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1#!/usr/bin/env python
2#
3# LSST Data Management System
4# Copyright 2008-2015 AURA/LSST.
5#
6# This product includes software developed by the
7# LSST Project (http://www.lsst.org/).
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the LSST License Statement and
20# the GNU General Public License along with this program. If not,
21# see <https://www.lsstcorp.org/LegalNotices/>.
22#
23from lsst.coadd.utils.coaddDataIdContainer import ExistingCoaddDataIdContainer
24from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner,
25 PipelineTask, PipelineTaskConfig, PipelineTaskConnections)
26import lsst.pipe.base.connectionTypes as cT
27from lsst.pex.config import Config, Field, ConfigurableField
28from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader
29from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask
30from lsst.meas.deblender import SourceDeblendTask
31from lsst.meas.extensions.scarlet import ScarletDeblendTask
32from lsst.pipe.tasks.coaddBase import getSkyInfo
33from lsst.pipe.tasks.scaleVariance import ScaleVarianceTask
34from lsst.meas.astrom import DirectMatchTask, denormalizeMatches
35from lsst.pipe.tasks.fakes import BaseFakeSourcesTask
36from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
37from lsst.pipe.tasks.propagateVisitFlags import PropagateVisitFlagsTask
38import lsst.afw.image as afwImage
39import lsst.afw.table as afwTable
40import lsst.afw.math as afwMath
41from lsst.daf.base import PropertyList
43from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401
44from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401
45from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401
46from .multiBandUtils import getInputSchema, getShortFilterName, readCatalog, _makeMakeIdFactory # noqa: F401
47from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401
48from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401
49from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401
50from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401
53"""
54New set types:
55* deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter)
56* deepCoadd_mergeDet: merged detections (tract, patch)
57* deepCoadd_meas: measurements of merged detections (tract, patch, filter)
58* deepCoadd_ref: reference sources (tract, patch)
59All of these have associated *_schema catalogs that require no data ID and hold no records.
61In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in
62the mergeDet, meas, and ref dataset Footprints:
63* deepCoadd_peak_schema
64"""
67##############################################################################################################
68class DetectCoaddSourcesConnections(PipelineTaskConnections,
69 dimensions=("tract", "patch", "abstract_filter", "skymap"),
70 defaultTemplates={"inputCoaddName": "deep", "outputCoaddName": "deep"}):
71 detectionSchema = cT.InitOutput(
72 doc="Schema of the detection catalog",
73 name="{outputCoaddName}Coadd_det_schema",
74 storageClass="SourceCatalog",
75 )
76 exposure = cT.Input(
77 doc="Exposure on which detections are to be performed",
78 name="{inputCoaddName}Coadd",
79 storageClass="ExposureF",
80 dimensions=("tract", "patch", "abstract_filter", "skymap")
81 )
82 outputBackgrounds = cT.Output(
83 doc="Output Backgrounds used in detection",
84 name="{outputCoaddName}Coadd_calexp_background",
85 storageClass="Background",
86 dimensions=("tract", "patch", "abstract_filter", "skymap")
87 )
88 outputSources = cT.Output(
89 doc="Detected sources catalog",
90 name="{outputCoaddName}Coadd_det",
91 storageClass="SourceCatalog",
92 dimensions=("tract", "patch", "abstract_filter", "skymap")
93 )
94 outputExposure = cT.Output(
95 doc="Exposure post detection",
96 name="{outputCoaddName}Coadd_calexp",
97 storageClass="ExposureF",
98 dimensions=("tract", "patch", "abstract_filter", "skymap")
99 )
102class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections):
103 """!
104 @anchor DetectCoaddSourcesConfig_
106 @brief Configuration parameters for the DetectCoaddSourcesTask
107 """
108 doScaleVariance = Field(dtype=bool, default=True, doc="Scale variance plane using empirical noise?")
109 scaleVariance = ConfigurableField(target=ScaleVarianceTask, doc="Variance rescaling")
110 detection = ConfigurableField(target=DynamicDetectionTask, doc="Source detection")
111 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
112 doInsertFakes = Field(dtype=bool, default=False,
113 doc="Run fake sources injection task")
114 insertFakes = ConfigurableField(target=BaseFakeSourcesTask,
115 doc="Injection of fake sources for testing "
116 "purposes (must be retargeted)")
117 hasFakes = Field(
118 dtype=bool,
119 default=False,
120 doc="Should be set to True if fake sources have been inserted into the input data."
121 )
123 def setDefaults(self):
124 super().setDefaults()
125 self.detection.thresholdType = "pixel_stdev"
126 self.detection.isotropicGrow = True
127 # Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic
128 self.detection.reEstimateBackground = False
129 self.detection.background.useApprox = False
130 self.detection.background.binSize = 4096
131 self.detection.background.undersampleStyle = 'REDUCE_INTERP_ORDER'
132 self.detection.doTempWideBackground = True # Suppress large footprints that overwhelm the deblender
134## @addtogroup LSST_task_documentation
135## @{
136## @page DetectCoaddSourcesTask
137## @ref DetectCoaddSourcesTask_ "DetectCoaddSourcesTask"
138## @copybrief DetectCoaddSourcesTask
139## @}
142class DetectCoaddSourcesTask(PipelineTask, CmdLineTask):
143 r"""!
144 @anchor DetectCoaddSourcesTask_
146 @brief Detect sources on a coadd
148 @section pipe_tasks_multiBand_Contents Contents
150 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose
151 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize
152 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run
153 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config
154 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug
155 - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example
157 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description
159 Command-line task that detects sources on a coadd of exposures obtained with a single filter.
161 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise
162 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane
163 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should
164 propagate the full covariance matrix -- but it is simple and works well in practice.
166 After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref
167 SourceDetectionTask_ "detection" subtask.
169 @par Inputs:
170 deepCoadd{tract,patch,filter}: ExposureF
171 @par Outputs:
172 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints)
173 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input
174 exposure (ExposureF)
175 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList
176 @par Data Unit:
177 tract, patch, filter
179 DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask.
180 You can retarget this subtask if you wish.
182 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization
184 @copydoc \_\_init\_\_
186 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task
188 @copydoc run
190 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters
192 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig"
194 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables
196 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a
197 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py
198 files.
200 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to
201 @ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for
202 @ref SourceDetectionTask_ "SourceDetectionTask" for further information.
204 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example
205 of using DetectCoaddSourcesTask
207 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of
208 the task is to update the background, detect all sources in a single band and generate a set of parent
209 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and,
210 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data
211 reference to the coadd to be processed. A list of the available optional arguments can be obtained by
212 calling detectCoaddSources.py with the `--help` command line argument:
213 @code
214 detectCoaddSources.py --help
215 @endcode
217 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we
218 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has followed
219 steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows:
220 @code
221 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I
222 @endcode
223 that will process the HSC-I band data. The results are written to
224 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`.
226 It is also necessary to run:
227 @code
228 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R
229 @endcode
230 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band
231 processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask".
232 """
233 _DefaultName = "detectCoaddSources"
234 ConfigClass = DetectCoaddSourcesConfig
235 getSchemaCatalogs = _makeGetSchemaCatalogs("det")
236 makeIdFactory = _makeMakeIdFactory("CoaddId")
238 @classmethod
239 def _makeArgumentParser(cls):
240 parser = ArgumentParser(name=cls._DefaultName)
241 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
242 ContainerClass=ExistingCoaddDataIdContainer)
243 return parser
245 def __init__(self, schema=None, **kwargs):
246 """!
247 @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask.
249 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
251 @param[in] schema: initial schema for the output catalog, modified-in place to include all
252 fields set by this task. If None, the source minimal schema will be used.
253 @param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__
254 """
255 # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree
256 # call structure has been reviewed carefully to be sure super will work as intended.
257 super().__init__(**kwargs)
258 if schema is None:
259 schema = afwTable.SourceTable.makeMinimalSchema()
260 if self.config.doInsertFakes:
261 self.makeSubtask("insertFakes")
262 self.schema = schema
263 self.makeSubtask("detection", schema=self.schema)
264 if self.config.doScaleVariance:
265 self.makeSubtask("scaleVariance")
267 self.detectionSchema = afwTable.SourceCatalog(self.schema)
269 def runDataRef(self, patchRef):
270 """!
271 @brief Run detection on a coadd.
273 Invokes @ref run and then uses @ref write to output the
274 results.
276 @param[in] patchRef: data reference for patch
277 """
278 if self.config.hasFakes:
279 exposure = patchRef.get("fakes_" + self.config.coaddName + "Coadd", immediate=True)
280 else:
281 exposure = patchRef.get(self.config.coaddName + "Coadd", immediate=True)
282 expId = int(patchRef.get(self.config.coaddName + "CoaddId"))
283 results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId)
284 self.write(results, patchRef)
285 return results
287 def runQuantum(self, butlerQC, inputRefs, outputRefs):
288 inputs = butlerQC.get(inputRefs)
289 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch_abstract_filter", returnMaxBits=True)
290 inputs["idFactory"] = afwTable.IdFactory.makeSource(packedId, 64 - maxBits)
291 inputs["expId"] = packedId
292 outputs = self.run(**inputs)
293 butlerQC.put(outputs, outputRefs)
295 def run(self, exposure, idFactory, expId):
296 """!
297 @brief Run detection on an exposure.
299 First scale the variance plane to match the observed variance
300 using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to
301 detect sources.
303 @param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled,
304 depending on configuration).
305 @param[in] idFactory: IdFactory to set source identifiers
306 @param[in] expId: Exposure identifier (integer) for RNG seed
308 @return a pipe.base.Struct with fields
309 - sources: catalog of detections
310 - backgrounds: list of backgrounds
311 """
312 if self.config.doScaleVariance:
313 varScale = self.scaleVariance.run(exposure.maskedImage)
314 exposure.getMetadata().add("VARIANCE_SCALE", varScale)
315 backgrounds = afwMath.BackgroundList()
316 if self.config.doInsertFakes:
317 self.insertFakes.run(exposure, background=backgrounds)
318 table = afwTable.SourceTable.make(self.schema, idFactory)
319 detections = self.detection.run(table, exposure, expId=expId)
320 sources = detections.sources
321 fpSets = detections.fpSets
322 if hasattr(fpSets, "background") and fpSets.background:
323 for bg in fpSets.background:
324 backgrounds.append(bg)
325 return Struct(outputSources=sources, outputBackgrounds=backgrounds, outputExposure=exposure)
327 def write(self, results, patchRef):
328 """!
329 @brief Write out results from runDetection.
331 @param[in] exposure: Exposure to write out
332 @param[in] results: Struct returned from runDetection
333 @param[in] patchRef: data reference for patch
334 """
335 coaddName = self.config.coaddName + "Coadd"
336 patchRef.put(results.outputBackgrounds, coaddName + "_calexp_background")
337 patchRef.put(results.outputSources, coaddName + "_det")
338 if self.config.hasFakes:
339 patchRef.put(results.outputExposure, "fakes_" + coaddName + "_calexp")
340 else:
341 patchRef.put(results.outputExposure, coaddName + "_calexp")
343##############################################################################################################
346class DeblendCoaddSourcesConfig(Config):
347 """DeblendCoaddSourcesConfig
349 Configuration parameters for the `DeblendCoaddSourcesTask`.
350 """
351 singleBandDeblend = ConfigurableField(target=SourceDeblendTask,
352 doc="Deblend sources separately in each band")
353 multiBandDeblend = ConfigurableField(target=ScarletDeblendTask,
354 doc="Deblend sources simultaneously across bands")
355 simultaneous = Field(dtype=bool, default=False, doc="Simultaneously deblend all bands?")
356 coaddName = Field(dtype=str, default="deep", doc="Name of coadd")
357 hasFakes = Field(dtype=bool,
358 default=False,
359 doc="Should be set to True if fake sources have been inserted into the input data.")
361 def setDefaults(self):
362 Config.setDefaults(self)
363 self.singleBandDeblend.propagateAllPeaks = True
366class DeblendCoaddSourcesRunner(MergeSourcesRunner):
367 """Task runner for the `MergeSourcesTask`
369 Required because the run method requires a list of
370 dataRefs rather than a single dataRef.
371 """
372 @staticmethod
373 def getTargetList(parsedCmd, **kwargs):
374 """Provide a list of patch references for each patch, tract, filter combo.
376 Parameters
377 ----------
378 parsedCmd:
379 The parsed command
380 kwargs:
381 Keyword arguments passed to the task
383 Returns
384 -------
385 targetList: list
386 List of tuples, where each tuple is a (dataRef, kwargs) pair.
387 """
388 refDict = MergeSourcesRunner.buildRefDict(parsedCmd)
389 kwargs["psfCache"] = parsedCmd.psfCache
390 return [(list(p.values()), kwargs) for t in refDict.values() for p in t.values()]
393class DeblendCoaddSourcesTask(CmdLineTask):
394 """Deblend the sources in a merged catalog
396 Deblend sources from master catalog in each coadd.
397 This can either be done separately in each band using the HSC-SDSS deblender
398 (`DeblendCoaddSourcesTask.config.simultaneous==False`)
399 or use SCARLET to simultaneously fit the blend in all bands
400 (`DeblendCoaddSourcesTask.config.simultaneous==True`).
401 The task will set its own `self.schema` atribute to the `Schema` of the
402 output deblended catalog.
403 This will include all fields from the input `Schema`, as well as additional fields
404 from the deblender.
406 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description
407 ---------------------------------------------------------
408 `
410 Parameters
411 ----------
412 butler: `Butler`
413 Butler used to read the input schemas from disk or
414 construct the reference catalog loader, if `schema` or `peakSchema` or
415 schema: `Schema`
416 The schema of the merged detection catalog as an input to this task.
417 peakSchema: `Schema`
418 The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog
419 """
420 ConfigClass = DeblendCoaddSourcesConfig
421 RunnerClass = DeblendCoaddSourcesRunner
422 _DefaultName = "deblendCoaddSources"
423 makeIdFactory = _makeMakeIdFactory("MergedCoaddId")
425 @classmethod
426 def _makeArgumentParser(cls):
427 parser = ArgumentParser(name=cls._DefaultName)
428 parser.add_id_argument("--id", "deepCoadd_calexp",
429 help="data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i",
430 ContainerClass=ExistingCoaddDataIdContainer)
431 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
432 return parser
434 def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs):
435 CmdLineTask.__init__(self, **kwargs)
436 if schema is None:
437 assert butler is not None, "Neither butler nor schema is defined"
438 schema = butler.get(self.config.coaddName + "Coadd_mergeDet_schema", immediate=True).schema
439 self.schemaMapper = afwTable.SchemaMapper(schema)
440 self.schemaMapper.addMinimalSchema(schema)
441 self.schema = self.schemaMapper.getOutputSchema()
442 if peakSchema is None:
443 assert butler is not None, "Neither butler nor peakSchema is defined"
444 peakSchema = butler.get(self.config.coaddName + "Coadd_peak_schema", immediate=True).schema
446 if self.config.simultaneous:
447 self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema)
448 else:
449 self.makeSubtask("singleBandDeblend", schema=self.schema, peakSchema=peakSchema)
451 def getSchemaCatalogs(self):
452 """Return a dict of empty catalogs for each catalog dataset produced by this task.
454 Returns
455 -------
456 result: dict
457 Dictionary of empty catalogs, with catalog names as keys.
458 """
459 catalog = afwTable.SourceCatalog(self.schema)
460 return {self.config.coaddName + "Coadd_deblendedFlux": catalog,
461 self.config.coaddName + "Coadd_deblendedModel": catalog}
463 def runDataRef(self, patchRefList, psfCache=100):
464 """Deblend the patch
466 Deblend each source simultaneously or separately
467 (depending on `DeblendCoaddSourcesTask.config.simultaneous`).
468 Set `is-primary` and related flags.
469 Propagate flags from individual visits.
470 Write the deblended sources out.
472 Parameters
473 ----------
474 patchRefList: list
475 List of data references for each filter
476 """
478 if self.config.hasFakes:
479 coaddType = "fakes_" + self.config.coaddName
480 else:
481 coaddType = self.config.coaddName
483 if self.config.simultaneous:
484 # Use SCARLET to simultaneously deblend across filters
485 filters = []
486 exposures = []
487 for patchRef in patchRefList:
488 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
489 filters.append(patchRef.dataId["filter"])
490 exposures.append(exposure)
491 # The input sources are the same for all bands, since it is a merged catalog
492 sources = self.readSources(patchRef)
493 exposure = afwImage.MultibandExposure.fromExposures(filters, exposures)
494 fluxCatalogs, templateCatalogs = self.multiBandDeblend.run(exposure, sources)
495 for n in range(len(patchRefList)):
496 fluxCat = fluxCatalogs if fluxCatalogs is None else fluxCatalogs[filters[n]]
497 self.write(patchRefList[n], fluxCat, templateCatalogs[filters[n]])
498 else:
499 # Use the singeband deblender to deblend each band separately
500 for patchRef in patchRefList:
501 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
502 exposure.getPsf().setCacheCapacity(psfCache)
503 sources = self.readSources(patchRef)
504 self.singleBandDeblend.run(exposure, sources)
505 self.write(patchRef, sources)
507 def readSources(self, dataRef):
508 """Read merged catalog
510 Read the catalog of merged detections and create a catalog
511 in a single band.
513 Parameters
514 ----------
515 dataRef: data reference
516 Data reference for catalog of merged detections
518 Returns
519 -------
520 sources: `SourceCatalog`
521 List of sources in merged catalog
523 We also need to add columns to hold the measurements we're about to make
524 so we can measure in-place.
525 """
526 merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=True)
527 self.log.info("Read %d detections: %s" % (len(merged), dataRef.dataId))
528 idFactory = self.makeIdFactory(dataRef)
529 for s in merged:
530 idFactory.notify(s.getId())
531 table = afwTable.SourceTable.make(self.schema, idFactory)
532 sources = afwTable.SourceCatalog(table)
533 sources.extend(merged, self.schemaMapper)
534 return sources
536 def write(self, dataRef, flux_sources, template_sources=None):
537 """Write the source catalog(s)
539 Parameters
540 ----------
541 dataRef: Data Reference
542 Reference to the output catalog.
543 flux_sources: `SourceCatalog`
544 Flux conserved sources to write to file.
545 If using the single band deblender, this is the catalog
546 generated.
547 template_sources: `SourceCatalog`
548 Source catalog using the multiband template models
549 as footprints.
550 """
551 # The multiband deblender does not have to conserve flux,
552 # so only write the flux conserved catalog if it exists
553 if flux_sources is not None:
554 assert not self.config.simultaneous or self.config.multiBandDeblend.conserveFlux
555 dataRef.put(flux_sources, self.config.coaddName + "Coadd_deblendedFlux")
556 self.log.info("Wrote %d sources: %s" % (len(flux_sources), dataRef.dataId))
557 # Only the multiband deblender has the option to output the
558 # template model catalog, which can optionally be used
559 # in MeasureMergedCoaddSources
560 if template_sources is not None:
561 assert self.config.multiBandDeblend.saveTemplates
562 dataRef.put(template_sources, self.config.coaddName + "Coadd_deblendedModel")
563 self.log.info("Wrote %d sources: %s" % (len(template_sources), dataRef.dataId))
565 def writeMetadata(self, dataRefList):
566 """Write the metadata produced from processing the data.
567 Parameters
568 ----------
569 dataRefList
570 List of Butler data references used to write the metadata.
571 The metadata is written to dataset type `CmdLineTask._getMetadataName`.
572 """
573 for dataRef in dataRefList:
574 try:
575 metadataName = self._getMetadataName()
576 if metadataName is not None:
577 dataRef.put(self.getFullMetadata(), metadataName)
578 except Exception as e:
579 self.log.warn("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e)
581 def getExposureId(self, dataRef):
582 """Get the ExposureId from a data reference
583 """
584 return int(dataRef.get(self.config.coaddName + "CoaddId"))
587class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections,
588 dimensions=("tract", "patch", "abstract_filter", "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", "abstract_filter", "skymap")
614 )
615 skyMap = cT.Input(
616 doc="SkyMap to use in processing",
617 name="{inputCoaddName}Coadd_skyMap",
618 storageClass="SkyMap",
619 dimensions=("skymap",),
620 )
621 visitCatalogs = cT.Input(
622 doc="Source catalogs for visits which overlap input tract, patch, abstract_filter. 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", "abstract_filter", "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", "abstract_filter", "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", "abstract_filter", "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", "abstract_filter", "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 makeIdFactory = _makeMakeIdFactory("MergedCoaddId") # The IDs we already have are of this type
887 @classmethod
888 def _makeArgumentParser(cls):
889 parser = ArgumentParser(name=cls._DefaultName)
890 parser.add_id_argument("--id", "deepCoadd_calexp",
891 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r",
892 ContainerClass=ExistingCoaddDataIdContainer)
893 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache")
894 return parser
896 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None,
897 **kwargs):
898 """!
899 @brief Initialize the task.
901 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__):
902 @param[in] schema: the schema of the merged detection catalog used as input to this one
903 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog
904 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference
905 catalog. May be None if the loader can be constructed from the butler argument or all steps
906 requiring a reference catalog are disabled.
907 @param[in] butler: a butler used to read the input schemas from disk or construct the reference
908 catalog loader, if schema or peakSchema or refObjLoader is None
910 The task will set its own self.schema attribute to the schema of the output measurement catalog.
911 This will include all fields from the input schema, as well as additional fields for all the
912 measurements.
913 """
914 super().__init__(**kwargs)
915 self.deblended = self.config.inputCatalog.startswith("deblended")
916 self.inputCatalog = "Coadd_" + self.config.inputCatalog
917 if initInputs is not None:
918 schema = initInputs['inputSchema'].schema
919 if schema is None:
920 assert butler is not None, "Neither butler nor schema is defined"
921 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema
922 self.schemaMapper = afwTable.SchemaMapper(schema)
923 self.schemaMapper.addMinimalSchema(schema)
924 self.schema = self.schemaMapper.getOutputSchema()
925 self.algMetadata = PropertyList()
926 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata)
927 self.makeSubtask("setPrimaryFlags", schema=self.schema)
928 if self.config.doMatchSources:
929 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader)
930 if self.config.doPropagateFlags:
931 self.makeSubtask("propagateFlags", schema=self.schema)
932 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
933 if self.config.doApCorr:
934 self.makeSubtask("applyApCorr", schema=self.schema)
935 if self.config.doRunCatalogCalculation:
936 self.makeSubtask("catalogCalculation", schema=self.schema)
938 self.outputSchema = afwTable.SourceCatalog(self.schema)
940 def runQuantum(self, butlerQC, inputRefs, outputRefs):
941 inputs = butlerQC.get(inputRefs)
943 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat],
944 inputs.pop('refCat'), config=self.config.refObjLoader,
945 log=self.log)
946 self.match.setRefObjLoader(refObjLoader)
948 # Set psfcache
949 # move this to run after gen2 deprecation
950 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache)
952 # Get unique integer ID for IdFactory and RNG seeds
953 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch", returnMaxBits=True)
954 inputs['exposureId'] = packedId
955 idFactory = afwTable.IdFactory.makeSource(packedId, 64 - maxBits)
956 # Transform inputCatalog
957 table = afwTable.SourceTable.make(self.schema, idFactory)
958 sources = afwTable.SourceCatalog(table)
959 sources.extend(inputs.pop('inputCatalog'), self.schemaMapper)
960 table = sources.getTable()
961 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
962 inputs['sources'] = sources
964 skyMap = inputs.pop('skyMap')
965 tractNumber = inputRefs.inputCatalog.dataId['tract']
966 tractInfo = skyMap[tractNumber]
967 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId['patch'])
968 skyInfo = Struct(
969 skyMap=skyMap,
970 tractInfo=tractInfo,
971 patchInfo=patchInfo,
972 wcs=tractInfo.getWcs(),
973 bbox=patchInfo.getOuterBBox()
974 )
975 inputs['skyInfo'] = skyInfo
977 if self.config.doPropagateFlags:
978 # Filter out any visit catalog that is not coadd inputs
979 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds
980 visitKey = ccdInputs.schema.find("visit").key
981 ccdKey = ccdInputs.schema.find("ccd").key
982 inputVisitIds = set()
983 ccdRecordsWcs = {}
984 for ccdRecord in ccdInputs:
985 visit = ccdRecord.get(visitKey)
986 ccd = ccdRecord.get(ccdKey)
987 inputVisitIds.add((visit, ccd))
988 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs()
990 inputCatalogsToKeep = []
991 inputCatalogWcsUpdate = []
992 for i, dataRef in enumerate(inputRefs.visitCatalogs):
993 key = (dataRef.dataId['visit'], dataRef.dataId['detector'])
994 if key in inputVisitIds:
995 inputCatalogsToKeep.append(inputs['visitCatalogs'][i])
996 inputCatalogWcsUpdate.append(ccdRecordsWcs[key])
997 inputs['visitCatalogs'] = inputCatalogsToKeep
998 inputs['wcsUpdates'] = inputCatalogWcsUpdate
999 inputs['ccdInputs'] = ccdInputs
1001 outputs = self.run(**inputs)
1002 butlerQC.put(outputs, outputRefs)
1004 def runDataRef(self, patchRef, psfCache=100):
1005 """!
1006 @brief Deblend and measure.
1008 @param[in] patchRef: Patch reference.
1010 Set 'is-primary' and related flags. Propagate flags
1011 from individual visits. Optionally match the sources to a reference catalog and write the matches.
1012 Finally, write the deblended sources and measurements out.
1013 """
1014 if self.config.hasFakes:
1015 coaddType = "fakes_" + self.config.coaddName
1016 else:
1017 coaddType = self.config.coaddName
1018 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True)
1019 exposure.getPsf().setCacheCapacity(psfCache)
1020 sources = self.readSources(patchRef)
1021 table = sources.getTable()
1022 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog.
1023 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
1025 if self.config.doPropagateFlags:
1026 ccdInputs = self.propagateFlags.getCcdInputs(exposure)
1027 else:
1028 ccdInputs = None
1030 results = self.run(exposure=exposure, sources=sources,
1031 ccdInputs=ccdInputs,
1032 skyInfo=skyInfo, butler=patchRef.getButler(),
1033 exposureId=self.getExposureId(patchRef))
1035 if self.config.doMatchSources:
1036 self.writeMatches(patchRef, results)
1037 self.write(patchRef, results.outputSources)
1039 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None,
1040 butler=None):
1041 """Run measurement algorithms on the input exposure, and optionally populate the
1042 resulting catalog with extra information.
1044 Parameters
1045 ----------
1046 exposure : `lsst.afw.exposure.Exposure`
1047 The input exposure on which measurements are to be performed
1048 sources : `lsst.afw.table.SourceCatalog`
1049 A catalog built from the results of merged detections, or
1050 deblender outputs.
1051 skyInfo : `lsst.pipe.base.Struct`
1052 A struct containing information about the position of the input exposure within
1053 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box
1054 exposureId : `int` or `bytes`
1055 packed unique number or bytes unique to the input exposure
1056 ccdInputs : `lsst.afw.table.ExposureCatalog`
1057 Catalog containing information on the individual visits which went into making
1058 the exposure
1059 visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None`
1060 A list of source catalogs corresponding to measurements made on the individual
1061 visits which went into the input exposure. If None and butler is `None` then
1062 the task cannot propagate visit flags to the output catalog.
1063 wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None`
1064 If visitCatalogs is not `None` this should be a list of wcs objects which correspond
1065 to the input visits. Used to put all coordinates to common system. If `None` and
1066 butler is `None` then the task cannot propagate visit flags to the output catalog.
1067 butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler`
1068 Either a gen2 or gen3 butler used to load visit catalogs
1070 Returns
1071 -------
1072 results : `lsst.pipe.base.Struct`
1073 Results of running measurement task. Will contain the catalog in the
1074 sources attribute. Optionally will have results of matching to a
1075 reference catalog in the matchResults attribute, and denormalized
1076 matches in the denormMatches attribute.
1077 """
1078 self.measurement.run(sources, exposure, exposureId=exposureId)
1080 if self.config.doApCorr:
1081 self.applyApCorr.run(
1082 catalog=sources,
1083 apCorrMap=exposure.getInfo().getApCorrMap()
1084 )
1086 # TODO DM-11568: this contiguous check-and-copy could go away if we
1087 # reserve enough space during SourceDetection and/or SourceDeblend.
1088 # NOTE: sourceSelectors require contiguous catalogs, so ensure
1089 # contiguity now, so views are preserved from here on.
1090 if not sources.isContiguous():
1091 sources = sources.copy(deep=True)
1093 if self.config.doRunCatalogCalculation:
1094 self.catalogCalculation.run(sources)
1096 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo,
1097 patchInfo=skyInfo.patchInfo, includeDeblend=self.deblended)
1098 if self.config.doPropagateFlags:
1099 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates)
1101 results = Struct()
1103 if self.config.doMatchSources:
1104 matchResult = self.match.run(sources, exposure.getInfo().getFilter().getName())
1105 matches = afwTable.packMatches(matchResult.matches)
1106 matches.table.setMetadata(matchResult.matchMeta)
1107 results.matchResult = matches
1108 if self.config.doWriteMatchesDenormalized:
1109 if matchResult.matches:
1110 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta)
1111 else:
1112 self.log.warn("No matches, so generating dummy denormalized matches file")
1113 denormMatches = afwTable.BaseCatalog(afwTable.Schema())
1114 denormMatches.setMetadata(PropertyList())
1115 denormMatches.getMetadata().add("COMMENT",
1116 "This catalog is empty because no matches were found.")
1117 results.denormMatches = denormMatches
1118 results.denormMatches = denormMatches
1120 results.outputSources = sources
1121 return results
1123 def readSources(self, dataRef):
1124 """!
1125 @brief Read input sources.
1127 @param[in] dataRef: Data reference for catalog of merged detections
1128 @return List of sources in merged catalog
1130 We also need to add columns to hold the measurements we're about to make
1131 so we can measure in-place.
1132 """
1133 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True)
1134 self.log.info("Read %d detections: %s" % (len(merged), dataRef.dataId))
1135 idFactory = self.makeIdFactory(dataRef)
1136 for s in merged:
1137 idFactory.notify(s.getId())
1138 table = afwTable.SourceTable.make(self.schema, idFactory)
1139 sources = afwTable.SourceCatalog(table)
1140 sources.extend(merged, self.schemaMapper)
1141 return sources
1143 def writeMatches(self, dataRef, results):
1144 """!
1145 @brief Write matches of the sources to the astrometric reference catalog.
1147 @param[in] dataRef: data reference
1148 @param[in] results: results struct from run method
1149 """
1150 if hasattr(results, "matchResult"):
1151 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch")
1152 if hasattr(results, "denormMatches"):
1153 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull")
1155 def write(self, dataRef, sources):
1156 """!
1157 @brief Write the source catalog.
1159 @param[in] dataRef: data reference
1160 @param[in] sources: source catalog
1161 """
1162 dataRef.put(sources, self.config.coaddName + "Coadd_meas")
1163 self.log.info("Wrote %d sources: %s" % (len(sources), dataRef.dataId))
1165 def getExposureId(self, dataRef):
1166 return int(dataRef.get(self.config.coaddName + "CoaddId"))