Coverage for python/lsst/pipe/tasks/multiBand.py: 27%
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1#!/usr/bin/env python
2#
3# LSST Data Management System
4# Copyright 2008-2015 AURA/LSST.
5#
6# This product includes software developed by the
7# LSST Project (http://www.lsst.org/).
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the LSST License Statement and
20# the GNU General Public License along with this program. If not,
21# see <https://www.lsstcorp.org/LegalNotices/>.
22#
23import numpy as np
25from lsst.coadd.utils.coaddDataIdContainer import ExistingCoaddDataIdContainer
26from lsst.coadd.utils.getGen3CoaddExposureId import getGen3CoaddExposureId
27from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner,
28 PipelineTask, PipelineTaskConfig, PipelineTaskConnections)
29import lsst.pipe.base.connectionTypes as cT
30from lsst.pex.config import Config, Field, ConfigurableField
31from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader
32from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask
33from lsst.meas.deblender import SourceDeblendTask
34from lsst.meas.extensions.scarlet import ScarletDeblendTask
35from lsst.pipe.tasks.coaddBase import getSkyInfo
36from lsst.pipe.tasks.scaleVariance import ScaleVarianceTask
37from lsst.meas.astrom import DirectMatchTask, denormalizeMatches
38from lsst.pipe.tasks.fakes import BaseFakeSourcesTask
39from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
40from lsst.pipe.tasks.propagateSourceFlags import PropagateSourceFlagsTask
41import lsst.afw.image as afwImage
42import lsst.afw.table as afwTable
43import lsst.afw.math as afwMath
44from lsst.daf.base import PropertyList
45from lsst.skymap import BaseSkyMap
46from lsst.obs.base import ExposureIdInfo
48# NOTE: these imports are a convenience so multiband users only have to import this file.
49from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401
50from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401
51from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401
52from .multiBandUtils import getInputSchema, readCatalog, _makeMakeIdFactory # noqa: F401
53from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401
54from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401
55from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401
56from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401
59"""
60New set types:
61* deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter)
62* deepCoadd_mergeDet: merged detections (tract, patch)
63* deepCoadd_meas: measurements of merged detections (tract, patch, filter)
64* deepCoadd_ref: reference sources (tract, patch)
65All of these have associated *_schema catalogs that require no data ID and hold no records.
67In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in
68the mergeDet, meas, and ref dataset Footprints:
69* deepCoadd_peak_schema
70"""
73##############################################################################################################
74class DetectCoaddSourcesConnections(PipelineTaskConnections,
75 dimensions=("tract", "patch", "band", "skymap"),
76 defaultTemplates={"inputCoaddName": "deep", "outputCoaddName": "deep"}):
77 detectionSchema = cT.InitOutput(
78 doc="Schema of the detection catalog",
79 name="{outputCoaddName}Coadd_det_schema",
80 storageClass="SourceCatalog",
81 )
82 exposure = cT.Input(
83 doc="Exposure on which detections are to be performed",
84 name="{inputCoaddName}Coadd",
85 storageClass="ExposureF",
86 dimensions=("tract", "patch", "band", "skymap")
87 )
88 outputBackgrounds = cT.Output(
89 doc="Output Backgrounds used in detection",
90 name="{outputCoaddName}Coadd_calexp_background",
91 storageClass="Background",
92 dimensions=("tract", "patch", "band", "skymap")
93 )
94 outputSources = cT.Output(
95 doc="Detected sources catalog",
96 name="{outputCoaddName}Coadd_det",
97 storageClass="SourceCatalog",
98 dimensions=("tract", "patch", "band", "skymap")
99 )
100 outputExposure = cT.Output(
101 doc="Exposure post detection",
102 name="{outputCoaddName}Coadd_calexp",
103 storageClass="ExposureF",
104 dimensions=("tract", "patch", "band", "skymap")
105 )
108class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections):
109 """!
110 @anchor DetectCoaddSourcesConfig_
112 @brief Configuration parameters for the DetectCoaddSourcesTask
113 """
114 doScaleVariance = Field(dtype=bool, default=True, doc="Scale variance plane using empirical noise?")
115 scaleVariance = ConfigurableField(target=ScaleVarianceTask, doc="Variance rescaling")
116 detection = ConfigurableField(target=DynamicDetectionTask, doc="Source detection")
117 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
118 doInsertFakes = Field(dtype=bool, default=False,
119 doc="Run fake sources injection task")
120 insertFakes = ConfigurableField(target=BaseFakeSourcesTask,
121 doc="Injection of fake sources for testing "
122 "purposes (must be retargeted)")
123 hasFakes = Field(
124 dtype=bool,
125 default=False,
126 doc="Should be set to True if fake sources have been inserted into the input data."
127 )
129 def setDefaults(self):
130 super().setDefaults()
131 self.detection.thresholdType = "pixel_stdev"
132 self.detection.isotropicGrow = True
133 # Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic
134 self.detection.reEstimateBackground = False
135 self.detection.background.useApprox = False
136 self.detection.background.binSize = 4096
137 self.detection.background.undersampleStyle = 'REDUCE_INTERP_ORDER'
138 self.detection.doTempWideBackground = True # Suppress large footprints that overwhelm the deblender
140## @addtogroup LSST_task_documentation
141## @{
142## @page page_DetectCoaddSourcesTask DetectCoaddSourcesTask
143## @ref DetectCoaddSourcesTask_ "DetectCoaddSourcesTask"
144## @copybrief DetectCoaddSourcesTask
145## @}
148class DetectCoaddSourcesTask(PipelineTask, CmdLineTask):
149 r"""!
150 @anchor DetectCoaddSourcesTask_
152 @brief Detect sources on a coadd
154 @section pipe_tasks_multiBand_Contents Contents
156 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose
157 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize
158 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run
159 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config
160 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug
161 - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example
163 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
165 Command-line task that detects sources on a coadd of exposures obtained with a single filter.
167 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise
168 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane
169 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should
170 propagate the full covariance matrix -- but it is simple and works well in practice.
172 After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref
173 SourceDetectionTask_ "detection" subtask.
175 @par Inputs:
176 deepCoadd{tract,patch,filter}: ExposureF
177 @par Outputs:
178 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
179 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input
180 exposure (ExposureF)
181 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList
182 @par Data Unit:
183 tract, patch, filter
185 DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask.
186 You can retarget this subtask if you wish.
188 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
190 @copydoc \_\_init\_\_
192 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
194 @copydoc run
196 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
198 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig"
200 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
202 The command line task interface supports a
203 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
204 files.
206 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to
207 @ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for
208 @ref SourceDetectionTask_ "SourceDetectionTask" for further information.
210 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example
211 of using DetectCoaddSourcesTask
213 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of
214 the task is to update the background, detect all sources in a single band and generate a set of parent
215 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and,
216 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data
217 reference to the coadd to be processed. A list of the available optional arguments can be obtained by
218 calling detectCoaddSources.py with the `--help` command line argument:
219 @code
220 detectCoaddSources.py --help
221 @endcode
223 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
224 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed
225 steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows:
226 @code
227 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
228 @endcode
229 that will process the HSC-I band data. The results are written to
230 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
232 It is also necessary to run:
233 @code
234 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
235 @endcode
236 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
237 processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask".
238 """
239 _DefaultName = "detectCoaddSources"
240 ConfigClass = DetectCoaddSourcesConfig
241 getSchemaCatalogs = _makeGetSchemaCatalogs("det")
242 makeIdFactory = _makeMakeIdFactory("CoaddId")
244 @classmethod
245 def _makeArgumentParser(cls):
246 parser = ArgumentParser(name=cls._DefaultName)
247 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
248 ContainerClass=ExistingCoaddDataIdContainer)
249 return parser
251 def __init__(self, schema=None, **kwargs):
252 """!
253 @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask.
255 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
257 @param[in] schema: initial schema for the output catalog, modified-in place to include all
258 fields set by this task. If None, the source minimal schema will be used.
259 @param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__
260 """
261 # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree
262 # call structure has been reviewed carefully to be sure super will work as intended.
263 super().__init__(**kwargs)
264 if schema is None:
265 schema = afwTable.SourceTable.makeMinimalSchema()
266 if self.config.doInsertFakes:
267 self.makeSubtask("insertFakes")
268 self.schema = schema
269 self.makeSubtask("detection", schema=self.schema)
270 if self.config.doScaleVariance:
271 self.makeSubtask("scaleVariance")
273 self.detectionSchema = afwTable.SourceCatalog(self.schema)
275 def runDataRef(self, patchRef):
276 """!
277 @brief Run detection on a coadd.
279 Invokes @ref run and then uses @ref write to output the
280 results.
282 @param[in] patchRef: data reference for patch
283 """
284 if self.config.hasFakes:
285 exposure = patchRef.get("fakes_" + self.config.coaddName + "Coadd", immediate=True)
286 else:
287 exposure = patchRef.get(self.config.coaddName + "Coadd", immediate=True)
288 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, log=self.log)
289 results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId)
290 self.write(results, patchRef)
291 return results
293 def runQuantum(self, butlerQC, inputRefs, outputRefs):
294 inputs = butlerQC.get(inputRefs)
295 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch_band")
296 inputs["idFactory"] = exposureIdInfo.makeSourceIdFactory()
297 inputs["expId"] = exposureIdInfo.expId
298 outputs = self.run(**inputs)
299 butlerQC.put(outputs, outputRefs)
301 def run(self, exposure, idFactory, expId):
302 """!
303 @brief Run detection on an exposure.
305 First scale the variance plane to match the observed variance
306 using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to
307 detect sources.
309 @param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled,
310 depending on configuration).
311 @param[in] idFactory: IdFactory to set source identifiers
312 @param[in] expId: Exposure identifier (integer) for RNG seed
314 @return a pipe.base.Struct with fields
315 - sources: catalog of detections
316 - backgrounds: list of backgrounds
317 """
318 if self.config.doScaleVariance:
319 varScale = self.scaleVariance.run(exposure.maskedImage)
320 exposure.getMetadata().add("VARIANCE_SCALE", varScale)
321 backgrounds = afwMath.BackgroundList()
322 if self.config.doInsertFakes:
323 self.insertFakes.run(exposure, background=backgrounds)
324 table = afwTable.SourceTable.make(self.schema, idFactory)
325 detections = self.detection.run(table, exposure, expId=expId)
326 sources = detections.sources
327 fpSets = detections.fpSets
328 if hasattr(fpSets, "background") and fpSets.background:
329 for bg in fpSets.background:
330 backgrounds.append(bg)
331 return Struct(outputSources=sources, outputBackgrounds=backgrounds, outputExposure=exposure)
333 def write(self, results, patchRef):
334 """!
335 @brief Write out results from runDetection.
337 @param[in] exposure: Exposure to write out
338 @param[in] results: Struct returned from runDetection
339 @param[in] patchRef: data reference for patch
340 """
341 coaddName = self.config.coaddName + "Coadd"
342 patchRef.put(results.outputBackgrounds, coaddName + "_calexp_background")
343 patchRef.put(results.outputSources, coaddName + "_det")
344 if self.config.hasFakes:
345 patchRef.put(results.outputExposure, "fakes_" + coaddName + "_calexp")
346 else:
347 patchRef.put(results.outputExposure, coaddName + "_calexp")
349##############################################################################################################
352class DeblendCoaddSourcesConfig(Config):
353 """DeblendCoaddSourcesConfig
355 Configuration parameters for the `DeblendCoaddSourcesTask`.
356 """
357 singleBandDeblend = ConfigurableField(target=SourceDeblendTask,
358 doc="Deblend sources separately in each band")
359 multiBandDeblend = ConfigurableField(target=ScarletDeblendTask,
360 doc="Deblend sources simultaneously across bands")
361 simultaneous = Field(dtype=bool,
362 default=True,
363 doc="Simultaneously deblend all bands? "
364 "True uses `multibandDeblend` while False uses `singleBandDeblend`")
365 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
366 hasFakes = Field(dtype=bool,
367 default=False,
368 doc="Should be set to True if fake sources have been inserted into the input data.")
370 def setDefaults(self):
371 Config.setDefaults(self)
372 self.singleBandDeblend.propagateAllPeaks = True
375class DeblendCoaddSourcesRunner(MergeSourcesRunner):
376 """Task runner for the `MergeSourcesTask`
378 Required because the run method requires a list of
379 dataRefs rather than a single dataRef.
380 """
381 @staticmethod
382 def getTargetList(parsedCmd, **kwargs):
383 """Provide a list of patch references for each patch, tract, filter combo.
385 Parameters
386 ----------
387 parsedCmd:
388 The parsed command
389 kwargs:
390 Keyword arguments passed to the task
392 Returns
393 -------
394 targetList: list
395 List of tuples, where each tuple is a (dataRef, kwargs) pair.
396 """
397 refDict = MergeSourcesRunner.buildRefDict(parsedCmd)
398 kwargs["psfCache"] = parsedCmd.psfCache
399 return [(list(p.values()), kwargs) for t in refDict.values() for p in t.values()]
402class DeblendCoaddSourcesTask(CmdLineTask):
403 """Deblend the sources in a merged catalog
405 Deblend sources from master catalog in each coadd.
406 This can either be done separately in each band using the HSC-SDSS deblender
407 (`DeblendCoaddSourcesTask.config.simultaneous==False`)
408 or use SCARLET to simultaneously fit the blend in all bands
409 (`DeblendCoaddSourcesTask.config.simultaneous==True`).
410 The task will set its own `self.schema` atribute to the `Schema` of the
411 output deblended catalog.
412 This will include all fields from the input `Schema`, as well as additional fields
413 from the deblender.
415 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description
416 ---------------------------------------------------------
417 `
419 Parameters
420 ----------
421 butler: `Butler`
422 Butler used to read the input schemas from disk or
423 construct the reference catalog loader, if `schema` or `peakSchema` or
424 schema: `Schema`
425 The schema of the merged detection catalog as an input to this task.
426 peakSchema: `Schema`
427 The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog
428 """
429 ConfigClass = DeblendCoaddSourcesConfig
430 RunnerClass = DeblendCoaddSourcesRunner
431 _DefaultName = "deblendCoaddSources"
432 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False)
434 @classmethod
435 def _makeArgumentParser(cls):
436 parser = ArgumentParser(name=cls._DefaultName)
437 parser.add_id_argument("--id", "deepCoadd_calexp",
438 help="data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i",
439 ContainerClass=ExistingCoaddDataIdContainer)
440 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
441 return parser
443 def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs):
444 CmdLineTask.__init__(self, **kwargs)
445 if schema is None:
446 assert butler is not None, "Neither butler nor schema is defined"
447 schema = butler.get(self.config.coaddName + "Coadd_mergeDet_schema", immediate=True).schema
448 self.schemaMapper = afwTable.SchemaMapper(schema)
449 self.schemaMapper.addMinimalSchema(schema)
450 self.schema = self.schemaMapper.getOutputSchema()
451 if peakSchema is None:
452 assert butler is not None, "Neither butler nor peakSchema is defined"
453 peakSchema = butler.get(self.config.coaddName + "Coadd_peak_schema", immediate=True).schema
455 if self.config.simultaneous:
456 self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema)
457 else:
458 self.makeSubtask("singleBandDeblend", schema=self.schema, peakSchema=peakSchema)
460 def getSchemaCatalogs(self):
461 """Return a dict of empty catalogs for each catalog dataset produced by this task.
463 Returns
464 -------
465 result: dict
466 Dictionary of empty catalogs, with catalog names as keys.
467 """
468 catalog = afwTable.SourceCatalog(self.schema)
469 return {self.config.coaddName + "Coadd_deblendedFlux": catalog,
470 self.config.coaddName + "Coadd_deblendedModel": catalog}
472 def runDataRef(self, patchRefList, psfCache=100):
473 """Deblend the patch
475 Deblend each source simultaneously or separately
476 (depending on `DeblendCoaddSourcesTask.config.simultaneous`).
477 Set `is-primary` and related flags.
478 Propagate flags from individual visits.
479 Write the deblended sources out.
481 Parameters
482 ----------
483 patchRefList: list
484 List of data references for each filter
485 """
487 if self.config.hasFakes:
488 coaddType = "fakes_" + self.config.coaddName
489 else:
490 coaddType = self.config.coaddName
492 if self.config.simultaneous:
493 # Use SCARLET to simultaneously deblend across filters
494 filters = []
495 exposures = []
496 for patchRef in patchRefList:
497 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
498 filter = patchRef.get(coaddType + "Coadd_filterLabel", immediate=True)
499 filters.append(filter.bandLabel)
500 exposures.append(exposure)
501 # Sort inputs by band to match Gen3 order of inputs
502 exposures = [exposure for _, exposure in sorted(zip(filters, exposures))]
503 patchRefList = [patchRef for _, patchRef in sorted(zip(filters, patchRefList))]
504 filters.sort()
505 # The input sources are the same for all bands, since it is a merged catalog
506 sources = self.readSources(patchRef)
507 exposure = afwImage.MultibandExposure.fromExposures(filters, exposures)
508 templateCatalogs, fluxCatalogs = self.multiBandDeblend.run(exposure, sources)
509 for n in range(len(patchRefList)):
510 self.write(patchRefList[n], templateCatalogs[filters[n]], "Model")
511 if filters[n] in fluxCatalogs:
512 self.write(patchRefList[n], fluxCatalogs[filters[n]], "Flux")
513 else:
514 # Use the singeband deblender to deblend each band separately
515 for patchRef in patchRefList:
516 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
517 exposure.getPsf().setCacheCapacity(psfCache)
518 sources = self.readSources(patchRef)
519 self.singleBandDeblend.run(exposure, sources)
520 self.write(patchRef, sources)
522 def readSources(self, dataRef):
523 """Read merged catalog
525 Read the catalog of merged detections and create a catalog
526 in a single band.
528 Parameters
529 ----------
530 dataRef: data reference
531 Data reference for catalog of merged detections
533 Returns
534 -------
535 sources: `SourceCatalog`
536 List of sources in merged catalog
538 We also need to add columns to hold the measurements we're about to make
539 so we can measure in-place.
540 """
541 merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=True)
542 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
543 idFactory = self.makeIdFactory(dataRef)
544 # There may be gaps in the mergeDet catalog, which will cause the
545 # source ids to be inconsistent. So we update the id factory
546 # with the largest id already in the catalog.
547 maxId = np.max(merged["id"])
548 idFactory.notify(maxId)
549 table = afwTable.SourceTable.make(self.schema, idFactory)
550 sources = afwTable.SourceCatalog(table)
551 sources.extend(merged, self.schemaMapper)
552 return sources
554 def write(self, dataRef, sources, catalogType):
555 """Write the source catalog(s)
557 Parameters
558 ----------
559 dataRef: Data Reference
560 Reference to the output catalog.
561 sources: `SourceCatalog`
562 Flux conserved sources to write to file.
563 If using the single band deblender, this is the catalog
564 generated.
565 template_sources: `SourceCatalog`
566 Source catalog using the multiband template models
567 as footprints.
568 """
569 dataRef.put(sources, self.config.coaddName + f"Coadd_deblended{catalogType}")
570 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)
572 def writeMetadata(self, dataRefList):
573 """Write the metadata produced from processing the data.
574 Parameters
575 ----------
576 dataRefList
577 List of Butler data references used to write the metadata.
578 The metadata is written to dataset type `CmdLineTask._getMetadataName`.
579 """
580 for dataRef in dataRefList:
581 try:
582 metadataName = self._getMetadataName()
583 if metadataName is not None:
584 dataRef.put(self.getFullMetadata(), metadataName)
585 except Exception as e:
586 self.log.warning("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
589class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections,
590 dimensions=("tract", "patch", "band", "skymap"),
591 defaultTemplates={"inputCoaddName": "deep",
592 "outputCoaddName": "deep",
593 "deblendedCatalog": "deblendedFlux"}):
594 inputSchema = cT.InitInput(
595 doc="Input schema for measure merged task produced by a deblender or detection task",
596 name="{inputCoaddName}Coadd_deblendedFlux_schema",
597 storageClass="SourceCatalog"
598 )
599 outputSchema = cT.InitOutput(
600 doc="Output schema after all new fields are added by task",
601 name="{inputCoaddName}Coadd_meas_schema",
602 storageClass="SourceCatalog"
603 )
604 refCat = cT.PrerequisiteInput(
605 doc="Reference catalog used to match measured sources against known sources",
606 name="ref_cat",
607 storageClass="SimpleCatalog",
608 dimensions=("skypix",),
609 deferLoad=True,
610 multiple=True
611 )
612 exposure = cT.Input(
613 doc="Input coadd image",
614 name="{inputCoaddName}Coadd_calexp",
615 storageClass="ExposureF",
616 dimensions=("tract", "patch", "band", "skymap")
617 )
618 skyMap = cT.Input(
619 doc="SkyMap to use in processing",
620 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
621 storageClass="SkyMap",
622 dimensions=("skymap",),
623 )
624 visitCatalogs = cT.Input(
625 doc="Source catalogs for visits which overlap input tract, patch, band. Will be "
626 "further filtered in the task for the purpose of propagating flags from image calibration "
627 "and characterization to coadd objects. Only used in legacy PropagateVisitFlagsTask.",
628 name="src",
629 dimensions=("instrument", "visit", "detector"),
630 storageClass="SourceCatalog",
631 multiple=True
632 )
633 sourceTableHandles = cT.Input(
634 doc=("Source tables that are derived from the ``CalibrateTask`` sources. "
635 "These tables contain astrometry and photometry flags, and optionally "
636 "PSF flags."),
637 name="sourceTable_visit",
638 storageClass="DataFrame",
639 dimensions=("instrument", "visit"),
640 multiple=True,
641 deferLoad=True,
642 )
643 finalizedSourceTableHandles = cT.Input(
644 doc=("Finalized source tables from ``FinalizeCalibrationTask``. These "
645 "tables contain PSF flags from the finalized PSF estimation."),
646 name="finalized_src_table",
647 storageClass="DataFrame",
648 dimensions=("instrument", "visit"),
649 multiple=True,
650 deferLoad=True,
651 )
652 inputCatalog = cT.Input(
653 doc=("Name of the input catalog to use."
654 "If the single band deblender was used this should be 'deblendedFlux."
655 "If the multi-band deblender was used this should be 'deblendedModel, "
656 "or deblendedFlux if the multiband deblender was configured to output "
657 "deblended flux catalogs. If no deblending was performed this should "
658 "be 'mergeDet'"),
659 name="{inputCoaddName}Coadd_{deblendedCatalog}",
660 storageClass="SourceCatalog",
661 dimensions=("tract", "patch", "band", "skymap"),
662 )
663 outputSources = cT.Output(
664 doc="Source catalog containing all the measurement information generated in this task",
665 name="{outputCoaddName}Coadd_meas",
666 dimensions=("tract", "patch", "band", "skymap"),
667 storageClass="SourceCatalog",
668 )
669 matchResult = cT.Output(
670 doc="Match catalog produced by configured matcher, optional on doMatchSources",
671 name="{outputCoaddName}Coadd_measMatch",
672 dimensions=("tract", "patch", "band", "skymap"),
673 storageClass="Catalog",
674 )
675 denormMatches = cT.Output(
676 doc="Denormalized Match catalog produced by configured matcher, optional on "
677 "doWriteMatchesDenormalized",
678 name="{outputCoaddName}Coadd_measMatchFull",
679 dimensions=("tract", "patch", "band", "skymap"),
680 storageClass="Catalog",
681 )
683 def __init__(self, *, config=None):
684 super().__init__(config=config)
685 if config.doPropagateFlags is False:
686 self.inputs -= set(("visitCatalogs",))
687 self.inputs -= set(("sourceTableHandles",))
688 self.inputs -= set(("finalizedSourceTableHandles",))
689 elif config.propagateFlags.target == PropagateSourceFlagsTask:
690 # New PropagateSourceFlagsTask does not use visitCatalogs.
691 self.inputs -= set(("visitCatalogs",))
692 # Check for types of flags required.
693 if not config.propagateFlags.source_flags:
694 self.inputs -= set(("sourceTableHandles",))
695 if not config.propagateFlags.finalized_source_flags:
696 self.inputs -= set(("finalizedSourceTableHandles",))
697 else:
698 # Deprecated PropagateVisitFlagsTask uses visitCatalogs.
699 self.inputs -= set(("sourceTableHandles",))
700 self.inputs -= set(("finalizedSourceTableHandles",))
702 if config.doMatchSources is False:
703 self.outputs -= set(("matchResult",))
705 if config.doWriteMatchesDenormalized is False:
706 self.outputs -= set(("denormMatches",))
709class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
710 pipelineConnections=MeasureMergedCoaddSourcesConnections):
711 """!
712 @anchor MeasureMergedCoaddSourcesConfig_
714 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask
715 """
716 inputCatalog = Field(dtype=str, default="deblendedFlux",
717 doc=("Name of the input catalog to use."
718 "If the single band deblender was used this should be 'deblendedFlux."
719 "If the multi-band deblender was used this should be 'deblendedModel."
720 "If no deblending was performed this should be 'mergeDet'"))
721 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement")
722 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch")
723 doPropagateFlags = Field(
724 dtype=bool, default=True,
725 doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
726 )
727 propagateFlags = ConfigurableField(target=PropagateSourceFlagsTask, doc="Propagate source flags to coadd")
728 doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?")
729 match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog")
730 doWriteMatchesDenormalized = Field(
731 dtype=bool,
732 default=False,
733 doc=("Write reference matches in denormalized format? "
734 "This format uses more disk space, but is more convenient to read."),
735 )
736 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
737 psfCache = Field(dtype=int, default=100, doc="Size of psfCache")
738 checkUnitsParseStrict = Field(
739 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
740 dtype=str,
741 default="raise",
742 )
743 doApCorr = Field(
744 dtype=bool,
745 default=True,
746 doc="Apply aperture corrections"
747 )
748 applyApCorr = ConfigurableField(
749 target=ApplyApCorrTask,
750 doc="Subtask to apply aperture corrections"
751 )
752 doRunCatalogCalculation = Field(
753 dtype=bool,
754 default=True,
755 doc='Run catalogCalculation task'
756 )
757 catalogCalculation = ConfigurableField(
758 target=CatalogCalculationTask,
759 doc="Subtask to run catalogCalculation plugins on catalog"
760 )
762 hasFakes = Field(
763 dtype=bool,
764 default=False,
765 doc="Should be set to True if fake sources have been inserted into the input data."
766 )
768 @property
769 def refObjLoader(self):
770 return self.match.refObjLoader
772 def setDefaults(self):
773 super().setDefaults()
774 self.measurement.plugins.names |= ['base_InputCount',
775 'base_Variance',
776 'base_LocalPhotoCalib',
777 'base_LocalWcs']
778 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE',
779 'INEXACT_PSF']
780 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE',
781 'INEXACT_PSF']
783 def validate(self):
784 super().validate()
785 refCatGen2 = getattr(self.refObjLoader, "ref_dataset_name", None)
786 if refCatGen2 is not None and refCatGen2 != self.connections.refCat:
787 raise ValueError(
788 f"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
789 f"are different. These options must be kept in sync until Gen2 is retired."
790 )
793## @addtogroup LSST_task_documentation
794## @{
795## @page page_MeasureMergedCoaddSourcesTask MeasureMergedCoaddSourcesTask
796## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask"
797## @copybrief MeasureMergedCoaddSourcesTask
798## @}
801class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
802 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
803 @staticmethod
804 def getTargetList(parsedCmd, **kwargs):
805 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
808class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
809 r"""!
810 @anchor MeasureMergedCoaddSourcesTask_
812 @brief Deblend sources from master catalog in each coadd seperately and measure.
814 @section pipe_tasks_multiBand_Contents Contents
816 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
817 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
818 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
819 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
820 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
821 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
823 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
825 Command-line task that uses peaks and footprints from a master catalog to perform deblending and
826 measurement in each coadd.
828 Given a master input catalog of sources (peaks and footprints) or deblender outputs
829 (including a HeavyFootprint in each band), measure each source on the
830 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a
831 consistent set of child sources.
833 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source
834 properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit
835 flags are propagated to the coadd sources.
837 Optionally, we can match the coadd sources to an external reference catalog.
839 @par Inputs:
840 deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog
841 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
842 @par Outputs:
843 deepCoadd_meas{tract,patch,filter}: SourceCatalog
844 @par Data Unit:
845 tract, patch, filter
847 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
849 <DL>
850 <DT> @ref SingleFrameMeasurementTask_ "measurement"
851 <DD> Measure source properties of deblended sources.</DD>
852 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags"
853 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are
854 not at the edge of the field and that have either not been deblended or are the children of deblended
855 sources</DD>
856 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags"
857 <DD> Propagate flags set in individual visits to the coadd.</DD>
858 <DT> @ref DirectMatchTask_ "match"
859 <DD> Match input sources to a reference catalog (optional).
860 </DD>
861 </DL>
862 These subtasks may be retargeted as required.
864 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
866 @copydoc \_\_init\_\_
868 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
870 @copydoc run
872 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
874 See @ref MeasureMergedCoaddSourcesConfig_
876 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
878 The command line task interface supports a
879 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
880 files.
882 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
883 the various sub-tasks. See the documetation for individual sub-tasks for more information.
885 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
886 MeasureMergedCoaddSourcesTask
888 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
889 The next stage in the multi-band processing procedure will merge these measurements into a suitable
890 catalog for driving forced photometry.
892 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
893 to be processed.
894 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the
895 `--help` command line argument:
896 @code
897 measureCoaddSources.py --help
898 @endcode
900 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
901 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
902 step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band
903 coadd as follows:
904 @code
905 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
906 @endcode
907 This will process the HSC-I band data. The results are written in
908 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
910 It is also necessary to run
911 @code
912 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
913 @endcode
914 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
915 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask".
916 """
917 _DefaultName = "measureCoaddSources"
918 ConfigClass = MeasureMergedCoaddSourcesConfig
919 RunnerClass = MeasureMergedCoaddSourcesRunner
920 getSchemaCatalogs = _makeGetSchemaCatalogs("meas")
921 # The IDs we already have are of this type
922 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False)
924 @classmethod
925 def _makeArgumentParser(cls):
926 parser = ArgumentParser(name=cls._DefaultName)
927 parser.add_id_argument("--id", "deepCoadd_calexp",
928 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
929 ContainerClass=ExistingCoaddDataIdContainer)
930 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
931 return parser
933 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
934 **kwargs):
935 """!
936 @brief Initialize the task.
938 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
939 @param[in] schema: the schema of the merged detection catalog used as input to this one
940 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog
941 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
942 catalog. May be None if the loader can be constructed from the butler argument or all steps
943 requiring a reference catalog are disabled.
944 @param[in] butler: a butler used to read the input schemas from disk or construct the reference
945 catalog loader, if schema or peakSchema or refObjLoader is None
947 The task will set its own self.schema attribute to the schema of the output measurement catalog.
948 This will include all fields from the input schema, as well as additional fields for all the
949 measurements.
950 """
951 super().__init__(**kwargs)
952 self.deblended = self.config.inputCatalog.startswith("deblended")
953 self.inputCatalog = "Coadd_" + self.config.inputCatalog
954 if initInputs is not None:
955 schema = initInputs['inputSchema'].schema
956 if schema is None:
957 assert butler is not None, "Neither butler nor schema is defined"
958 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema
959 self.schemaMapper = afwTable.SchemaMapper(schema)
960 self.schemaMapper.addMinimalSchema(schema)
961 self.schema = self.schemaMapper.getOutputSchema()
962 self.algMetadata = PropertyList()
963 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata)
964 self.makeSubtask("setPrimaryFlags", schema=self.schema)
965 if self.config.doMatchSources:
966 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
967 if self.config.doPropagateFlags:
968 self.makeSubtask("propagateFlags", schema=self.schema)
969 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
970 if self.config.doApCorr:
971 self.makeSubtask("applyApCorr", schema=self.schema)
972 if self.config.doRunCatalogCalculation:
973 self.makeSubtask("catalogCalculation", schema=self.schema)
975 self.outputSchema = afwTable.SourceCatalog(self.schema)
977 def runQuantum(self, butlerQC, inputRefs, outputRefs):
978 inputs = butlerQC.get(inputRefs)
980 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat],
981 inputs.pop('refCat'), config=self.config.refObjLoader,
982 log=self.log)
983 self.match.setRefObjLoader(refObjLoader)
985 # Set psfcache
986 # move this to run after gen2 deprecation
987 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
989 # Get unique integer ID for IdFactory and RNG seeds
990 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch")
991 inputs['exposureId'] = exposureIdInfo.expId
992 idFactory = exposureIdInfo.makeSourceIdFactory()
993 # Transform inputCatalog
994 table = afwTable.SourceTable.make(self.schema, idFactory)
995 sources = afwTable.SourceCatalog(table)
996 sources.extend(inputs.pop('inputCatalog'), self.schemaMapper)
997 table = sources.getTable()
998 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
999 inputs['sources'] = sources
1001 skyMap = inputs.pop('skyMap')
1002 tractNumber = inputRefs.inputCatalog.dataId['tract']
1003 tractInfo = skyMap[tractNumber]
1004 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId['patch'])
1005 skyInfo = Struct(
1006 skyMap=skyMap,
1007 tractInfo=tractInfo,
1008 patchInfo=patchInfo,
1009 wcs=tractInfo.getWcs(),
1010 bbox=patchInfo.getOuterBBox()
1011 )
1012 inputs['skyInfo'] = skyInfo
1014 if self.config.doPropagateFlags:
1015 if self.config.propagateFlags.target == PropagateSourceFlagsTask:
1016 # New version
1017 ccdInputs = inputs["exposure"].getInfo().getCoaddInputs().ccds
1018 inputs["ccdInputs"] = ccdInputs
1020 if "sourceTableHandles" in inputs:
1021 sourceTableHandles = inputs.pop("sourceTableHandles")
1022 sourceTableHandleDict = {handle.dataId["visit"]: handle
1023 for handle in sourceTableHandles}
1024 inputs["sourceTableHandleDict"] = sourceTableHandleDict
1025 if "finalizedSourceTableHandles" in inputs:
1026 finalizedSourceTableHandles = inputs.pop("finalizedSourceTableHandles")
1027 finalizedSourceTableHandleDict = {handle.dataId["visit"]: handle
1028 for handle in finalizedSourceTableHandles}
1029 inputs["finalizedSourceTableHandleDict"] = finalizedSourceTableHandleDict
1030 else:
1031 # Deprecated legacy version
1032 # Filter out any visit catalog that is not coadd inputs
1033 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds
1034 visitKey = ccdInputs.schema.find("visit").key
1035 ccdKey = ccdInputs.schema.find("ccd").key
1036 inputVisitIds = set()
1037 ccdRecordsWcs = {}
1038 for ccdRecord in ccdInputs:
1039 visit = ccdRecord.get(visitKey)
1040 ccd = ccdRecord.get(ccdKey)
1041 inputVisitIds.add((visit, ccd))
1042 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
1044 inputCatalogsToKeep = []
1045 inputCatalogWcsUpdate = []
1046 for i, dataRef in enumerate(inputRefs.visitCatalogs):
1047 key = (dataRef.dataId['visit'], dataRef.dataId['detector'])
1048 if key in inputVisitIds:
1049 inputCatalogsToKeep.append(inputs['visitCatalogs'][i])
1050 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
1051 inputs['visitCatalogs'] = inputCatalogsToKeep
1052 inputs['wcsUpdates'] = inputCatalogWcsUpdate
1053 inputs['ccdInputs'] = ccdInputs
1055 outputs = self.run(**inputs)
1056 butlerQC.put(outputs, outputRefs)
1058 def runDataRef(self, patchRef, psfCache=100):
1059 """!
1060 @brief Deblend and measure.
1062 @param[in] patchRef: Patch reference.
1064 Set 'is-primary' and related flags. Propagate flags
1065 from individual visits. Optionally match the sources to a reference catalog and write the matches.
1066 Finally, write the deblended sources and measurements out.
1067 """
1068 if self.config.hasFakes:
1069 coaddType = "fakes_" + self.config.coaddName
1070 else:
1071 coaddType = self.config.coaddName
1072 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
1073 exposure.getPsf().setCacheCapacity(psfCache)
1074 sources = self.readSources(patchRef)
1075 table = sources.getTable()
1076 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1077 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1079 if self.config.doPropagateFlags:
1080 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1081 else:
1082 ccdInputs = None
1084 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=False,
1085 log=self.log)
1086 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId,
1087 ccdInputs=ccdInputs, butler=patchRef.getButler())
1089 if self.config.doMatchSources:
1090 self.writeMatches(patchRef, results)
1091 self.write(patchRef, results.outputSources)
1093 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1094 butler=None, sourceTableHandleDict=None, finalizedSourceTableHandleDict=None):
1095 """Run measurement algorithms on the input exposure, and optionally populate the
1096 resulting catalog with extra information.
1098 Parameters
1099 ----------
1100 exposure : `lsst.afw.exposure.Exposure`
1101 The input exposure on which measurements are to be performed
1102 sources : `lsst.afw.table.SourceCatalog`
1103 A catalog built from the results of merged detections, or
1104 deblender outputs.
1105 skyInfo : `lsst.pipe.base.Struct`
1106 A struct containing information about the position of the input exposure within
1107 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box
1108 exposureId : `int` or `bytes`
1109 packed unique number or bytes unique to the input exposure
1110 ccdInputs : `lsst.afw.table.ExposureCatalog`
1111 Catalog containing information on the individual visits which went into making
1112 the coadd.
1113 sourceTableHandleDict : `dict` [`int`: `lsst.daf.butler.DeferredDatasetHandle`]
1114 Dict for sourceTable_visit handles (key is visit) for propagating flags.
1115 These tables are derived from the ``CalibrateTask`` sources, and contain
1116 astrometry and photometry flags, and optionally PSF flags.
1117 finalizedSourceTableHandleDict : `dict` [`int`: `lsst.daf.butler.DeferredDatasetHandle`], optional
1118 Dict for finalized_src_table handles (key is visit) for propagating flags.
1119 These tables are derived from ``FinalizeCalibrationTask`` and contain
1120 PSF flags from the finalized PSF estimation.
1121 visitCatalogs : list of `lsst.afw.table.SourceCatalogs`
1122 A list of source catalogs corresponding to measurements made on the individual
1123 visits which went into the input exposure. If None and butler is `None` then
1124 the task cannot propagate visit flags to the output catalog.
1125 Deprecated, to be removed with PropagateVisitFlagsTask.
1126 wcsUpdates : list of `lsst.afw.geom.SkyWcs`
1127 If visitCatalogs is not `None` this should be a list of wcs objects which correspond
1128 to the input visits. Used to put all coordinates to common system. If `None` and
1129 butler is `None` then the task cannot propagate visit flags to the output catalog.
1130 Deprecated, to be removed with PropagateVisitFlagsTask.
1131 butler : `lsst.daf.persistence.Butler`
1132 A gen2 butler used to load visit catalogs.
1133 Deprecated, to be removed with Gen2.
1135 Returns
1136 -------
1137 results : `lsst.pipe.base.Struct`
1138 Results of running measurement task. Will contain the catalog in the
1139 sources attribute. Optionally will have results of matching to a
1140 reference catalog in the matchResults attribute, and denormalized
1141 matches in the denormMatches attribute.
1142 """
1143 self.measurement.run(sources, exposure, exposureId=exposureId)
1145 if self.config.doApCorr:
1146 self.applyApCorr.run(
1147 catalog=sources,
1148 apCorrMap=exposure.getInfo().getApCorrMap()
1149 )
1151 # TODO DM-11568: this contiguous check-and-copy could go away if we
1152 # reserve enough space during SourceDetection and/or SourceDeblend.
1153 # NOTE: sourceSelectors require contiguous catalogs, so ensure
1154 # contiguity now, so views are preserved from here on.
1155 if not sources.isContiguous():
1156 sources = sources.copy(deep=True)
1158 if self.config.doRunCatalogCalculation:
1159 self.catalogCalculation.run(sources)
1161 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1162 patchInfo=skyInfo.patchInfo)
1163 if self.config.doPropagateFlags:
1164 if self.config.propagateFlags.target == PropagateSourceFlagsTask:
1165 # New version
1166 self.propagateFlags.run(
1167 sources,
1168 ccdInputs,
1169 sourceTableHandleDict,
1170 finalizedSourceTableHandleDict
1171 )
1172 else:
1173 # Legacy deprecated version
1174 self.propagateFlags.run(
1175 butler,
1176 sources,
1177 ccdInputs,
1178 exposure.getWcs(),
1179 visitCatalogs,
1180 wcsUpdates
1181 )
1183 results = Struct()
1185 if self.config.doMatchSources:
1186 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel)
1187 matches = afwTable.packMatches(matchResult.matches)
1188 matches.table.setMetadata(matchResult.matchMeta)
1189 results.matchResult = matches
1190 if self.config.doWriteMatchesDenormalized:
1191 if matchResult.matches:
1192 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1193 else:
1194 self.log.warning("No matches, so generating dummy denormalized matches file")
1195 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1196 denormMatches.setMetadata(PropertyList())
1197 denormMatches.getMetadata().add("COMMENT",
1198 "This catalog is empty because no matches were found.")
1199 results.denormMatches = denormMatches
1200 results.denormMatches = denormMatches
1202 results.outputSources = sources
1203 return results
1205 def readSources(self, dataRef):
1206 """!
1207 @brief Read input sources.
1209 @param[in] dataRef: Data reference for catalog of merged detections
1210 @return List of sources in merged catalog
1212 We also need to add columns to hold the measurements we're about to make
1213 so we can measure in-place.
1214 """
1215 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1216 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
1217 idFactory = self.makeIdFactory(dataRef)
1218 for s in merged:
1219 idFactory.notify(s.getId())
1220 table = afwTable.SourceTable.make(self.schema, idFactory)
1221 sources = afwTable.SourceCatalog(table)
1222 sources.extend(merged, self.schemaMapper)
1223 return sources
1225 def writeMatches(self, dataRef, results):
1226 """!
1227 @brief Write matches of the sources to the astrometric reference catalog.
1229 @param[in] dataRef: data reference
1230 @param[in] results: results struct from run method
1231 """
1232 if hasattr(results, "matchResult"):
1233 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1234 if hasattr(results, "denormMatches"):
1235 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1237 def write(self, dataRef, sources):
1238 """!
1239 @brief Write the source catalog.
1241 @param[in] dataRef: data reference
1242 @param[in] sources: source catalog
1243 """
1244 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1245 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)