Coverage for python/lsst/pipe/tasks/calibrate.py: 21%
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1#
2# LSST Data Management System
3# Copyright 2008-2016 AURA/LSST.
4#
5# This product includes software developed by the
6# LSST Project (http://www.lsst.org/).
7#
8# This program is free software: you can redistribute it and/or modify
9# it under the terms of the GNU General Public License as published by
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11# (at your option) any later version.
12#
13# This program is distributed in the hope that it will be useful,
14# but WITHOUT ANY WARRANTY; without even the implied warranty of
15# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16# GNU General Public License for more details.
17#
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20# see <https://www.lsstcorp.org/LegalNotices/>.
21#
22import math
23import warnings
25from lsstDebug import getDebugFrame
26import lsst.pex.config as pexConfig
27import lsst.pipe.base as pipeBase
28import lsst.pipe.base.connectionTypes as cT
29import lsst.afw.table as afwTable
30from lsst.meas.astrom import AstrometryTask, displayAstrometry, denormalizeMatches
31from lsst.meas.algorithms import LoadReferenceObjectsConfig, SkyObjectsTask
32from lsst.obs.base import ExposureIdInfo
33import lsst.daf.base as dafBase
34from lsst.afw.math import BackgroundList
35from lsst.afw.table import SourceTable
36from lsst.meas.algorithms import SourceDetectionTask, ReferenceObjectLoader
37from lsst.meas.base import (SingleFrameMeasurementTask,
38 ApplyApCorrTask,
39 CatalogCalculationTask)
40from lsst.meas.deblender import SourceDeblendTask
41from lsst.utils.timer import timeMethod
42from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
43from .fakes import BaseFakeSourcesTask
44from .photoCal import PhotoCalTask
45from .computeExposureSummaryStats import ComputeExposureSummaryStatsTask
48__all__ = ["CalibrateConfig", "CalibrateTask"]
51class CalibrateConnections(pipeBase.PipelineTaskConnections, dimensions=("instrument", "visit", "detector"),
52 defaultTemplates={}):
54 icSourceSchema = cT.InitInput(
55 doc="Schema produced by characterize image task, used to initialize this task",
56 name="icSrc_schema",
57 storageClass="SourceCatalog",
58 )
60 outputSchema = cT.InitOutput(
61 doc="Schema after CalibrateTask has been initialized",
62 name="src_schema",
63 storageClass="SourceCatalog",
64 )
66 exposure = cT.Input(
67 doc="Input image to calibrate",
68 name="icExp",
69 storageClass="ExposureF",
70 dimensions=("instrument", "visit", "detector"),
71 )
73 background = cT.Input(
74 doc="Backgrounds determined by characterize task",
75 name="icExpBackground",
76 storageClass="Background",
77 dimensions=("instrument", "visit", "detector"),
78 )
80 icSourceCat = cT.Input(
81 doc="Source catalog created by characterize task",
82 name="icSrc",
83 storageClass="SourceCatalog",
84 dimensions=("instrument", "visit", "detector"),
85 )
87 astromRefCat = cT.PrerequisiteInput(
88 doc="Reference catalog to use for astrometry",
89 name="gaia_dr2_20200414",
90 storageClass="SimpleCatalog",
91 dimensions=("skypix",),
92 deferLoad=True,
93 multiple=True,
94 )
96 photoRefCat = cT.PrerequisiteInput(
97 doc="Reference catalog to use for photometric calibration",
98 name="ps1_pv3_3pi_20170110",
99 storageClass="SimpleCatalog",
100 dimensions=("skypix",),
101 deferLoad=True,
102 multiple=True
103 )
105 outputExposure = cT.Output(
106 doc="Exposure after running calibration task",
107 name="calexp",
108 storageClass="ExposureF",
109 dimensions=("instrument", "visit", "detector"),
110 )
112 outputCat = cT.Output(
113 doc="Source catalog produced in calibrate task",
114 name="src",
115 storageClass="SourceCatalog",
116 dimensions=("instrument", "visit", "detector"),
117 )
119 outputBackground = cT.Output(
120 doc="Background models estimated in calibration task",
121 name="calexpBackground",
122 storageClass="Background",
123 dimensions=("instrument", "visit", "detector"),
124 )
126 matches = cT.Output(
127 doc="Source/refObj matches from the astrometry solver",
128 name="srcMatch",
129 storageClass="Catalog",
130 dimensions=("instrument", "visit", "detector"),
131 )
133 matchesDenormalized = cT.Output(
134 doc="Denormalized matches from astrometry solver",
135 name="srcMatchFull",
136 storageClass="Catalog",
137 dimensions=("instrument", "visit", "detector"),
138 )
140 def __init__(self, *, config=None):
141 super().__init__(config=config)
143 if config.doAstrometry is False:
144 self.prerequisiteInputs.remove("astromRefCat")
145 if config.doPhotoCal is False:
146 self.prerequisiteInputs.remove("photoRefCat")
148 if config.doWriteMatches is False or config.doAstrometry is False:
149 self.outputs.remove("matches")
150 if config.doWriteMatchesDenormalized is False or config.doAstrometry is False:
151 self.outputs.remove("matchesDenormalized")
154class CalibrateConfig(pipeBase.PipelineTaskConfig, pipelineConnections=CalibrateConnections):
155 """Config for CalibrateTask"""
156 doWrite = pexConfig.Field(
157 dtype=bool,
158 default=True,
159 doc="Save calibration results?",
160 )
161 doWriteHeavyFootprintsInSources = pexConfig.Field(
162 dtype=bool,
163 default=True,
164 doc="Include HeavyFootprint data in source table? If false then heavy "
165 "footprints are saved as normal footprints, which saves some space"
166 )
167 doWriteMatches = pexConfig.Field(
168 dtype=bool,
169 default=True,
170 doc="Write reference matches (ignored if doWrite or doAstrometry false)?",
171 )
172 doWriteMatchesDenormalized = pexConfig.Field(
173 dtype=bool,
174 default=False,
175 doc=("Write reference matches in denormalized format? "
176 "This format uses more disk space, but is more convenient to "
177 "read. Ignored if doWriteMatches=False or doWrite=False."),
178 )
179 doAstrometry = pexConfig.Field(
180 dtype=bool,
181 default=True,
182 doc="Perform astrometric calibration?",
183 )
184 astromRefObjLoader = pexConfig.ConfigField(
185 dtype=LoadReferenceObjectsConfig,
186 doc="reference object loader for astrometric calibration",
187 )
188 photoRefObjLoader = pexConfig.ConfigField(
189 dtype=LoadReferenceObjectsConfig,
190 doc="reference object loader for photometric calibration",
191 )
192 astrometry = pexConfig.ConfigurableField(
193 target=AstrometryTask,
194 doc="Perform astrometric calibration to refine the WCS",
195 )
196 requireAstrometry = pexConfig.Field(
197 dtype=bool,
198 default=True,
199 doc=("Raise an exception if astrometry fails? Ignored if doAstrometry "
200 "false."),
201 )
202 doPhotoCal = pexConfig.Field(
203 dtype=bool,
204 default=True,
205 doc="Perform phometric calibration?",
206 )
207 requirePhotoCal = pexConfig.Field(
208 dtype=bool,
209 default=True,
210 doc=("Raise an exception if photoCal fails? Ignored if doPhotoCal "
211 "false."),
212 )
213 photoCal = pexConfig.ConfigurableField(
214 target=PhotoCalTask,
215 doc="Perform photometric calibration",
216 )
217 icSourceFieldsToCopy = pexConfig.ListField(
218 dtype=str,
219 default=("calib_psf_candidate", "calib_psf_used", "calib_psf_reserved"),
220 doc=("Fields to copy from the icSource catalog to the output catalog "
221 "for matching sources Any missing fields will trigger a "
222 "RuntimeError exception. Ignored if icSourceCat is not provided.")
223 )
224 matchRadiusPix = pexConfig.Field(
225 dtype=float,
226 default=3,
227 doc=("Match radius for matching icSourceCat objects to sourceCat "
228 "objects (pixels)"),
229 )
230 checkUnitsParseStrict = pexConfig.Field(
231 doc=("Strictness of Astropy unit compatibility check, can be 'raise', "
232 "'warn' or 'silent'"),
233 dtype=str,
234 default="raise",
235 )
236 detection = pexConfig.ConfigurableField(
237 target=SourceDetectionTask,
238 doc="Detect sources"
239 )
240 doDeblend = pexConfig.Field(
241 dtype=bool,
242 default=True,
243 doc="Run deblender input exposure"
244 )
245 deblend = pexConfig.ConfigurableField(
246 target=SourceDeblendTask,
247 doc="Split blended sources into their components"
248 )
249 doSkySources = pexConfig.Field(
250 dtype=bool,
251 default=True,
252 doc="Generate sky sources?",
253 )
254 skySources = pexConfig.ConfigurableField(
255 target=SkyObjectsTask,
256 doc="Generate sky sources",
257 )
258 measurement = pexConfig.ConfigurableField(
259 target=SingleFrameMeasurementTask,
260 doc="Measure sources"
261 )
262 postCalibrationMeasurement = pexConfig.ConfigurableField(
263 target=SingleFrameMeasurementTask,
264 doc="Second round of measurement for plugins that need to be run after photocal"
265 )
266 setPrimaryFlags = pexConfig.ConfigurableField(
267 target=SetPrimaryFlagsTask,
268 doc=("Set flags for primary source classification in single frame "
269 "processing. True if sources are not sky sources and not a parent.")
270 )
271 doApCorr = pexConfig.Field(
272 dtype=bool,
273 default=True,
274 doc="Run subtask to apply aperture correction"
275 )
276 applyApCorr = pexConfig.ConfigurableField(
277 target=ApplyApCorrTask,
278 doc="Subtask to apply aperture corrections"
279 )
280 # If doApCorr is False, and the exposure does not have apcorrections
281 # already applied, the active plugins in catalogCalculation almost
282 # certainly should not contain the characterization plugin
283 catalogCalculation = pexConfig.ConfigurableField(
284 target=CatalogCalculationTask,
285 doc="Subtask to run catalogCalculation plugins on catalog"
286 )
287 doInsertFakes = pexConfig.Field(
288 dtype=bool,
289 default=False,
290 doc="Run fake sources injection task",
291 deprecated=("doInsertFakes is no longer supported. This config will be removed after v24. "
292 "Please use ProcessCcdWithFakesTask instead.")
293 )
294 insertFakes = pexConfig.ConfigurableField(
295 target=BaseFakeSourcesTask,
296 doc="Injection of fake sources for testing purposes (must be "
297 "retargeted)",
298 deprecated=("insertFakes is no longer supported. This config will be removed after v24. "
299 "Please use ProcessCcdWithFakesTask instead.")
300 )
301 doComputeSummaryStats = pexConfig.Field(
302 dtype=bool,
303 default=True,
304 doc="Run subtask to measure exposure summary statistics?"
305 )
306 computeSummaryStats = pexConfig.ConfigurableField(
307 target=ComputeExposureSummaryStatsTask,
308 doc="Subtask to run computeSummaryStats on exposure"
309 )
310 doWriteExposure = pexConfig.Field(
311 dtype=bool,
312 default=True,
313 doc="Write the calexp? If fakes have been added then we do not want to write out the calexp as a "
314 "normal calexp but as a fakes_calexp."
315 )
317 def setDefaults(self):
318 super().setDefaults()
319 self.detection.doTempLocalBackground = False
320 self.deblend.maxFootprintSize = 2000
321 self.postCalibrationMeasurement.plugins.names = ["base_LocalPhotoCalib", "base_LocalWcs"]
322 self.postCalibrationMeasurement.doReplaceWithNoise = False
323 for key in self.postCalibrationMeasurement.slots:
324 setattr(self.postCalibrationMeasurement.slots, key, None)
325 self.astromRefObjLoader.anyFilterMapsToThis = "phot_g_mean"
326 # The photoRefCat connection is the name to use for the colorterms.
327 self.photoCal.photoCatName = self.connections.photoRefCat
329 # NOTE: these two lines are for gen2, and are only here for compatibility.
330 self.astromRefObjLoader.ref_dataset_name = "gaia_dr2_20200414"
331 self.photoRefObjLoader.ref_dataset_name = "ps1_pv3_3pi_20170110"
333 def validate(self):
334 super().validate()
335 astromRefCatGen2 = getattr(self.astromRefObjLoader, "ref_dataset_name", None)
336 if astromRefCatGen2 is not None and astromRefCatGen2 != self.connections.astromRefCat:
337 raise ValueError(
338 f"Gen2 ({astromRefCatGen2}) and Gen3 ({self.connections.astromRefCat}) astrometry reference "
339 f"catalogs are different. These options must be kept in sync until Gen2 is retired."
340 )
341 photoRefCatGen2 = getattr(self.photoRefObjLoader, "ref_dataset_name", None)
342 if photoRefCatGen2 is not None and photoRefCatGen2 != self.connections.photoRefCat:
343 raise ValueError(
344 f"Gen2 ({photoRefCatGen2}) and Gen3 ({self.connections.photoRefCat}) photometry reference "
345 f"catalogs are different. These options must be kept in sync until Gen2 is retired."
346 )
349class CalibrateTask(pipeBase.PipelineTask):
350 """Task to calibrate an exposure.
352 Parameters
353 ----------
354 butler : `None`
355 Compatibility parameter. Should always be `None`.
356 astromRefObjLoader : `lsst.meas.algorithms.ReferenceObjectLoader`, optional
357 Reference object loader for astrometry task. Must be None if
358 run as part of PipelineTask.
359 photoRefObjLoader : `lsst.meas.algorithms.ReferenceObjectLoader`, optional
360 Reference object loader for photometry task. Must be None if
361 run as part of PipelineTask.
362 icSourceSchema : `lsst.afw.table.Schema`, optional
363 Schema for the icSource catalog.
364 initInputs : `dict`, optional
365 Dictionary that can contain a key ``icSourceSchema`` containing the
366 input schema. If present will override the value of ``icSourceSchema``.
367 """
368 ConfigClass = CalibrateConfig
369 _DefaultName = "calibrate"
371 def __init__(self, butler=None, astromRefObjLoader=None,
372 photoRefObjLoader=None, icSourceSchema=None,
373 initInputs=None, **kwargs):
374 super().__init__(**kwargs)
376 if butler is not None:
377 warnings.warn("The 'butler' parameter is no longer used and can be safely removed.",
378 category=FutureWarning, stacklevel=2)
379 butler = None
381 if initInputs is not None:
382 icSourceSchema = initInputs['icSourceSchema'].schema
384 if icSourceSchema is not None:
385 # use a schema mapper to avoid copying each field separately
386 self.schemaMapper = afwTable.SchemaMapper(icSourceSchema)
387 minimumSchema = afwTable.SourceTable.makeMinimalSchema()
388 self.schemaMapper.addMinimalSchema(minimumSchema, False)
390 # Add fields to copy from an icSource catalog
391 # and a field to indicate that the source matched a source in that
392 # catalog. If any fields are missing then raise an exception, but
393 # first find all missing fields in order to make the error message
394 # more useful.
395 self.calibSourceKey = self.schemaMapper.addOutputField(
396 afwTable.Field["Flag"]("calib_detected",
397 "Source was detected as an icSource"))
398 missingFieldNames = []
399 for fieldName in self.config.icSourceFieldsToCopy:
400 try:
401 schemaItem = icSourceSchema.find(fieldName)
402 except Exception:
403 missingFieldNames.append(fieldName)
404 else:
405 # field found; if addMapping fails then raise an exception
406 self.schemaMapper.addMapping(schemaItem.getKey())
408 if missingFieldNames:
409 raise RuntimeError("isSourceCat is missing fields {} "
410 "specified in icSourceFieldsToCopy"
411 .format(missingFieldNames))
413 # produce a temporary schema to pass to the subtasks; finalize it
414 # later
415 self.schema = self.schemaMapper.editOutputSchema()
416 else:
417 self.schemaMapper = None
418 self.schema = afwTable.SourceTable.makeMinimalSchema()
419 self.makeSubtask('detection', schema=self.schema)
421 self.algMetadata = dafBase.PropertyList()
423 if self.config.doDeblend:
424 self.makeSubtask("deblend", schema=self.schema)
425 if self.config.doSkySources:
426 self.makeSubtask("skySources")
427 self.skySourceKey = self.schema.addField("sky_source", type="Flag", doc="Sky objects.")
428 self.makeSubtask('measurement', schema=self.schema,
429 algMetadata=self.algMetadata)
430 self.makeSubtask('postCalibrationMeasurement', schema=self.schema,
431 algMetadata=self.algMetadata)
432 self.makeSubtask("setPrimaryFlags", schema=self.schema, isSingleFrame=True)
433 if self.config.doApCorr:
434 self.makeSubtask('applyApCorr', schema=self.schema)
435 self.makeSubtask('catalogCalculation', schema=self.schema)
437 if self.config.doAstrometry:
438 self.makeSubtask("astrometry", refObjLoader=astromRefObjLoader,
439 schema=self.schema)
440 if self.config.doPhotoCal:
441 self.makeSubtask("photoCal", refObjLoader=photoRefObjLoader,
442 schema=self.schema)
443 if self.config.doComputeSummaryStats:
444 self.makeSubtask('computeSummaryStats')
446 if initInputs is not None and (astromRefObjLoader is not None or photoRefObjLoader is not None):
447 raise RuntimeError("PipelineTask form of this task should not be initialized with "
448 "reference object loaders.")
450 if self.schemaMapper is not None:
451 # finalize the schema
452 self.schema = self.schemaMapper.getOutputSchema()
453 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
455 sourceCatSchema = afwTable.SourceCatalog(self.schema)
456 sourceCatSchema.getTable().setMetadata(self.algMetadata)
457 self.outputSchema = sourceCatSchema
459 def runQuantum(self, butlerQC, inputRefs, outputRefs):
460 inputs = butlerQC.get(inputRefs)
461 inputs['exposureIdInfo'] = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "visit_detector")
463 if self.config.doAstrometry:
464 refObjLoader = ReferenceObjectLoader(dataIds=[ref.datasetRef.dataId
465 for ref in inputRefs.astromRefCat],
466 refCats=inputs.pop('astromRefCat'),
467 config=self.config.astromRefObjLoader, log=self.log)
468 self.astrometry.setRefObjLoader(refObjLoader)
470 if self.config.doPhotoCal:
471 photoRefObjLoader = ReferenceObjectLoader(dataIds=[ref.datasetRef.dataId
472 for ref in inputRefs.photoRefCat],
473 refCats=inputs.pop('photoRefCat'),
474 config=self.config.photoRefObjLoader,
475 log=self.log)
476 self.photoCal.match.setRefObjLoader(photoRefObjLoader)
478 outputs = self.run(**inputs)
480 if self.config.doWriteMatches and self.config.doAstrometry:
481 normalizedMatches = afwTable.packMatches(outputs.astromMatches)
482 normalizedMatches.table.setMetadata(outputs.matchMeta)
483 if self.config.doWriteMatchesDenormalized:
484 denormMatches = denormalizeMatches(outputs.astromMatches, outputs.matchMeta)
485 outputs.matchesDenormalized = denormMatches
486 outputs.matches = normalizedMatches
487 butlerQC.put(outputs, outputRefs)
489 @timeMethod
490 def run(self, exposure, exposureIdInfo=None, background=None,
491 icSourceCat=None):
492 """Calibrate an exposure.
494 Parameters
495 ----------
496 exposure : `lsst.afw.image.ExposureF`
497 Exposure to calibrate.
498 exposureIdInfo : `lsst.obs.baseExposureIdInfo`, optional
499 Exposure ID info. If not provided, returned SourceCatalog IDs will not
500 be globally unique.
501 background : `lsst.afw.math.BackgroundList`, optional
502 Initial model of background already subtracted from exposure.
503 icSourceCat : `lsst.afw.image.SourceCatalog`, optional
504 SourceCatalog from CharacterizeImageTask from which we can copy some fields.
506 Returns
507 -------
508 result : `lsst.pipe.base.Struct`
509 Result structure with the following attributes:
511 ``exposure``
512 Characterized exposure (`lsst.afw.image.ExposureF`).
513 ``sourceCat``
514 Detected sources (`lsst.afw.table.SourceCatalog`).
515 ``outputBackground``
516 Model of subtracted background (`lsst.afw.math.BackgroundList`).
517 ``astromMatches``
518 List of source/ref matches from astrometry solver.
519 ``matchMeta``
520 Metadata from astrometry matches.
521 ``outputExposure``
522 Another reference to ``exposure`` for compatibility.
523 ``outputCat``
524 Another reference to ``sourceCat`` for compatibility.
525 """
526 # detect, deblend and measure sources
527 if exposureIdInfo is None:
528 exposureIdInfo = ExposureIdInfo()
530 if background is None:
531 background = BackgroundList()
532 sourceIdFactory = exposureIdInfo.makeSourceIdFactory()
533 table = SourceTable.make(self.schema, sourceIdFactory)
534 table.setMetadata(self.algMetadata)
536 detRes = self.detection.run(table=table, exposure=exposure,
537 doSmooth=True)
538 sourceCat = detRes.sources
539 if detRes.fpSets.background:
540 for bg in detRes.fpSets.background:
541 background.append(bg)
542 if self.config.doSkySources:
543 skySourceFootprints = self.skySources.run(mask=exposure.mask, seed=exposureIdInfo.expId)
544 if skySourceFootprints:
545 for foot in skySourceFootprints:
546 s = sourceCat.addNew()
547 s.setFootprint(foot)
548 s.set(self.skySourceKey, True)
549 if self.config.doDeblend:
550 self.deblend.run(exposure=exposure, sources=sourceCat)
551 self.measurement.run(
552 measCat=sourceCat,
553 exposure=exposure,
554 exposureId=exposureIdInfo.expId
555 )
556 if self.config.doApCorr:
557 self.applyApCorr.run(
558 catalog=sourceCat,
559 apCorrMap=exposure.getInfo().getApCorrMap()
560 )
561 self.catalogCalculation.run(sourceCat)
563 self.setPrimaryFlags.run(sourceCat)
565 if icSourceCat is not None and \
566 len(self.config.icSourceFieldsToCopy) > 0:
567 self.copyIcSourceFields(icSourceCat=icSourceCat,
568 sourceCat=sourceCat)
570 # TODO DM-11568: this contiguous check-and-copy could go away if we
571 # reserve enough space during SourceDetection and/or SourceDeblend.
572 # NOTE: sourceSelectors require contiguous catalogs, so ensure
573 # contiguity now, so views are preserved from here on.
574 if not sourceCat.isContiguous():
575 sourceCat = sourceCat.copy(deep=True)
577 # perform astrometry calibration:
578 # fit an improved WCS and update the exposure's WCS in place
579 astromMatches = None
580 matchMeta = None
581 if self.config.doAstrometry:
582 try:
583 astromRes = self.astrometry.run(
584 exposure=exposure,
585 sourceCat=sourceCat,
586 )
587 astromMatches = astromRes.matches
588 matchMeta = astromRes.matchMeta
589 except Exception as e:
590 if self.config.requireAstrometry:
591 raise
592 self.log.warning("Unable to perform astrometric calibration "
593 "(%s): attempting to proceed", e)
595 # compute photometric calibration
596 if self.config.doPhotoCal:
597 try:
598 photoRes = self.photoCal.run(exposure, sourceCat=sourceCat, expId=exposureIdInfo.expId)
599 exposure.setPhotoCalib(photoRes.photoCalib)
600 # TODO: reword this to phrase it in terms of the calibration factor?
601 self.log.info("Photometric zero-point: %f",
602 photoRes.photoCalib.instFluxToMagnitude(1.0))
603 self.setMetadata(exposure=exposure, photoRes=photoRes)
604 except Exception as e:
605 if self.config.requirePhotoCal:
606 raise
607 self.log.warning("Unable to perform photometric calibration "
608 "(%s): attempting to proceed", e)
609 self.setMetadata(exposure=exposure, photoRes=None)
611 self.postCalibrationMeasurement.run(
612 measCat=sourceCat,
613 exposure=exposure,
614 exposureId=exposureIdInfo.expId
615 )
617 if self.config.doComputeSummaryStats:
618 summary = self.computeSummaryStats.run(exposure=exposure,
619 sources=sourceCat,
620 background=background)
621 exposure.getInfo().setSummaryStats(summary)
623 frame = getDebugFrame(self._display, "calibrate")
624 if frame:
625 displayAstrometry(
626 sourceCat=sourceCat,
627 exposure=exposure,
628 matches=astromMatches,
629 frame=frame,
630 pause=False,
631 )
633 return pipeBase.Struct(
634 sourceCat=sourceCat,
635 astromMatches=astromMatches,
636 matchMeta=matchMeta,
637 outputExposure=exposure,
638 outputCat=sourceCat,
639 outputBackground=background,
640 )
642 def getSchemaCatalogs(self):
643 """Return a dict of empty catalogs for each catalog dataset produced
644 by this task.
645 """
646 sourceCat = afwTable.SourceCatalog(self.schema)
647 sourceCat.getTable().setMetadata(self.algMetadata)
648 return {"src": sourceCat}
650 def setMetadata(self, exposure, photoRes=None):
651 """Set task and exposure metadata.
653 Logs a warning continues if needed data is missing.
655 Parameters
656 ----------
657 exposure : `lsst.afw.image.ExposureF`
658 Exposure to set metadata on.
659 photoRes : `lsst.pipe.base.Struct`, optional
660 Result of running photoCal task.
661 """
662 if photoRes is None:
663 return
665 metadata = exposure.getMetadata()
667 # convert zero-point to (mag/sec/adu) for task MAGZERO metadata
668 try:
669 exposureTime = exposure.getInfo().getVisitInfo().getExposureTime()
670 magZero = photoRes.zp - 2.5*math.log10(exposureTime)
671 except Exception:
672 self.log.warning("Could not set normalized MAGZERO in header: no "
673 "exposure time")
674 magZero = math.nan
676 try:
677 metadata.set('MAGZERO', magZero)
678 metadata.set('MAGZERO_RMS', photoRes.sigma)
679 metadata.set('MAGZERO_NOBJ', photoRes.ngood)
680 metadata.set('COLORTERM1', 0.0)
681 metadata.set('COLORTERM2', 0.0)
682 metadata.set('COLORTERM3', 0.0)
683 except Exception as e:
684 self.log.warning("Could not set exposure metadata: %s", e)
686 def copyIcSourceFields(self, icSourceCat, sourceCat):
687 """Match sources in an icSourceCat and a sourceCat and copy fields.
689 The fields copied are those specified by ``config.icSourceFieldsToCopy``.
691 Parameters
692 ----------
693 icSourceCat : `lsst.afw.table.SourceCatalog`
694 Catalog from which to copy fields.
695 sourceCat : `lsst.afw.table.SourceCatalog`
696 Catalog to which to copy fields.
697 """
698 if self.schemaMapper is None:
699 raise RuntimeError("To copy icSource fields you must specify "
700 "icSourceSchema nd icSourceKeys when "
701 "constructing this task")
702 if icSourceCat is None or sourceCat is None:
703 raise RuntimeError("icSourceCat and sourceCat must both be "
704 "specified")
705 if len(self.config.icSourceFieldsToCopy) == 0:
706 self.log.warning("copyIcSourceFields doing nothing because "
707 "icSourceFieldsToCopy is empty")
708 return
710 mc = afwTable.MatchControl()
711 mc.findOnlyClosest = False # return all matched objects
712 matches = afwTable.matchXy(icSourceCat, sourceCat,
713 self.config.matchRadiusPix, mc)
714 if self.config.doDeblend:
715 deblendKey = sourceCat.schema["deblend_nChild"].asKey()
716 # if deblended, keep children
717 matches = [m for m in matches if m[1].get(deblendKey) == 0]
719 # Because we had to allow multiple matches to handle parents, we now
720 # need to prune to the best matches
721 # closest matches as a dict of icSourceCat source ID:
722 # (icSourceCat source, sourceCat source, distance in pixels)
723 bestMatches = {}
724 for m0, m1, d in matches:
725 id0 = m0.getId()
726 match = bestMatches.get(id0)
727 if match is None or d <= match[2]:
728 bestMatches[id0] = (m0, m1, d)
729 matches = list(bestMatches.values())
731 # Check that no sourceCat sources are listed twice (we already know
732 # that each match has a unique icSourceCat source ID, due to using
733 # that ID as the key in bestMatches)
734 numMatches = len(matches)
735 numUniqueSources = len(set(m[1].getId() for m in matches))
736 if numUniqueSources != numMatches:
737 self.log.warning("%d icSourceCat sources matched only %d sourceCat "
738 "sources", numMatches, numUniqueSources)
740 self.log.info("Copying flags from icSourceCat to sourceCat for "
741 "%d sources", numMatches)
743 # For each match: set the calibSourceKey flag and copy the desired
744 # fields
745 for icSrc, src, d in matches:
746 src.setFlag(self.calibSourceKey, True)
747 # src.assign copies the footprint from icSrc, which we don't want
748 # (DM-407)
749 # so set icSrc's footprint to src's footprint before src.assign,
750 # then restore it
751 icSrcFootprint = icSrc.getFootprint()
752 try:
753 icSrc.setFootprint(src.getFootprint())
754 src.assign(icSrc, self.schemaMapper)
755 finally:
756 icSrc.setFootprint(icSrcFootprint)