs['inputSchema'].schema
911 if schema is None: 911 ↛ 914line 911 didn't jump to line 914, because the condition on line 911 was never false
912 assert butler is not None, "Neither butler nor schema is defined"
913 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema
914 self.schemaMapper = afwTable.SchemaMapper(schema)
915 self.schemaMapper.addMinimalSchema(schema)
916 self.schema = self.schemaMapper.getOutputSchema()
917 self.algMetadata = PropertyList()
918 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata)
919 self.makeSubtask("setPrimaryFlags", schema=self.schema)
920 if self.config.doMatchSources: 920 ↛ 921line 920 didn't jump to line 921, because the condition on line 920 was never true
921 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
922 if self.config.doPropagateFlags: 922 ↛ 924line 922 didn't jump to line 924, because the condition on line 922 was never false
923 self.makeSubtask("propagateFlags", schema=self.schema)
924 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
925 if self.config.doApCorr: 925 ↛ 927line 925 didn't jump to line 927, because the condition on line 925 was never false
926 self.makeSubtask("applyApCorr", schema=self.schema)
927 if self.config.doRunCatalogCalculation: 927 ↛ 930line 927 didn't jump to line 930, because the condition on line 927 was never false
928 self.makeSubtask("catalogCalculation", schema=self.schema)
930 self.outputSchema = afwTable.SourceCatalog(self.schema)
932 def runQuantum(self, butlerQC, inputRefs, outputRefs):
933 inputs = butlerQC.get(inputRefs)
935 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat],
936 inputs.pop('refCat'), config=self.config.refObjLoader,
937 log=self.log)
938 self.match.setRefObjLoader(refObjLoader)
940 # Set psfcache
941 # move this to run after gen2 deprecation
942 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
944 # Get unique integer ID for IdFactory and RNG seeds
945 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch", returnMaxBits=True)
946 inputs['exposureId'] = packedId
947 idFactory = afwTable.IdFactory.makeSource(packedId, 64 - maxBits)
948 # Transform inputCatalog
949 table = afwTable.SourceTable.make(self.schema, idFactory)
950 sources = afwTable.SourceCatalog(table)
951 sources.extend(inputs.pop('inputCatalog'), self.schemaMapper)
952 table = sources.getTable()
953 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
954 inputs['sources'] = sources
956 skyMap = inputs.pop('skyMap')
957 tractNumber = inputRefs.inputCatalog.dataId['tract']
958 tractInfo = skyMap[tractNumber]
959 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId['patch'])
960 skyInfo = Struct(
961 skyMap=skyMap,
962 tractInfo=tractInfo,
963 patchInfo=patchInfo,
964 wcs=tractInfo.getWcs(),
965 bbox=patchInfo.getOuterBBox()
966 )
967 inputs['skyInfo'] = skyInfo
969 if self.config.doPropagateFlags:
970 # Filter out any visit catalog that is not coadd inputs
971 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds
972 visitKey = ccdInputs.schema.find("visit").key
973 ccdKey = ccdInputs.schema.find("ccd").key
974 inputVisitIds = set()
975 ccdRecordsWcs = {}
976 for ccdRecord in ccdInputs:
977 visit = ccdRecord.get(visitKey)
978 ccd = ccdRecord.get(ccdKey)
979 inputVisitIds.add((visit, ccd))
980 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
982 inputCatalogsToKeep = []
983 inputCatalogWcsUpdate = []
984 for i, dataRef in enumerate(inputRefs.visitCatalogs):
985 key = (dataRef.dataId['visit'], dataRef.dataId['detector'])
986 if key in inputVisitIds:
987 inputCatalogsToKeep.append(inputs['visitCatalogs'][i])
988 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
989 inputs['visitCatalogs'] = inputCatalogsToKeep
990 inputs['wcsUpdates'] = inputCatalogWcsUpdate
991 inputs['ccdInputs'] = ccdInputs
993 outputs = self.run(**inputs)
994 butlerQC.put(outputs, outputRefs)
996 def runDataRef(self, patchRef, psfCache=100):
997 """!
998 @brief Deblend and measure.
1000 @param[in] patchRef: Patch reference.
1002 Set 'is-primary' and related flags. Propagate flags
1003 from individual visits. Optionally match the sources to a reference catalog and write the matches.
1004 Finally, write the deblended sources and measurements out.
1005 """
1006 if self.config.hasFakes: 1006 ↛ 1007line 1006 didn't jump to line 1007, because the condition on line 1006 was never true
1007 coaddType = "fakes_" + self.config.coaddName
1008 else:
1009 coaddType = self.config.coaddName
1010 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
1011 exposure.getPsf().setCacheCapacity(psfCache)
1012 sources = self.readSources(patchRef)
1013 table = sources.getTable()
1014 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1015 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1017 if self.config.doPropagateFlags: 1017 ↛ 1020line 1017 didn't jump to line 1020, because the condition on line 1017 was never false
1018 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1019 else:
1020 ccdInputs = None
1022 results = self.run(exposure=exposure, sources=sources,
1023 ccdInputs=ccdInputs,
1024 skyInfo=skyInfo, butler=patchRef.getButler(),
1025 exposureId=self.getExposureId(patchRef))
1027 if self.config.doMatchSources: 1027 ↛ 1028line 1027 didn't jump to line 1028, because the condition on line 1027 was never true
1028 self.writeMatches(patchRef, results)
1029 self.write(patchRef, results.outputSources)
1031 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1032 butler=None):
1033 """Run measurement algorithms on the input exposure, and optionally populate the
1034 resulting catalog with extra information.
1036 Parameters
1037 ----------
1038 exposure : `lsst.afw.exposure.Exposure`
1039 The input exposure on which measurements are to be performed
1040 sources : `lsst.afw.table.SourceCatalog`
1041 A catalog built from the results of merged detections, or
1042 deblender outputs.
1043 skyInfo : `lsst.pipe.base.Struct`
1044 A struct containing information about the position of the input exposure within
1045 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box
1046 exposureId : `int` or `bytes`
1047 packed unique number or bytes unique to the input exposure
1048 ccdInputs : `lsst.afw.table.ExposureCatalog`
1049 Catalog containing information on the individual visits which went into making
1050 the exposure
1051 visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None`
1052 A list of source catalogs corresponding to measurements made on the individual
1053 visits which went into the input exposure. If None and butler is `None` then
1054 the task cannot propagate visit flags to the output catalog.
1055 wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None`
1056 If visitCatalogs is not `None` this should be a list of wcs objects which correspond
1057 to the input visits. Used to put all coordinates to common system. If `None` and
1058 butler is `None` then the task cannot propagate visit flags to the output catalog.
1059 butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler`
1060 Either a gen2 or gen3 butler used to load visit catalogs
1062 Returns
1063 -------
1064 results : `lsst.pipe.base.Struct`
1065 Results of running measurement task. Will contain the catalog in the
1066 sources attribute. Optionally will have results of matching to a
1067 reference catalog in the matchResults attribute, and denormalized
1068 matches in the denormMatches attribute.
1069 """
1070 self.measurement.run(sources, exposure, exposureId=exposureId)
1072 if self.config.doApCorr: 1072 ↛ 1082line 1072 didn't jump to line 1082, because the condition on line 1072 was never false
1073 self.applyApCorr.run(
1074 catalog=sources,
1075 apCorrMap=exposure.getInfo().getApCorrMap()
1076 )
1078 # TODO DM-11568: this contiguous check-and-copy could go away if we
1079 # reserve enough space during SourceDetection and/or SourceDeblend.
1080 # NOTE: sourceSelectors require contiguous catalogs, so ensure
1081 # contiguity now, so views are preserved from here on.
1082 if not sources.isContiguous(): 1082 ↛ 1083line 1082 didn't jump to line 1083, because the condition on line 1082 was never true
1083 sources = sources.copy(deep=True)
1085 if self.config.doRunCatalogCalculation: 1085 ↛ 1088line 1085 didn't jump to line 1088, because the condition on line 1085 was never false
1086 self.catalogCalculation.run(sources)
1088 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1089 patchInfo=skyInfo.patchInfo, includeDeblend=self.deblended)
1090 if self.config.doPropagateFlags: 1090 ↛ 1093line 1090 didn't jump to line 1093, because the condition on line 1090 was never false
1091 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates)
1093 results = Struct()
1095 if self.config.doMatchSources: 1095 ↛ 1096line 1095 didn't jump to line 1096, because the condition on line 1095 was never true
1096 matchResult = self.match.run(sources, exposure.getInfo().getFilter().getName())
1097 matches = afwTable.packMatches(matchResult.matches)
1098 matches.table.setMetadata(matchResult.matchMeta)
1099 results.matchResult = matches
1100 if self.config.doWriteMatchesDenormalized:
1101 if matchResult.matches:
1102 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1103 else:
1104 self.log.warn("No matches, so generating dummy denormalized matches file")
1105 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1106 denormMatches.setMetadata(PropertyList())
1107 denormMatches.getMetadata().add("COMMENT",
1108 "This catalog is empty because no matches were found.")
1109 results.denormMatches = denormMatches
1110 results.denormMatches = denormMatches
1112 results.outputSources = sources
1113 return results
1115 def readSources(self, dataRef):
1116 """!
1117 @brief Read input sources.
1119 @param[in] dataRef: Data reference for catalog of merged detections
1120 @return List of sources in merged catalog
1122 We also need to add columns to hold the measurements we're about to make
1123 so we can measure in-place.
1124 """
1125 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1126 self.log.info("Read %d detections: %s" % (len(merged), dataRef.dataId))
1127 idFactory = self.makeIdFactory(dataRef)
1128 for s in merged:
1129 idFactory.notify(s.getId())
1130 table = afwTable.SourceTable.make(self.schema, idFactory)
1131 sources = afwTable.SourceCatalog(table)
1132 sources.extend(merged, self.schemaMapper)
1133 return sources
1135 def writeMatches(self, dataRef, results):
1136 """!
1137 @brief Write matches of the sources to the astrometric reference catalog.
1139 @param[in] dataRef: data reference
1140 @param[in] results: results struct from run method
1141 """
1142 if hasattr(results, "matchResult"):
1143 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1144 if hasattr(results, "denormMatches"):
1145 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1147 def write(self, dataRef, sources):
1148 """!
1149 @brief Write the source catalog.
1151 @param[in] dataRef: data reference
1152 @param[in] sources: source catalog
1153 """
1154 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1155 self.log.info("Wrote %d sources: %s" % (len(sources), dataRef.dataId))
1157 def getExposureId(self, dataRef):
1158 return int(dataRef.get(self.config.coaddName + "CoaddId"))