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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
44# NOTE: these imports are a convenience so multiband users only have to import this file.
45from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401
46from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401
47from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401
48from .multiBandUtils import getInputSchema, readCatalog, _makeMakeIdFactory # noqa: F401
49from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401
50from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401
51from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401
52from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401
55"""
56New set types:
57* deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter)
58* deepCoadd_mergeDet: merged detections (tract, patch)
59* deepCoadd_meas: measurements of merged detections (tract, patch, filter)
60* deepCoadd_ref: reference sources (tract, patch)
61All of these have associated *_schema catalogs that require no data ID and hold no records.
63In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in
64the mergeDet, meas, and ref dataset Footprints:
65* deepCoadd_peak_schema
66"""
69##############################################################################################################
70class DetectCoaddSourcesConnections(PipelineTaskConnections,
71 dimensions=("tract", "patch", "band", "skymap"),
72 defaultTemplates={"inputCoaddName": "deep", "outputCoaddName": "deep"}):
73 detectionSchema = cT.InitOutput(
74 doc="Schema of the detection catalog",
75 name="{outputCoaddName}Coadd_det_schema",
76 storageClass="SourceCatalog",
77 )
78 exposure = cT.Input(
79 doc="Exposure on which detections are to be performed",
80 name="{inputCoaddName}Coadd",
81 storageClass="ExposureF",
82 dimensions=("tract", "patch", "band", "skymap")
83 )
84 outputBackgrounds = cT.Output(
85 doc="Output Backgrounds used in detection",
86 name="{outputCoaddName}Coadd_calexp_background",
87 storageClass="Background",
88 dimensions=("tract", "patch", "band", "skymap")
89 )
90 outputSources = cT.Output(
91 doc="Detected sources catalog",
92 name="{outputCoaddName}Coadd_det",
93 storageClass="SourceCatalog",
94 dimensions=("tract", "patch", "band", "skymap")
95 )
96 outputExposure = cT.Output(
97 doc="Exposure post detection",
98 name="{outputCoaddName}Coadd_calexp",
99 storageClass="ExposureF",
100 dimensions=("tract", "patch", "band", "skymap")
101 )
104class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections):
105 """!
106 @anchor DetectCoaddSourcesConfig_
108 @brief Configuration parameters for the DetectCoaddSourcesTask
109 """
110 doScaleVariance = Field(dtype=bool, default=True, doc="Scale variance plane using empirical noise?")
111 scaleVariance = ConfigurableField(target=ScaleVarianceTask, doc="Variance rescaling")
112 detection = ConfigurableField(target=DynamicDetectionTask, doc="Source detection")
113 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
114 doInsertFakes = Field(dtype=bool, default=False,
115 doc="Run fake sources injection task")
116 insertFakes = ConfigurableField(target=BaseFakeSourcesTask,
117 doc="Injection of fake sources for testing "
118 "purposes (must be retargeted)")
119 hasFakes = Field(
120 dtype=bool,
121 default=False,
122 doc="Should be set to True if fake sources have been inserted into the input data."
123 )
125 def setDefaults(self):
126 super().setDefaults()
127 self.detection.thresholdType = "pixel_stdev"
128 self.detection.isotropicGrow = True
129 # Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic
130 self.detection.reEstimateBackground = False
131 self.detection.background.useApprox = False
132 self.detection.background.binSize = 4096
133 self.detection.background.undersampleStyle = 'REDUCE_INTERP_ORDER'
134 self.detection.doTempWideBackground = True # Suppress large footprints that overwhelm the deblender
136## @addtogroup LSST_task_documentation
137## @{
138## @page DetectCoaddSourcesTask
139## @ref DetectCoaddSourcesTask_ "DetectCoaddSourcesTask"
140## @copybrief DetectCoaddSourcesTask
141## @}
144class DetectCoaddSourcesTask(PipelineTask, CmdLineTask):
145 r"""!
146 @anchor DetectCoaddSourcesTask_
148 @brief Detect sources on a coadd
150 @section pipe_tasks_multiBand_Contents Contents
152 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose
153 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize
154 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run
155 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config
156 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug
157 - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example
159 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
161 Command-line task that detects sources on a coadd of exposures obtained with a single filter.
163 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise
164 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane
165 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should
166 propagate the full covariance matrix -- but it is simple and works well in practice.
168 After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref
169 SourceDetectionTask_ "detection" subtask.
171 @par Inputs:
172 deepCoadd{tract,patch,filter}: ExposureF
173 @par Outputs:
174 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
175 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input
176 exposure (ExposureF)
177 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList
178 @par Data Unit:
179 tract, patch, filter
181 DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask.
182 You can retarget this subtask if you wish.
184 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
186 @copydoc \_\_init\_\_
188 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
190 @copydoc run
192 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
194 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig"
196 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
198 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
199 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
200 files.
202 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to
203 @ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for
204 @ref SourceDetectionTask_ "SourceDetectionTask" for further information.
206 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example
207 of using DetectCoaddSourcesTask
209 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of
210 the task is to update the background, detect all sources in a single band and generate a set of parent
211 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and,
212 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data
213 reference to the coadd to be processed. A list of the available optional arguments can be obtained by
214 calling detectCoaddSources.py with the `--help` command line argument:
215 @code
216 detectCoaddSources.py --help
217 @endcode
219 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
220 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed
221 steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows:
222 @code
223 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
224 @endcode
225 that will process the HSC-I band data. The results are written to
226 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
228 It is also necessary to run:
229 @code
230 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
231 @endcode
232 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
233 processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask".
234 """
235 _DefaultName = "detectCoaddSources"
236 ConfigClass = DetectCoaddSourcesConfig
237 getSchemaCatalogs = _makeGetSchemaCatalogs("det")
238 makeIdFactory = _makeMakeIdFactory("CoaddId")
240 @classmethod
241 def _makeArgumentParser(cls):
242 parser = ArgumentParser(name=cls._DefaultName)
243 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
244 ContainerClass=ExistingCoaddDataIdContainer)
245 return parser
247 def __init__(self, schema=None, **kwargs):
248 """!
249 @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask.
251 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
253 @param[in] schema: initial schema for the output catalog, modified-in place to include all
254 fields set by this task. If None, the source minimal schema will be used.
255 @param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__
256 """
257 # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree
258 # call structure has been reviewed carefully to be sure super will work as intended.
259 super().__init__(**kwargs)
260 if schema is None: 260 ↛ 262line 260 didn't jump to line 262, because the condition on line 260 was never false
261 schema = afwTable.SourceTable.makeMinimalSchema()
262 if self.config.doInsertFakes: 262 ↛ 263line 262 didn't jump to line 263, because the condition on line 262 was never true
263 self.makeSubtask("insertFakes")
264 self.schema = schema
265 self.makeSubtask("detection", schema=self.schema)
266 if self.config.doScaleVariance: 266 ↛ 269line 266 didn't jump to line 269, because the condition on line 266 was never false
267 self.makeSubtask("scaleVariance")
269 self.detectionSchema = afwTable.SourceCatalog(self.schema)
271 def runDataRef(self, patchRef):
272 """!
273 @brief Run detection on a coadd.
275 Invokes @ref run and then uses @ref write to output the
276 results.
278 @param[in] patchRef: data reference for patch
279 """
280 if self.config.hasFakes: 280 ↛ 281line 280 didn't jump to line 281, because the condition on line 280 was never true
281 exposure = patchRef.get("fakes_" + self.config.coaddName + "Coadd", immediate=True)
282 else:
283 exposure = patchRef.get(self.config.coaddName + "Coadd", immediate=True)
284 expId = int(patchRef.get(self.config.coaddName + "CoaddId"))
285 results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId)
286 self.write(results, patchRef)
287 return results
289 def runQuantum(self, butlerQC, inputRefs, outputRefs):
290 inputs = butlerQC.get(inputRefs)
291 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch_band", returnMaxBits=True)
292 inputs["idFactory"] = afwTable.IdFactory.makeSource(packedId, 64 - maxBits)
293 inputs["expId"] = packedId
294 outputs = self.run(**inputs)
295 butlerQC.put(outputs, outputRefs)
297 def run(self, exposure, idFactory, expId):
298 """!
299 @brief Run detection on an exposure.
301 First scale the variance plane to match the observed variance
302 using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to
303 detect sources.
305 @param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled,
306 depending on configuration).
307 @param[in] idFactory: IdFactory to set source identifiers
308 @param[in] expId: Exposure identifier (integer) for RNG seed
310 @return a pipe.base.Struct with fields
311 - sources: catalog of detections
312 - backgrounds: list of backgrounds
313 """
314 if self.config.doScaleVariance: 314 ↛ 317line 314 didn't jump to line 317, because the condition on line 314 was never false
315 varScale = self.scaleVariance.run(exposure.maskedImage)
316 exposure.getMetadata().add("VARIANCE_SCALE", varScale)
317 backgrounds = afwMath.BackgroundList()
318 if self.config.doInsertFakes: 318 ↛ 319line 318 didn't jump to line 319, because the condition on line 318 was never true
319 self.insertFakes.run(exposure, background=backgrounds)
320 table = afwTable.SourceTable.make(self.schema, idFactory)
321 detections = self.detection.run(table, exposure, expId=expId)
322 sources = detections.sources
323 fpSets = detections.fpSets
324 if hasattr(fpSets, "background") and fpSets.background: 324 ↛ 327line 324 didn't jump to line 327, because the condition on line 324 was never false
325 for bg in fpSets.background:
326 backgrounds.append(bg)
327 return Struct(outputSources=sources, outputBackgrounds=backgrounds, outputExposure=exposure)
329 def write(self, results, patchRef):
330 """!
331 @brief Write out results from runDetection.
333 @param[in] exposure: Exposure to write out
334 @param[in] results: Struct returned from runDetection
335 @param[in] patchRef: data reference for patch
336 """
337 coaddName = self.config.coaddName + "Coadd"
338 patchRef.put(results.outputBackgrounds, coaddName + "_calexp_background")
339 patchRef.put(results.outputSources, coaddName + "_det")
340 if self.config.hasFakes: 340 ↛ 341line 340 didn't jump to line 341, because the condition on line 340 was never true
341 patchRef.put(results.outputExposure, "fakes_" + coaddName + "_calexp")
342 else:
343 patchRef.put(results.outputExposure, coaddName + "_calexp")
345##############################################################################################################
348class DeblendCoaddSourcesConfig(Config):
349 """DeblendCoaddSourcesConfig
351 Configuration parameters for the `DeblendCoaddSourcesTask`.
352 """
353 singleBandDeblend = ConfigurableField(target=SourceDeblendTask,
354 doc="Deblend sources separately in each band")
355 multiBandDeblend = ConfigurableField(target=ScarletDeblendTask,
356 doc="Deblend sources simultaneously across bands")
357 simultaneous = Field(dtype=bool,
358 default=True,
359 doc="Simultaneously deblend all bands? "
360 "True uses 'singleBandDeblend' while False uses 'multibandDeblend'")
361 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
362 hasFakes = Field(dtype=bool,
363 default=False,
364 doc="Should be set to True if fake sources have been inserted into the input data.")
366 def setDefaults(self):
367 Config.setDefaults(self)
368 self.singleBandDeblend.propagateAllPeaks = True
371class DeblendCoaddSourcesRunner(MergeSourcesRunner):
372 """Task runner for the `MergeSourcesTask`
374 Required because the run method requires a list of
375 dataRefs rather than a single dataRef.
376 """
377 @staticmethod
378 def getTargetList(parsedCmd, **kwargs):
379 """Provide a list of patch references for each patch, tract, filter combo.
381 Parameters
382 ----------
383 parsedCmd:
384 The parsed command
385 kwargs:
386 Keyword arguments passed to the task
388 Returns
389 -------
390 targetList: list
391 List of tuples, where each tuple is a (dataRef, kwargs) pair.
392 """
393 refDict = MergeSourcesRunner.buildRefDict(parsedCmd)
394 kwargs["psfCache"] = parsedCmd.psfCache
395 return [(list(p.values()), kwargs) for t in refDict.values() for p in t.values()]
398class DeblendCoaddSourcesTask(CmdLineTask):
399 """Deblend the sources in a merged catalog
401 Deblend sources from master catalog in each coadd.
402 This can either be done separately in each band using the HSC-SDSS deblender
403 (`DeblendCoaddSourcesTask.config.simultaneous==False`)
404 or use SCARLET to simultaneously fit the blend in all bands
405 (`DeblendCoaddSourcesTask.config.simultaneous==True`).
406 The task will set its own `self.schema` atribute to the `Schema` of the
407 output deblended catalog.
408 This will include all fields from the input `Schema`, as well as additional fields
409 from the deblender.
411 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description
412 ---------------------------------------------------------
413 `
415 Parameters
416 ----------
417 butler: `Butler`
418 Butler used to read the input schemas from disk or
419 construct the reference catalog loader, if `schema` or `peakSchema` or
420 schema: `Schema`
421 The schema of the merged detection catalog as an input to this task.
422 peakSchema: `Schema`
423 The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog
424 """
425 ConfigClass = DeblendCoaddSourcesConfig
426 RunnerClass = DeblendCoaddSourcesRunner
427 _DefaultName = "deblendCoaddSources"
428 makeIdFactory = _makeMakeIdFactory("MergedCoaddId")
430 @classmethod
431 def _makeArgumentParser(cls):
432 parser = ArgumentParser(name=cls._DefaultName)
433 parser.add_id_argument("--id", "deepCoadd_calexp",
434 help="data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i",
435 ContainerClass=ExistingCoaddDataIdContainer)
436 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
437 return parser
439 def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs):
440 CmdLineTask.__init__(self, **kwargs)
441 if schema is None: 441 ↛ 444line 441 didn't jump to line 444, because the condition on line 441 was never false
442 assert butler is not None, "Neither butler nor schema is defined"
443 schema = butler.get(self.config.coaddName + "Coadd_mergeDet_schema", immediate=True).schema
444 self.schemaMapper = afwTable.SchemaMapper(schema)
445 self.schemaMapper.addMinimalSchema(schema)
446 self.schema = self.schemaMapper.getOutputSchema()
447 if peakSchema is None: 447 ↛ 451line 447 didn't jump to line 451, because the condition on line 447 was never false
448 assert butler is not None, "Neither butler nor peakSchema is defined"
449 peakSchema = butler.get(self.config.coaddName + "Coadd_peak_schema", immediate=True).schema
451 if self.config.simultaneous: 451 ↛ 454line 451 didn't jump to line 454, because the condition on line 451 was never false
452 self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema)
453 else:
454 self.makeSubtask("singleBandDeblend", schema=self.schema, peakSchema=peakSchema)
456 def getSchemaCatalogs(self):
457 """Return a dict of empty catalogs for each catalog dataset produced by this task.
459 Returns
460 -------
461 result: dict
462 Dictionary of empty catalogs, with catalog names as keys.
463 """
464 catalog = afwTable.SourceCatalog(self.schema)
465 return {self.config.coaddName + "Coadd_deblendedFlux": catalog,
466 self.config.coaddName + "Coadd_deblendedModel": catalog}
468 def runDataRef(self, patchRefList, psfCache=100):
469 """Deblend the patch
471 Deblend each source simultaneously or separately
472 (depending on `DeblendCoaddSourcesTask.config.simultaneous`).
473 Set `is-primary` and related flags.
474 Propagate flags from individual visits.
475 Write the deblended sources out.
477 Parameters
478 ----------
479 patchRefList: list
480 List of data references for each filter
481 """
483 if self.config.hasFakes: 483 ↛ 484line 483 didn't jump to line 484, because the condition on line 483 was never true
484 coaddType = "fakes_" + self.config.coaddName
485 else:
486 coaddType = self.config.coaddName
488 if self.config.simultaneous: 488 ↛ 505line 488 didn't jump to line 505, because the condition on line 488 was never false
489 # Use SCARLET to simultaneously deblend across filters
490 filters = []
491 exposures = []
492 for patchRef in patchRefList:
493 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
494 filter = patchRef.get(coaddType + "Coadd_filterLabel", immediate=True)
495 filters.append(filter.bandLabel)
496 exposures.append(exposure)
497 # The input sources are the same for all bands, since it is a merged catalog
498 sources = self.readSources(patchRef)
499 exposure = afwImage.MultibandExposure.fromExposures(filters, exposures)
500 templateCatalogs = self.multiBandDeblend.run(exposure, sources)
501 for n in range(len(patchRefList)):
502 self.write(patchRefList[n], templateCatalogs[filters[n]])
503 else:
504 # Use the singeband deblender to deblend each band separately
505 for patchRef in patchRefList:
506 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
507 exposure.getPsf().setCacheCapacity(psfCache)
508 sources = self.readSources(patchRef)
509 self.singleBandDeblend.run(exposure, sources)
510 self.write(patchRef, sources)
512 def readSources(self, dataRef):
513 """Read merged catalog
515 Read the catalog of merged detections and create a catalog
516 in a single band.
518 Parameters
519 ----------
520 dataRef: data reference
521 Data reference for catalog of merged detections
523 Returns
524 -------
525 sources: `SourceCatalog`
526 List of sources in merged catalog
528 We also need to add columns to hold the measurements we're about to make
529 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
541 def write(self, dataRef, sources):
542 """Write the source catalog(s)
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))
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.warn("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
575 def getExposureId(self, dataRef):
576 """Get the ExposureId from a data reference
577 """
578 return int(dataRef.get(self.config.coaddName + "CoaddId"))
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 )
655 def __init__(self, *, config=None):
656 super().__init__(config=config)
657 if config.doPropagateFlags is False:
658 self.inputs -= set(("visitCatalogs",))
660 if config.doMatchSources is False:
661 self.outputs -= set(("matchResult",))
663 if config.doWriteMatchesDenormalized is False:
664 self.outputs -= set(("denormMatches",))
667class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
668 pipelineConnections=MeasureMergedCoaddSourcesConnections):
669 """!
670 @anchor MeasureMergedCoaddSourcesConfig_
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 )
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 )
726 @property
727 def refObjLoader(self):
728 return self.match.refObjLoader
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']
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 )
751## @addtogroup LSST_task_documentation
752## @{
753## @page MeasureMergedCoaddSourcesTask
754## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask"
755## @copybrief MeasureMergedCoaddSourcesTask
756## @}
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)
766class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
767 r"""!
768 @anchor MeasureMergedCoaddSourcesTask_
770 @brief Deblend sources from master catalog in each coadd seperately and measure.
772 @section pipe_tasks_multiBand_Contents Contents
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
781 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
783 Command-line task that uses peaks and footprints from a master catalog to perform deblending and
784 measurement in each coadd.
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.
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.
795 Optionally, we can match the coadd sources to an external reference catalog.
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
805 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
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.
822 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
824 @copydoc \_\_init\_\_
826 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
828 @copydoc run
830 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
832 See @ref MeasureMergedCoaddSourcesConfig_
834 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
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.
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.
843 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
844 MeasureMergedCoaddSourcesTask
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.
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
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
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
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
890 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
891 **kwargs):
892 """!
893 @brief Initialize the task.
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
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: 911 ↛ 912line 911 didn't jump to line 912, because the condition on line 911 was never true
912 schema = initInputs['inputSchema'].schema
913 if schema is None: 913 ↛ 916line 913 didn't jump to line 916, because the condition on line 913 was never false
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: 922 ↛ 923line 922 didn't jump to line 923, because the condition on line 922 was never true
923 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
924 if self.config.doPropagateFlags: 924 ↛ 926line 924 didn't jump to line 926, because the condition on line 924 was never false
925 self.makeSubtask("propagateFlags", schema=self.schema)
926 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
927 if self.config.doApCorr: 927 ↛ 929line 927 didn't jump to line 929, because the condition on line 927 was never false
928 self.makeSubtask("applyApCorr", schema=self.schema)
929 if self.config.doRunCatalogCalculation: 929 ↛ 932line 929 didn't jump to line 932, because the condition on line 929 was never false
930 self.makeSubtask("catalogCalculation", schema=self.schema)
932 self.outputSchema = afwTable.SourceCatalog(self.schema)
934 def runQuantum(self, butlerQC, inputRefs, outputRefs):
935 inputs = butlerQC.get(inputRefs)
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)
942 # Set psfcache
943 # move this to run after gen2 deprecation
944 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
946 # Get unique integer ID for IdFactory and RNG seeds
947 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch", returnMaxBits=True)
948 inputs['exposureId'] = packedId
949 idFactory = afwTable.IdFactory.makeSource(packedId, 64 - maxBits)
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
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
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()
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
995 outputs = self.run(**inputs)
996 butlerQC.put(outputs, outputRefs)
998 def runDataRef(self, patchRef, psfCache=100):
999 """!
1000 @brief Deblend and measure.
1002 @param[in] patchRef: Patch reference.
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: 1008 ↛ 1009line 1008 didn't jump to line 1009, because the condition on line 1008 was never true
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)
1019 if self.config.doPropagateFlags: 1019 ↛ 1022line 1019 didn't jump to line 1022, because the condition on line 1019 was never false
1020 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1021 else:
1022 ccdInputs = None
1024 results = self.run(exposure=exposure, sources=sources,
1025 ccdInputs=ccdInputs,
1026 skyInfo=skyInfo, butler=patchRef.getButler(),
1027 exposureId=self.getExposureId(patchRef))
1029 if self.config.doMatchSources: 1029 ↛ 1030line 1029 didn't jump to line 1030, because the condition on line 1029 was never true
1030 self.writeMatches(patchRef, results)
1031 self.write(patchRef, results.outputSources)
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.
1038 Parameters
1039 ----------
1040 exposure : `lsst.afw.exposure.Exposure`
1041 The input exposure on which measurements are to be performed
1042 sources : `lsst.afw.table.SourceCatalog`
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
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)
1074 if self.config.doApCorr: 1074 ↛ 1084line 1074 didn't jump to line 1084, because the condition on line 1074 was never false
1075 self.applyApCorr.run(
1076 catalog=sources,
1077 apCorrMap=exposure.getInfo().getApCorrMap()
1078 )
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(): 1084 ↛ 1085line 1084 didn't jump to line 1085, because the condition on line 1084 was never true
1085 sources = sources.copy(deep=True)
1087 if self.config.doRunCatalogCalculation: 1087 ↛ 1090line 1087 didn't jump to line 1090, because the condition on line 1087 was never false
1088 self.catalogCalculation.run(sources)
1090 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1091 patchInfo=skyInfo.patchInfo, includeDeblend=self.deblended)
1092 if self.config.doPropagateFlags: 1092 ↛ 1095line 1092 didn't jump to line 1095, because the condition on line 1092 was never false
1093 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates)
1095 results = Struct()
1097 if self.config.doMatchSources: 1097 ↛ 1098line 1097 didn't jump to line 1098, because the condition on line 1097 was never true
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.warn("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
1114 results.outputSources = sources
1115 return results
1117 def readSources(self, dataRef):
1118 """!
1119 @brief Read input sources.
1121 @param[in] dataRef: Data reference for catalog of merged detections
1122 @return List of sources in merged catalog
1124 We also need to add columns to hold the measurements we're about to make
1125 so we can measure in-place.
1126 """
1127 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1128 self.log.info("Read %d detections: %s" % (len(merged), dataRef.dataId))
1129 idFactory = self.makeIdFactory(dataRef)
1130 for s in merged:
1131 idFactory.notify(s.getId())
1132 table = afwTable.SourceTable.make(self.schema, idFactory)
1133 sources = afwTable.SourceCatalog(table)
1134 sources.extend(merged, self.schemaMapper)
1135 return sources
1137 def writeMatches(self, dataRef, results):
1138 """!
1139 @brief Write matches of the sources to the astrometric reference catalog.
1141 @param[in] dataRef: data reference
1142 @param[in] results: results struct from run method
1143 """
1144 if hasattr(results, "matchResult"):
1145 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1146 if hasattr(results, "denormMatches"):
1147 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1149 def write(self, dataRef, sources):
1150 """!
1151 @brief Write the source catalog.
1153 @param[in] dataRef: data reference
1154 @param[in] sources: source catalog
1155 """
1156 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1157 self.log.info("Wrote %d sources: %s" % (len(sources), dataRef.dataId))
1159 def getExposureId(self, dataRef):
1160 return int(dataRef.get(self.config.coaddName + "CoaddId"))