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 = self.multiBandDeblend.run(exposure, sources)
509 for n in range(len(patchRefList)):
510 self.write(patchRefList[n], templateCatalogs[filters[n]])
511 else:
512 # Use the singeband deblender to deblend each band separately
513 for patchRef in patchRefList:
514 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
515 exposure.getPsf().setCacheCapacity(psfCache)
516 sources = self.readSources(patchRef)
517 self.singleBandDeblend.run(exposure, sources)
518 self.write(patchRef, sources)
520 def readSources(self, dataRef):
521 """Read merged catalog
523 Read the catalog of merged detections and create a catalog
524 in a single band.
526 Parameters
527 ----------
528 dataRef: data reference
529 Data reference for catalog of merged detections
531 Returns
532 -------
533 sources: `SourceCatalog`
534 List of sources in merged catalog
536 We also need to add columns to hold the measurements we're about to make
537 so we can measure in-place.
538 """
539 merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=True)
540 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
541 idFactory = self.makeIdFactory(dataRef)
542 # There may be gaps in the mergeDet catalog, which will cause the
543 # source ids to be inconsistent. So we update the id factory
544 # with the largest id already in the catalog.
545 maxId = np.max(merged["id"])
546 idFactory.notify(maxId)
547 table = afwTable.SourceTable.make(self.schema, idFactory)
548 sources = afwTable.SourceCatalog(table)
549 sources.extend(merged, self.schemaMapper)
550 return sources
552 def write(self, dataRef, sources):
553 """Write the source catalog(s)
555 Parameters
556 ----------
557 dataRef: Data Reference
558 Reference to the output catalog.
559 sources: `SourceCatalog`
560 Flux conserved sources to write to file.
561 If using the single band deblender, this is the catalog
562 generated.
563 template_sources: `SourceCatalog`
564 Source catalog using the multiband template models
565 as footprints.
566 """
567 dataRef.put(sources, self.config.coaddName + "Coadd_deblendedFlux")
568 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)
570 def writeMetadata(self, dataRefList):
571 """Write the metadata produced from processing the data.
572 Parameters
573 ----------
574 dataRefList
575 List of Butler data references used to write the metadata.
576 The metadata is written to dataset type `CmdLineTask._getMetadataName`.
577 """
578 for dataRef in dataRefList:
579 try:
580 metadataName = self._getMetadataName()
581 if metadataName is not None:
582 dataRef.put(self.getFullMetadata(), metadataName)
583 except Exception as e:
584 self.log.warning("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
587class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections,
588 dimensions=("tract", "patch", "band", "skymap"),
589 defaultTemplates={"inputCoaddName": "deep",
590 "outputCoaddName": "deep"}):
591 inputSchema = cT.InitInput(
592 doc="Input schema for measure merged task produced by a deblender or detection task",
593 name="{inputCoaddName}Coadd_deblendedFlux_schema",
594 storageClass="SourceCatalog"
595 )
596 outputSchema = cT.InitOutput(
597 doc="Output schema after all new fields are added by task",
598 name="{inputCoaddName}Coadd_meas_schema",
599 storageClass="SourceCatalog"
600 )
601 refCat = cT.PrerequisiteInput(
602 doc="Reference catalog used to match measured sources against known sources",
603 name="ref_cat",
604 storageClass="SimpleCatalog",
605 dimensions=("skypix",),
606 deferLoad=True,
607 multiple=True
608 )
609 exposure = cT.Input(
610 doc="Input coadd image",
611 name="{inputCoaddName}Coadd_calexp",
612 storageClass="ExposureF",
613 dimensions=("tract", "patch", "band", "skymap")
614 )
615 skyMap = cT.Input(
616 doc="SkyMap to use in processing",
617 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
618 storageClass="SkyMap",
619 dimensions=("skymap",),
620 )
621 visitCatalogs = cT.Input(
622 doc="Source catalogs for visits which overlap input tract, patch, band. Will be "
623 "further filtered in the task for the purpose of propagating flags from image calibration "
624 "and characterization to codd objects",
625 name="src",
626 dimensions=("instrument", "visit", "detector"),
627 storageClass="SourceCatalog",
628 multiple=True
629 )
630 inputCatalog = cT.Input(
631 doc=("Name of the input catalog to use."
632 "If the single band deblender was used this should be 'deblendedFlux."
633 "If the multi-band deblender was used this should be 'deblendedModel, "
634 "or deblendedFlux if the multiband deblender was configured to output "
635 "deblended flux catalogs. If no deblending was performed this should "
636 "be 'mergeDet'"),
637 name="{inputCoaddName}Coadd_deblendedFlux",
638 storageClass="SourceCatalog",
639 dimensions=("tract", "patch", "band", "skymap"),
640 )
641 outputSources = cT.Output(
642 doc="Source catalog containing all the measurement information generated in this task",
643 name="{outputCoaddName}Coadd_meas",
644 dimensions=("tract", "patch", "band", "skymap"),
645 storageClass="SourceCatalog",
646 )
647 matchResult = cT.Output(
648 doc="Match catalog produced by configured matcher, optional on doMatchSources",
649 name="{outputCoaddName}Coadd_measMatch",
650 dimensions=("tract", "patch", "band", "skymap"),
651 storageClass="Catalog",
652 )
653 denormMatches = cT.Output(
654 doc="Denormalized Match catalog produced by configured matcher, optional on "
655 "doWriteMatchesDenormalized",
656 name="{outputCoaddName}Coadd_measMatchFull",
657 dimensions=("tract", "patch", "band", "skymap"),
658 storageClass="Catalog",
659 )
661 def __init__(self, *, config=None):
662 super().__init__(config=config)
663 if config.doPropagateFlags is False:
664 self.inputs -= set(("visitCatalogs",))
666 if config.doMatchSources is False:
667 self.outputs -= set(("matchResult",))
669 if config.doWriteMatchesDenormalized is False:
670 self.outputs -= set(("denormMatches",))
673class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig,
674 pipelineConnections=MeasureMergedCoaddSourcesConnections):
675 """!
676 @anchor MeasureMergedCoaddSourcesConfig_
678 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask
679 """
680 inputCatalog = Field(dtype=str, default="deblendedFlux",
681 doc=("Name of the input catalog to use."
682 "If the single band deblender was used this should be 'deblendedFlux."
683 "If the multi-band deblender was used this should be 'deblendedModel."
684 "If no deblending was performed this should be 'mergeDet'"))
685 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement")
686 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch")
687 doPropagateFlags = Field(
688 dtype=bool, default=True,
689 doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)"
690 )
691 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc="Propagate visit flags to coadd")
692 doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?")
693 match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog")
694 doWriteMatchesDenormalized = Field(
695 dtype=bool,
696 default=False,
697 doc=("Write reference matches in denormalized format? "
698 "This format uses more disk space, but is more convenient to read."),
699 )
700 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
701 psfCache = Field(dtype=int, default=100, doc="Size of psfCache")
702 checkUnitsParseStrict = Field(
703 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
704 dtype=str,
705 default="raise",
706 )
707 doApCorr = Field(
708 dtype=bool,
709 default=True,
710 doc="Apply aperture corrections"
711 )
712 applyApCorr = ConfigurableField(
713 target=ApplyApCorrTask,
714 doc="Subtask to apply aperture corrections"
715 )
716 doRunCatalogCalculation = Field(
717 dtype=bool,
718 default=True,
719 doc='Run catalogCalculation task'
720 )
721 catalogCalculation = ConfigurableField(
722 target=CatalogCalculationTask,
723 doc="Subtask to run catalogCalculation plugins on catalog"
724 )
726 hasFakes = Field(
727 dtype=bool,
728 default=False,
729 doc="Should be set to True if fake sources have been inserted into the input data."
730 )
732 @property
733 def refObjLoader(self):
734 return self.match.refObjLoader
736 def setDefaults(self):
737 super().setDefaults()
738 self.measurement.plugins.names |= ['base_InputCount',
739 'base_Variance',
740 'base_LocalPhotoCalib',
741 'base_LocalWcs']
742 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE',
743 'INEXACT_PSF']
744 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE',
745 'INEXACT_PSF']
747 def validate(self):
748 super().validate()
749 refCatGen2 = getattr(self.refObjLoader, "ref_dataset_name", None)
750 if refCatGen2 is not None and refCatGen2 != self.connections.refCat:
751 raise ValueError(
752 f"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs "
753 f"are different. These options must be kept in sync until Gen2 is retired."
754 )
757## @addtogroup LSST_task_documentation
758## @{
759## @page MeasureMergedCoaddSourcesTask
760## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask"
761## @copybrief MeasureMergedCoaddSourcesTask
762## @}
765class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner):
766 """Get the psfCache setting into MeasureMergedCoaddSourcesTask"""
767 @staticmethod
768 def getTargetList(parsedCmd, **kwargs):
769 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache)
772class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask):
773 r"""!
774 @anchor MeasureMergedCoaddSourcesTask_
776 @brief Deblend sources from master catalog in each coadd seperately and measure.
778 @section pipe_tasks_multiBand_Contents Contents
780 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose
781 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize
782 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run
783 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config
784 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug
785 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example
787 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description
789 Command-line task that uses peaks and footprints from a master catalog to perform deblending and
790 measurement in each coadd.
792 Given a master input catalog of sources (peaks and footprints) or deblender outputs
793 (including a HeavyFootprint in each band), measure each source on the
794 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a
795 consistent set of child sources.
797 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source
798 properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit
799 flags are propagated to the coadd sources.
801 Optionally, we can match the coadd sources to an external reference catalog.
803 @par Inputs:
804 deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog
805 @n deepCoadd_calexp{tract,patch,filter}: ExposureF
806 @par Outputs:
807 deepCoadd_meas{tract,patch,filter}: SourceCatalog
808 @par Data Unit:
809 tract, patch, filter
811 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks:
813 <DL>
814 <DT> @ref SingleFrameMeasurementTask_ "measurement"
815 <DD> Measure source properties of deblended sources.</DD>
816 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags"
817 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are
818 not at the edge of the field and that have either not been deblended or are the children of deblended
819 sources</DD>
820 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags"
821 <DD> Propagate flags set in individual visits to the coadd.</DD>
822 <DT> @ref DirectMatchTask_ "match"
823 <DD> Match input sources to a reference catalog (optional).
824 </DD>
825 </DL>
826 These subtasks may be retargeted as required.
828 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization
830 @copydoc \_\_init\_\_
832 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task
834 @copydoc run
836 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters
838 See @ref MeasureMergedCoaddSourcesConfig_
840 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables
842 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
843 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
844 files.
846 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to
847 the various sub-tasks. See the documetation for individual sub-tasks for more information.
849 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using
850 MeasureMergedCoaddSourcesTask
852 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs.
853 The next stage in the multi-band processing procedure will merge these measurements into a suitable
854 catalog for driving forced photometry.
856 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds
857 to be processed.
858 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the
859 `--help` command line argument:
860 @code
861 measureCoaddSources.py --help
862 @endcode
864 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
865 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished
866 step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band
867 coadd as follows:
868 @code
869 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
870 @endcode
871 This will process the HSC-I band data. The results are written in
872 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits
874 It is also necessary to run
875 @code
876 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
877 @endcode
878 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
879 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask".
880 """
881 _DefaultName = "measureCoaddSources"
882 ConfigClass = MeasureMergedCoaddSourcesConfig
883 RunnerClass = MeasureMergedCoaddSourcesRunner
884 getSchemaCatalogs = _makeGetSchemaCatalogs("meas")
885 # The IDs we already have are of this type
886 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False)
888 @classmethod
889 def _makeArgumentParser(cls):
890 parser = ArgumentParser(name=cls._DefaultName)
891 parser.add_id_argument("--id", "deepCoadd_calexp",
892 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
893 ContainerClass=ExistingCoaddDataIdContainer)
894 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
895 return parser
897 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
898 **kwargs):
899 """!
900 @brief Initialize the task.
902 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
903 @param[in] schema: the schema of the merged detection catalog used as input to this one
904 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog
905 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
906 catalog. May be None if the loader can be constructed from the butler argument or all steps
907 requiring a reference catalog are disabled.
908 @param[in] butler: a butler used to read the input schemas from disk or construct the reference
909 catalog loader, if schema or peakSchema or refObjLoader is None
911 The task will set its own self.schema attribute to the schema of the output measurement catalog.
912 This will include all fields from the input schema, as well as additional fields for all the
913 measurements.
914 """
915 super().__init__(**kwargs)
916 self.deblended = self.config.inputCatalog.startswith("deblended")
917 self.inputCatalog = "Coadd_" + self.config.inputCatalog
918 if initInputs is not None:
919 schema = initInputs['inputSchema'].schema
920 if schema is None:
921 assert butler is not None, "Neither butler nor schema is defined"
922 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema
923 self.schemaMapper = afwTable.SchemaMapper(schema)
924 self.schemaMapper.addMinimalSchema(schema)
925 self.schema = self.schemaMapper.getOutputSchema()
926 self.algMetadata = PropertyList()
927 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata)
928 self.makeSubtask("setPrimaryFlags", schema=self.schema)
929 if self.config.doMatchSources:
930 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
931 if self.config.doPropagateFlags:
932 self.makeSubtask("propagateFlags", schema=self.schema)
933 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
934 if self.config.doApCorr:
935 self.makeSubtask("applyApCorr", schema=self.schema)
936 if self.config.doRunCatalogCalculation:
937 self.makeSubtask("catalogCalculation", schema=self.schema)
939 self.outputSchema = afwTable.SourceCatalog(self.schema)
941 def runQuantum(self, butlerQC, inputRefs, outputRefs):
942 inputs = butlerQC.get(inputRefs)
944 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat],
945 inputs.pop('refCat'), config=self.config.refObjLoader,
946 log=self.log)
947 self.match.setRefObjLoader(refObjLoader)
949 # Set psfcache
950 # move this to run after gen2 deprecation
951 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
953 # Get unique integer ID for IdFactory and RNG seeds
954 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch")
955 inputs['exposureId'] = exposureIdInfo.expId
956 idFactory = exposureIdInfo.makeSourceIdFactory()
957 # Transform inputCatalog
958 table = afwTable.SourceTable.make(self.schema, idFactory)
959 sources = afwTable.SourceCatalog(table)
960 sources.extend(inputs.pop('inputCatalog'), self.schemaMapper)
961 table = sources.getTable()
962 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
963 inputs['sources'] = sources
965 skyMap = inputs.pop('skyMap')
966 tractNumber = inputRefs.inputCatalog.dataId['tract']
967 tractInfo = skyMap[tractNumber]
968 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId['patch'])
969 skyInfo = Struct(
970 skyMap=skyMap,
971 tractInfo=tractInfo,
972 patchInfo=patchInfo,
973 wcs=tractInfo.getWcs(),
974 bbox=patchInfo.getOuterBBox()
975 )
976 inputs['skyInfo'] = skyInfo
978 if self.config.doPropagateFlags:
979 # Filter out any visit catalog that is not coadd inputs
980 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds
981 visitKey = ccdInputs.schema.find("visit").key
982 ccdKey = ccdInputs.schema.find("ccd").key
983 inputVisitIds = set()
984 ccdRecordsWcs = {}
985 for ccdRecord in ccdInputs:
986 visit = ccdRecord.get(visitKey)
987 ccd = ccdRecord.get(ccdKey)
988 inputVisitIds.add((visit, ccd))
989 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
991 inputCatalogsToKeep = []
992 inputCatalogWcsUpdate = []
993 for i, dataRef in enumerate(inputRefs.visitCatalogs):
994 key = (dataRef.dataId['visit'], dataRef.dataId['detector'])
995 if key in inputVisitIds:
996 inputCatalogsToKeep.append(inputs['visitCatalogs'][i])
997 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
998 inputs['visitCatalogs'] = inputCatalogsToKeep
999 inputs['wcsUpdates'] = inputCatalogWcsUpdate
1000 inputs['ccdInputs'] = ccdInputs
1002 outputs = self.run(**inputs)
1003 butlerQC.put(outputs, outputRefs)
1005 def runDataRef(self, patchRef, psfCache=100):
1006 """!
1007 @brief Deblend and measure.
1009 @param[in] patchRef: Patch reference.
1011 Set 'is-primary' and related flags. Propagate flags
1012 from individual visits. Optionally match the sources to a reference catalog and write the matches.
1013 Finally, write the deblended sources and measurements out.
1014 """
1015 if self.config.hasFakes:
1016 coaddType = "fakes_" + self.config.coaddName
1017 else:
1018 coaddType = self.config.coaddName
1019 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
1020 exposure.getPsf().setCacheCapacity(psfCache)
1021 sources = self.readSources(patchRef)
1022 table = sources.getTable()
1023 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1024 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1026 if self.config.doPropagateFlags:
1027 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1028 else:
1029 ccdInputs = None
1031 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=False,
1032 log=self.log)
1033 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId,
1034 ccdInputs=ccdInputs, butler=patchRef.getButler())
1036 if self.config.doMatchSources:
1037 self.writeMatches(patchRef, results)
1038 self.write(patchRef, results.outputSources)
1040 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1041 butler=None):
1042 """Run measurement algorithms on the input exposure, and optionally populate the
1043 resulting catalog with extra information.
1045 Parameters
1046 ----------
1047 exposure : `lsst.afw.exposure.Exposure`
1048 The input exposure on which measurements are to be performed
1049 sources : `lsst.afw.table.SourceCatalog`
1050 A catalog built from the results of merged detections, or
1051 deblender outputs.
1052 skyInfo : `lsst.pipe.base.Struct`
1053 A struct containing information about the position of the input exposure within
1054 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box
1055 exposureId : `int` or `bytes`
1056 packed unique number or bytes unique to the input exposure
1057 ccdInputs : `lsst.afw.table.ExposureCatalog`
1058 Catalog containing information on the individual visits which went into making
1059 the exposure
1060 visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None`
1061 A list of source catalogs corresponding to measurements made on the individual
1062 visits which went into the input exposure. If None and butler is `None` then
1063 the task cannot propagate visit flags to the output catalog.
1064 wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None`
1065 If visitCatalogs is not `None` this should be a list of wcs objects which correspond
1066 to the input visits. Used to put all coordinates to common system. If `None` and
1067 butler is `None` then the task cannot propagate visit flags to the output catalog.
1068 butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler`
1069 Either a gen2 or gen3 butler used to load visit catalogs
1071 Returns
1072 -------
1073 results : `lsst.pipe.base.Struct`
1074 Results of running measurement task. Will contain the catalog in the
1075 sources attribute. Optionally will have results of matching to a
1076 reference catalog in the matchResults attribute, and denormalized
1077 matches in the denormMatches attribute.
1078 """
1079 self.measurement.run(sources, exposure, exposureId=exposureId)
1081 if self.config.doApCorr:
1082 self.applyApCorr.run(
1083 catalog=sources,
1084 apCorrMap=exposure.getInfo().getApCorrMap()
1085 )
1087 # TODO DM-11568: this contiguous check-and-copy could go away if we
1088 # reserve enough space during SourceDetection and/or SourceDeblend.
1089 # NOTE: sourceSelectors require contiguous catalogs, so ensure
1090 # contiguity now, so views are preserved from here on.
1091 if not sources.isContiguous():
1092 sources = sources.copy(deep=True)
1094 if self.config.doRunCatalogCalculation:
1095 self.catalogCalculation.run(sources)
1097 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1098 patchInfo=skyInfo.patchInfo)
1099 if self.config.doPropagateFlags:
1100 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates)
1102 results = Struct()
1104 if self.config.doMatchSources:
1105 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel)
1106 matches = afwTable.packMatches(matchResult.matches)
1107 matches.table.setMetadata(matchResult.matchMeta)
1108 results.matchResult = matches
1109 if self.config.doWriteMatchesDenormalized:
1110 if matchResult.matches:
1111 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1112 else:
1113 self.log.warning("No matches, so generating dummy denormalized matches file")
1114 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1115 denormMatches.setMetadata(PropertyList())
1116 denormMatches.getMetadata().add("COMMENT",
1117 "This catalog is empty because no matches were found.")
1118 results.denormMatches = denormMatches
1119 results.denormMatches = denormMatches
1121 results.outputSources = sources
1122 return results
1124 def readSources(self, dataRef):
1125 """!
1126 @brief Read input sources.
1128 @param[in] dataRef: Data reference for catalog of merged detections
1129 @return List of sources in merged catalog
1131 We also need to add columns to hold the measurements we're about to make
1132 so we can measure in-place.
1133 """
1134 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1135 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId)
1136 idFactory = self.makeIdFactory(dataRef)
1137 for s in merged:
1138 idFactory.notify(s.getId())
1139 table = afwTable.SourceTable.make(self.schema, idFactory)
1140 sources = afwTable.SourceCatalog(table)
1141 sources.extend(merged, self.schemaMapper)
1142 return sources
1144 def writeMatches(self, dataRef, results):
1145 """!
1146 @brief Write matches of the sources to the astrometric reference catalog.
1148 @param[in] dataRef: data reference
1149 @param[in] results: results struct from run method
1150 """
1151 if hasattr(results, "matchResult"):
1152 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1153 if hasattr(results, "denormMatches"):
1154 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1156 def write(self, dataRef, sources):
1157 """!
1158 @brief Write the source catalog.
1160 @param[in] dataRef: data reference
1161 @param[in] sources: source catalog
1162 """
1163 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1164 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)