Coverage for python/lsst/pipe/tasks/multiBand.py: 29%
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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.propagateVisitFlags import PropagateVisitFlagsTask
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 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 @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink 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 inputSchema = cT.InitInput(
594 doc="Input schema for measure merged task produced by a deblender or detection task",
595 name="{inputCoaddName}Coadd_deblendedFlux_schema",
596 storageClass="SourceCatalog"
597 )
598 outputSchema = cT.InitOutput(
599 doc="Output schema after all new fields are added by task",
600 name="{inputCoaddName}Coadd_meas_schema",
601 storageClass="SourceCatalog"
602 )
603 refCat = cT.PrerequisiteInput(
604 doc="Reference catalog used to match measured sources against known sources",
605 name="ref_cat",
606 storageClass="SimpleCatalog",
607 dimensions=("skypix",),
608 deferLoad=True,
609 multiple=True
610 )
611 exposure = cT.Input(
612 doc="Input coadd image",
613 name="{inputCoaddName}Coadd_calexp",
614 storageClass="ExposureF",
615 dimensions=("tract", "patch", "band", "skymap")
616 )
617 skyMap = cT.Input(
618 doc="SkyMap to use in processing",
619 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
620 storageClass="SkyMap",
621 dimensions=("skymap",),
622 )
623 visitCatalogs = cT.Input(
624 doc="Source catalogs for visits which overlap input tract, patch, band. Will be "
625 "further filtered in the task for the purpose of propagating flags from image calibration "
626 "and characterization to codd objects",
627 name="src",
628 dimensions=("instrument", "visit", "detector"),
629 storageClass="SourceCatalog",
630 multiple=True
631 )
632 inputCatalog = cT.Input(
633 doc=("Name of the input catalog to use."
634 "If the single band deblender was used this should be 'deblendedFlux."
635 "If the multi-band deblender was used this should be 'deblendedModel, "
636 "or deblendedFlux if the multiband deblender was configured to output "
637 "deblended flux catalogs. If no deblending was performed this should "
638 "be 'mergeDet'"),
639 name="{inputCoaddName}Coadd_deblendedFlux",
640 storageClass="SourceCatalog",
641 dimensions=("tract", "patch", "band", "skymap"),
642 )
643 outputSources = cT.Output(
644 doc="Source catalog containing all the measurement information generated in this task",
645 name="{outputCoaddName}Coadd_meas",
646 dimensions=("tract", "patch", "band", "skymap"),
647 storageClass="SourceCatalog",
648 )
649 matchResult = cT.Output(
650 doc="Match catalog produced by configured matcher, optional on doMatchSources",
651 name="{outputCoaddName}Coadd_measMatch",
652 dimensions=("tract", "patch", "band", "skymap"),
653 storageClass="Catalog",
654 )
655 denormMatches = cT.Output(
656 doc="Denormalized Match catalog produced by configured matcher, optional on "
657 "doWriteMatchesDenormalized",
658 name="{outputCoaddName}Coadd_measMatchFull",
659 dimensions=("tract", "patch", "band", "skymap"),
660 storageClass="Catalog",
661 )
663 def __init__(self, *, config=None):
664 super().__init__(config=config)
665 if config.doPropagateFlags is False:
666 self.inputs -= set(("visitCatalogs",))
668 if config.doMatchSources is False:
669 self.outputs -= set(("matchResult",))
671 if config.doWriteMatchesDenormalized is False:
672 self.outputs -= set(("denormMatches",))
675class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
676 pipelineConnections=MeasureMergedCoaddSourcesConnections):
677 """!
678 @anchor MeasureMergedCoaddSourcesConfig_
680 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask
681 """
682 inputCatalog = Field(dtype=str, default="deblendedFlux",
683 doc=("Name of the input catalog to use."
684 "If the single band deblender was used this should be 'deblendedFlux."
685 "If the multi-band deblender was used this should be 'deblendedModel."
686 "If no deblending was performed this should be 'mergeDet'"))
687 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement")
688 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch")
689 doPropagateFlags = Field(
690 dtype=bool, default=True,
691 doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
692 )
693 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc="Propagate visit flags to coadd")
694 doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?")
695 match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog")
696 doWriteMatchesDenormalized = Field(
697 dtype=bool,
698 default=False,
699 doc=("Write reference matches in denormalized format? "
700 "This format uses more disk space, but is more convenient to read."),
701 )
702 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
703 psfCache = Field(dtype=int, default=100, doc="Size of psfCache")
704 checkUnitsParseStrict = Field(
705 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
706 dtype=str,
707 default="raise",
708 )
709 doApCorr = Field(
710 dtype=bool,
711 default=True,
712 doc="Apply aperture corrections"
713 )
714 applyApCorr = ConfigurableField(
715 target=ApplyApCorrTask,
716 doc="Subtask to apply aperture corrections"
717 )
718 doRunCatalogCalculation = Field(
719 dtype=bool,
720 default=True,
721 doc='Run catalogCalculation task'
722 )
723 catalogCalculation = ConfigurableField(
724 target=CatalogCalculationTask,
725 doc="Subtask to run catalogCalculation plugins on catalog"
726 )
728 hasFakes = Field(
729 dtype=bool,
730 default=False,
731 doc="Should be set to True if fake sources have been inserted into the input data."
732 )
734 @property
735 def refObjLoader(self):
736 return self.match.refObjLoader
738 def setDefaults(self):
739 super().setDefaults()
740 self.measurement.plugins.names |= ['base_InputCount',
741 'base_Variance',
742 'base_LocalPhotoCalib',
743 'base_LocalWcs']
744 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE',
745 'INEXACT_PSF']
746 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE',
747 'INEXACT_PSF']
749 def validate(self):
750 super().validate()
751 refCatGen2 = getattr(self.refObjLoader, "ref_dataset_name", None)
752 if refCatGen2 is not None and refCatGen2 != self.connections.refCat:
753 raise ValueError(
754 f"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
755 f"are different. These options must be kept in sync until Gen2 is retired."
756 )
759## @addtogroup LSST_task_documentation
760## @{
761## @page MeasureMergedCoaddSourcesTask
762## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask"
763## @copybrief MeasureMergedCoaddSourcesTask
764## @}
767class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
768 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
769 @staticmethod
770 def getTargetList(parsedCmd, **kwargs):
771 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
774class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
775 r"""!
776 @anchor MeasureMergedCoaddSourcesTask_
778 @brief Deblend sources from master catalog in each coadd seperately and measure.
780 @section pipe_tasks_multiBand_Contents Contents
782 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
783 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
784 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
785 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
786 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
787 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
789 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
791 Command-line task that uses peaks and footprints from a master catalog to perform deblending and
792 measurement in each coadd.
794 Given a master input catalog of sources (peaks and footprints) or deblender outputs
795 (including a HeavyFootprint in each band), measure each source on the
796 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a
797 consistent set of child sources.
799 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source
800 properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit
801 flags are propagated to the coadd sources.
803 Optionally, we can match the coadd sources to an external reference catalog.
805 @par Inputs:
806 deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog
807 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
808 @par Outputs:
809 deepCoadd_meas{tract,patch,filter}: SourceCatalog
810 @par Data Unit:
811 tract, patch, filter
813 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
815 <DL>
816 <DT> @ref SingleFrameMeasurementTask_ "measurement"
817 <DD> Measure source properties of deblended sources.</DD>
818 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags"
819 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are
820 not at the edge of the field and that have either not been deblended or are the children of deblended
821 sources</DD>
822 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags"
823 <DD> Propagate flags set in individual visits to the coadd.</DD>
824 <DT> @ref DirectMatchTask_ "match"
825 <DD> Match input sources to a reference catalog (optional).
826 </DD>
827 </DL>
828 These subtasks may be retargeted as required.
830 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
832 @copydoc \_\_init\_\_
834 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
836 @copydoc run
838 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
840 See @ref MeasureMergedCoaddSourcesConfig_
842 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
844 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
845 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
846 files.
848 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
849 the various sub-tasks. See the documetation for individual sub-tasks for more information.
851 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
852 MeasureMergedCoaddSourcesTask
854 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
855 The next stage in the multi-band processing procedure will merge these measurements into a suitable
856 catalog for driving forced photometry.
858 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
859 to be processed.
860 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the
861 `--help` command line argument:
862 @code
863 measureCoaddSources.py --help
864 @endcode
866 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
867 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
868 step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band
869 coadd as follows:
870 @code
871 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
872 @endcode
873 This will process the HSC-I band data. The results are written in
874 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
876 It is also necessary to run
877 @code
878 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
879 @endcode
880 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
881 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask".
882 """
883 _DefaultName = "measureCoaddSources"
884 ConfigClass = MeasureMergedCoaddSourcesConfig
885 RunnerClass = MeasureMergedCoaddSourcesRunner
886 getSchemaCatalogs = _makeGetSchemaCatalogs("meas")
887 # The IDs we already have are of this type
888 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False)
890 @classmethod
891 def _makeArgumentParser(cls):
892 parser = ArgumentParser(name=cls._DefaultName)
893 parser.add_id_argument("--id", "deepCoadd_calexp",
894 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
895 ContainerClass=ExistingCoaddDataIdContainer)
896 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
897 return parser
899 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
900 **kwargs):
901 """!
902 @brief Initialize the task.
904 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
905 @param[in] schema: the schema of the merged detection catalog used as input to this one
906 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog
907 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
908 catalog. May be None if the loader can be constructed from the butler argument or all steps
909 requiring a reference catalog are disabled.
910 @param[in] butler: a butler used to read the input schemas from disk or construct the reference
911 catalog loader, if schema or peakSchema or refObjLoader is None
913 The task will set its own self.schema attribute to the schema of the output measurement catalog.
914 This will include all fields from the input schema, as well as additional fields for all the
915 measurements.
916 """
917 super().__init__(**kwargs)
918 self.deblended = self.config.inputCatalog.startswith("deblended")
919 self.inputCatalog = "Coadd_" + self.config.inputCatalog
920 if initInputs is not None:
921 schema = initInputs['inputSchema'].schema
922 if schema is None:
923 assert butler is not None, "Neither butler nor schema is defined"
924 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema
925 self.schemaMapper = afwTable.SchemaMapper(schema)
926 self.schemaMapper.addMinimalSchema(schema)
927 self.schema = self.schemaMapper.getOutputSchema()
928 self.algMetadata = PropertyList()
929 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata)
930 self.makeSubtask("setPrimaryFlags", schema=self.schema)
931 if self.config.doMatchSources:
932 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
933 if self.config.doPropagateFlags:
934 self.makeSubtask("propagateFlags", schema=self.schema)
935 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
936 if self.config.doApCorr:
937 self.makeSubtask("applyApCorr", schema=self.schema)
938 if self.config.doRunCatalogCalculation:
939 self.makeSubtask("catalogCalculation", schema=self.schema)
941 self.outputSchema = afwTable.SourceCatalog(self.schema)
943 def runQuantum(self, butlerQC, inputRefs, outputRefs):
944 inputs = butlerQC.get(inputRefs)
946 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat],
947 inputs.pop('refCat'), config=self.config.refObjLoader,
948 log=self.log)
949 self.match.setRefObjLoader(refObjLoader)
951 # Set psfcache
952 # move this to run after gen2 deprecation
953 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
955 # Get unique integer ID for IdFactory and RNG seeds
956 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch")
957 inputs['exposureId'] = exposureIdInfo.expId
958 idFactory = exposureIdInfo.makeSourceIdFactory()
959 # Transform inputCatalog
960 table = afwTable.SourceTable.make(self.schema, idFactory)
961 sources = afwTable.SourceCatalog(table)
962 sources.extend(inputs.pop('inputCatalog'), self.schemaMapper)
963 table = sources.getTable()
964 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
965 inputs['sources'] = sources
967 skyMap = inputs.pop('skyMap')
968 tractNumber = inputRefs.inputCatalog.dataId['tract']
969 tractInfo = skyMap[tractNumber]
970 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId['patch'])
971 skyInfo = Struct(
972 skyMap=skyMap,
973 tractInfo=tractInfo,
974 patchInfo=patchInfo,
975 wcs=tractInfo.getWcs(),
976 bbox=patchInfo.getOuterBBox()
977 )
978 inputs['skyInfo'] = skyInfo
980 if self.config.doPropagateFlags:
981 # Filter out any visit catalog that is not coadd inputs
982 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds
983 visitKey = ccdInputs.schema.find("visit").key
984 ccdKey = ccdInputs.schema.find("ccd").key
985 inputVisitIds = set()
986 ccdRecordsWcs = {}
987 for ccdRecord in ccdInputs:
988 visit = ccdRecord.get(visitKey)
989 ccd = ccdRecord.get(ccdKey)
990 inputVisitIds.add((visit, ccd))
991 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
993 inputCatalogsToKeep = []
994 inputCatalogWcsUpdate = []
995 for i, dataRef in enumerate(inputRefs.visitCatalogs):
996 key = (dataRef.dataId['visit'], dataRef.dataId['detector'])
997 if key in inputVisitIds:
998 inputCatalogsToKeep.append(inputs['visitCatalogs'][i])
999 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
1000 inputs['visitCatalogs'] = inputCatalogsToKeep
1001 inputs['wcsUpdates'] = inputCatalogWcsUpdate
1002 inputs['ccdInputs'] = ccdInputs
1004 outputs = self.run(**inputs)
1005 butlerQC.put(outputs, outputRefs)
1007 def runDataRef(self, patchRef, psfCache=100):
1008 """!
1009 @brief Deblend and measure.
1011 @param[in] patchRef: Patch reference.
1013 Set 'is-primary' and related flags. Propagate flags
1014 from individual visits. Optionally match the sources to a reference catalog and write the matches.
1015 Finally, write the deblended sources and measurements out.
1016 """
1017 if self.config.hasFakes:
1018 coaddType = "fakes_" + self.config.coaddName
1019 else:
1020 coaddType = self.config.coaddName
1021 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
1022 exposure.getPsf().setCacheCapacity(psfCache)
1023 sources = self.readSources(patchRef)
1024 table = sources.getTable()
1025 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1026 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1028 if self.config.doPropagateFlags:
1029 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1030 else:
1031 ccdInputs = None
1033 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=False,
1034 log=self.log)
1035 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId,
1036 ccdInputs=ccdInputs, butler=patchRef.getButler())
1038 if self.config.doMatchSources:
1039 self.writeMatches(patchRef, results)
1040 self.write(patchRef, results.outputSources)
1042 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1043 butler=None):
1044 """Run measurement algorithms on the input exposure, and optionally populate the
1045 resulting catalog with extra information.
1047 Parameters
1048 ----------
1049 exposure : `lsst.afw.exposure.Exposure`
1050 The input exposure on which measurements are to be performed
1051 sources : `lsst.afw.table.SourceCatalog`
1052 A catalog built from the results of merged detections, or
1053 deblender outputs.
1054 skyInfo : `lsst.pipe.base.Struct`
1055 A struct containing information about the position of the input exposure within
1056 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box
1057 exposureId : `int` or `bytes`
1058 packed unique number or bytes unique to the input exposure
1059 ccdInputs : `lsst.afw.table.ExposureCatalog`
1060 Catalog containing information on the individual visits which went into making
1061 the exposure
1062 visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None`
1063 A list of source catalogs corresponding to measurements made on the individual
1064 visits which went into the input exposure. If None and butler is `None` then
1065 the task cannot propagate visit flags to the output catalog.
1066 wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None`
1067 If visitCatalogs is not `None` this should be a list of wcs objects which correspond
1068 to the input visits. Used to put all coordinates to common system. If `None` and
1069 butler is `None` then the task cannot propagate visit flags to the output catalog.
1070 butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler`
1071 Either a gen2 or gen3 butler used to load visit catalogs
1073 Returns
1074 -------
1075 results : `lsst.pipe.base.Struct`
1076 Results of running measurement task. Will contain the catalog in the
1077 sources attribute. Optionally will have results of matching to a
1078 reference catalog in the matchResults attribute, and denormalized
1079 matches in the denormMatches attribute.
1080 """
1081 self.measurement.run(sources, exposure, exposureId=exposureId)
1083 if self.config.doApCorr:
1084 self.applyApCorr.run(
1085 catalog=sources,
1086 apCorrMap=exposure.getInfo().getApCorrMap()
1087 )
1089 # TODO DM-11568: this contiguous check-and-copy could go away if we
1090 # reserve enough space during SourceDetection and/or SourceDeblend.
1091 # NOTE: sourceSelectors require contiguous catalogs, so ensure
1092 # contiguity now, so views are preserved from here on.
1093 if not sources.isContiguous():
1094 sources = sources.copy(deep=True)
1096 if self.config.doRunCatalogCalculation:
1097 self.catalogCalculation.run(sources)
1099 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1100 patchInfo=skyInfo.patchInfo)
1101 if self.config.doPropagateFlags:
1102 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates)
1104 results = Struct()
1106 if self.config.doMatchSources:
1107 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel)
1108 matches = afwTable.packMatches(matchResult.matches)
1109 matches.table.setMetadata(matchResult.matchMeta)
1110 results.matchResult = matches
1111 if self.config.doWriteMatchesDenormalized:
1112 if matchResult.matches:
1113 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1114 else:
1115 self.log.warning("No matches, so generating dummy denormalized matches file")
1116 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1117 denormMatches.setMetadata(PropertyList())
1118 denormMatches.getMetadata().add("COMMENT",
1119 "This catalog is empty because no matches were found.")
1120 results.denormMatches = denormMatches
1121 results.denormMatches = denormMatches
1123 results.outputSources = sources
1124 return results
1126 def readSources(self, dataRef):
1127 """!
1128 @brief Read input sources.
1130 @param[in] dataRef: Data reference for catalog of merged detections
1131 @return List of sources in merged catalog
1133 We also need to add columns to hold the measurements we're about to make
1134 so we can measure in-place.
1135 """
1136 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1137 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
1138 idFactory = self.makeIdFactory(dataRef)
1139 for s in merged:
1140 idFactory.notify(s.getId())
1141 table = afwTable.SourceTable.make(self.schema, idFactory)
1142 sources = afwTable.SourceCatalog(table)
1143 sources.extend(merged, self.schemaMapper)
1144 return sources
1146 def writeMatches(self, dataRef, results):
1147 """!
1148 @brief Write matches of the sources to the astrometric reference catalog.
1150 @param[in] dataRef: data reference
1151 @param[in] results: results struct from run method
1152 """
1153 if hasattr(results, "matchResult"):
1154 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1155 if hasattr(results, "denormMatches"):
1156 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1158 def write(self, dataRef, sources):
1159 """!
1160 @brief Write the source catalog.
1162 @param[in] dataRef: data reference
1163 @param[in] sources: source catalog
1164 """
1165 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1166 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)