Coverage for python/lsst/pipe/tasks/calibrate.py: 22%
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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
330class CalibrateTask(pipeBase.PipelineTask):
331 """Task to calibrate an exposure.
333 Parameters
334 ----------
335 butler : `None`
336 Compatibility parameter. Should always be `None`.
337 astromRefObjLoader : `lsst.meas.algorithms.ReferenceObjectLoader`, optional
338 Reference object loader for astrometry task. Must be None if
339 run as part of PipelineTask.
340 photoRefObjLoader : `lsst.meas.algorithms.ReferenceObjectLoader`, optional
341 Reference object loader for photometry task. Must be None if
342 run as part of PipelineTask.
343 icSourceSchema : `lsst.afw.table.Schema`, optional
344 Schema for the icSource catalog.
345 initInputs : `dict`, optional
346 Dictionary that can contain a key ``icSourceSchema`` containing the
347 input schema. If present will override the value of ``icSourceSchema``.
348 """
349 ConfigClass = CalibrateConfig
350 _DefaultName = "calibrate"
352 def __init__(self, butler=None, astromRefObjLoader=None,
353 photoRefObjLoader=None, icSourceSchema=None,
354 initInputs=None, **kwargs):
355 super().__init__(**kwargs)
357 if butler is not None:
358 warnings.warn("The 'butler' parameter is no longer used and can be safely removed.",
359 category=FutureWarning, stacklevel=2)
360 butler = None
362 if initInputs is not None:
363 icSourceSchema = initInputs['icSourceSchema'].schema
365 if icSourceSchema is not None:
366 # use a schema mapper to avoid copying each field separately
367 self.schemaMapper = afwTable.SchemaMapper(icSourceSchema)
368 minimumSchema = afwTable.SourceTable.makeMinimalSchema()
369 self.schemaMapper.addMinimalSchema(minimumSchema, False)
371 # Add fields to copy from an icSource catalog
372 # and a field to indicate that the source matched a source in that
373 # catalog. If any fields are missing then raise an exception, but
374 # first find all missing fields in order to make the error message
375 # more useful.
376 self.calibSourceKey = self.schemaMapper.addOutputField(
377 afwTable.Field["Flag"]("calib_detected",
378 "Source was detected as an icSource"))
379 missingFieldNames = []
380 for fieldName in self.config.icSourceFieldsToCopy:
381 try:
382 schemaItem = icSourceSchema.find(fieldName)
383 except Exception:
384 missingFieldNames.append(fieldName)
385 else:
386 # field found; if addMapping fails then raise an exception
387 self.schemaMapper.addMapping(schemaItem.getKey())
389 if missingFieldNames:
390 raise RuntimeError("isSourceCat is missing fields {} "
391 "specified in icSourceFieldsToCopy"
392 .format(missingFieldNames))
394 # produce a temporary schema to pass to the subtasks; finalize it
395 # later
396 self.schema = self.schemaMapper.editOutputSchema()
397 else:
398 self.schemaMapper = None
399 self.schema = afwTable.SourceTable.makeMinimalSchema()
400 self.makeSubtask('detection', schema=self.schema)
402 self.algMetadata = dafBase.PropertyList()
404 if self.config.doDeblend:
405 self.makeSubtask("deblend", schema=self.schema)
406 if self.config.doSkySources:
407 self.makeSubtask("skySources")
408 self.skySourceKey = self.schema.addField("sky_source", type="Flag", doc="Sky objects.")
409 self.makeSubtask('measurement', schema=self.schema,
410 algMetadata=self.algMetadata)
411 self.makeSubtask('postCalibrationMeasurement', schema=self.schema,
412 algMetadata=self.algMetadata)
413 self.makeSubtask("setPrimaryFlags", schema=self.schema, isSingleFrame=True)
414 if self.config.doApCorr:
415 self.makeSubtask('applyApCorr', schema=self.schema)
416 self.makeSubtask('catalogCalculation', schema=self.schema)
418 if self.config.doAstrometry:
419 self.makeSubtask("astrometry", refObjLoader=astromRefObjLoader,
420 schema=self.schema)
421 if self.config.doPhotoCal:
422 self.makeSubtask("photoCal", refObjLoader=photoRefObjLoader,
423 schema=self.schema)
424 if self.config.doComputeSummaryStats:
425 self.makeSubtask('computeSummaryStats')
427 if initInputs is not None and (astromRefObjLoader is not None or photoRefObjLoader is not None):
428 raise RuntimeError("PipelineTask form of this task should not be initialized with "
429 "reference object loaders.")
431 if self.schemaMapper is not None:
432 # finalize the schema
433 self.schema = self.schemaMapper.getOutputSchema()
434 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
436 sourceCatSchema = afwTable.SourceCatalog(self.schema)
437 sourceCatSchema.getTable().setMetadata(self.algMetadata)
438 self.outputSchema = sourceCatSchema
440 def runQuantum(self, butlerQC, inputRefs, outputRefs):
441 inputs = butlerQC.get(inputRefs)
442 inputs['exposureIdInfo'] = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "visit_detector")
444 if self.config.doAstrometry:
445 refObjLoader = ReferenceObjectLoader(dataIds=[ref.datasetRef.dataId
446 for ref in inputRefs.astromRefCat],
447 refCats=inputs.pop('astromRefCat'),
448 name=self.config.connections.astromRefCat,
449 config=self.config.astromRefObjLoader, log=self.log)
450 self.astrometry.setRefObjLoader(refObjLoader)
452 if self.config.doPhotoCal:
453 photoRefObjLoader = ReferenceObjectLoader(dataIds=[ref.datasetRef.dataId
454 for ref in inputRefs.photoRefCat],
455 refCats=inputs.pop('photoRefCat'),
456 name=self.config.connections.photoRefCat,
457 config=self.config.photoRefObjLoader,
458 log=self.log)
459 self.photoCal.match.setRefObjLoader(photoRefObjLoader)
461 outputs = self.run(**inputs)
463 if self.config.doWriteMatches and self.config.doAstrometry:
464 normalizedMatches = afwTable.packMatches(outputs.astromMatches)
465 normalizedMatches.table.setMetadata(outputs.matchMeta)
466 if self.config.doWriteMatchesDenormalized:
467 denormMatches = denormalizeMatches(outputs.astromMatches, outputs.matchMeta)
468 outputs.matchesDenormalized = denormMatches
469 outputs.matches = normalizedMatches
470 butlerQC.put(outputs, outputRefs)
472 @timeMethod
473 def run(self, exposure, exposureIdInfo=None, background=None,
474 icSourceCat=None):
475 """Calibrate an exposure.
477 Parameters
478 ----------
479 exposure : `lsst.afw.image.ExposureF`
480 Exposure to calibrate.
481 exposureIdInfo : `lsst.obs.baseExposureIdInfo`, optional
482 Exposure ID info. If not provided, returned SourceCatalog IDs will not
483 be globally unique.
484 background : `lsst.afw.math.BackgroundList`, optional
485 Initial model of background already subtracted from exposure.
486 icSourceCat : `lsst.afw.image.SourceCatalog`, optional
487 SourceCatalog from CharacterizeImageTask from which we can copy some fields.
489 Returns
490 -------
491 result : `lsst.pipe.base.Struct`
492 Result structure with the following attributes:
494 ``exposure``
495 Characterized exposure (`lsst.afw.image.ExposureF`).
496 ``sourceCat``
497 Detected sources (`lsst.afw.table.SourceCatalog`).
498 ``outputBackground``
499 Model of subtracted background (`lsst.afw.math.BackgroundList`).
500 ``astromMatches``
501 List of source/ref matches from astrometry solver.
502 ``matchMeta``
503 Metadata from astrometry matches.
504 ``outputExposure``
505 Another reference to ``exposure`` for compatibility.
506 ``outputCat``
507 Another reference to ``sourceCat`` for compatibility.
508 """
509 # detect, deblend and measure sources
510 if exposureIdInfo is None:
511 exposureIdInfo = ExposureIdInfo()
513 if background is None:
514 background = BackgroundList()
515 sourceIdFactory = exposureIdInfo.makeSourceIdFactory()
516 table = SourceTable.make(self.schema, sourceIdFactory)
517 table.setMetadata(self.algMetadata)
519 detRes = self.detection.run(table=table, exposure=exposure,
520 doSmooth=True)
521 sourceCat = detRes.sources
522 if detRes.fpSets.background:
523 for bg in detRes.fpSets.background:
524 background.append(bg)
525 if self.config.doSkySources:
526 skySourceFootprints = self.skySources.run(mask=exposure.mask, seed=exposureIdInfo.expId)
527 if skySourceFootprints:
528 for foot in skySourceFootprints:
529 s = sourceCat.addNew()
530 s.setFootprint(foot)
531 s.set(self.skySourceKey, True)
532 if self.config.doDeblend:
533 self.deblend.run(exposure=exposure, sources=sourceCat)
534 self.measurement.run(
535 measCat=sourceCat,
536 exposure=exposure,
537 exposureId=exposureIdInfo.expId
538 )
539 if self.config.doApCorr:
540 self.applyApCorr.run(
541 catalog=sourceCat,
542 apCorrMap=exposure.getInfo().getApCorrMap()
543 )
544 self.catalogCalculation.run(sourceCat)
546 self.setPrimaryFlags.run(sourceCat)
548 if icSourceCat is not None and \
549 len(self.config.icSourceFieldsToCopy) > 0:
550 self.copyIcSourceFields(icSourceCat=icSourceCat,
551 sourceCat=sourceCat)
553 # TODO DM-11568: this contiguous check-and-copy could go away if we
554 # reserve enough space during SourceDetection and/or SourceDeblend.
555 # NOTE: sourceSelectors require contiguous catalogs, so ensure
556 # contiguity now, so views are preserved from here on.
557 if not sourceCat.isContiguous():
558 sourceCat = sourceCat.copy(deep=True)
560 # perform astrometry calibration:
561 # fit an improved WCS and update the exposure's WCS in place
562 astromMatches = None
563 matchMeta = None
564 if self.config.doAstrometry:
565 try:
566 astromRes = self.astrometry.run(
567 exposure=exposure,
568 sourceCat=sourceCat,
569 )
570 astromMatches = astromRes.matches
571 matchMeta = astromRes.matchMeta
572 except Exception as e:
573 if self.config.requireAstrometry:
574 raise
575 self.log.warning("Unable to perform astrometric calibration "
576 "(%s): attempting to proceed", e)
578 # compute photometric calibration
579 if self.config.doPhotoCal:
580 try:
581 photoRes = self.photoCal.run(exposure, sourceCat=sourceCat, expId=exposureIdInfo.expId)
582 exposure.setPhotoCalib(photoRes.photoCalib)
583 # TODO: reword this to phrase it in terms of the calibration factor?
584 self.log.info("Photometric zero-point: %f",
585 photoRes.photoCalib.instFluxToMagnitude(1.0))
586 self.setMetadata(exposure=exposure, photoRes=photoRes)
587 except Exception as e:
588 if self.config.requirePhotoCal:
589 raise
590 self.log.warning("Unable to perform photometric calibration "
591 "(%s): attempting to proceed", e)
592 self.setMetadata(exposure=exposure, photoRes=None)
594 self.postCalibrationMeasurement.run(
595 measCat=sourceCat,
596 exposure=exposure,
597 exposureId=exposureIdInfo.expId
598 )
600 if self.config.doComputeSummaryStats:
601 summary = self.computeSummaryStats.run(exposure=exposure,
602 sources=sourceCat,
603 background=background)
604 exposure.getInfo().setSummaryStats(summary)
606 frame = getDebugFrame(self._display, "calibrate")
607 if frame:
608 displayAstrometry(
609 sourceCat=sourceCat,
610 exposure=exposure,
611 matches=astromMatches,
612 frame=frame,
613 pause=False,
614 )
616 return pipeBase.Struct(
617 sourceCat=sourceCat,
618 astromMatches=astromMatches,
619 matchMeta=matchMeta,
620 outputExposure=exposure,
621 outputCat=sourceCat,
622 outputBackground=background,
623 )
625 def getSchemaCatalogs(self):
626 """Return a dict of empty catalogs for each catalog dataset produced
627 by this task.
628 """
629 sourceCat = afwTable.SourceCatalog(self.schema)
630 sourceCat.getTable().setMetadata(self.algMetadata)
631 return {"src": sourceCat}
633 def setMetadata(self, exposure, photoRes=None):
634 """Set task and exposure metadata.
636 Logs a warning continues if needed data is missing.
638 Parameters
639 ----------
640 exposure : `lsst.afw.image.ExposureF`
641 Exposure to set metadata on.
642 photoRes : `lsst.pipe.base.Struct`, optional
643 Result of running photoCal task.
644 """
645 if photoRes is None:
646 return
648 metadata = exposure.getMetadata()
650 # convert zero-point to (mag/sec/adu) for task MAGZERO metadata
651 try:
652 exposureTime = exposure.getInfo().getVisitInfo().getExposureTime()
653 magZero = photoRes.zp - 2.5*math.log10(exposureTime)
654 except Exception:
655 self.log.warning("Could not set normalized MAGZERO in header: no "
656 "exposure time")
657 magZero = math.nan
659 try:
660 metadata.set('MAGZERO', magZero)
661 metadata.set('MAGZERO_RMS', photoRes.sigma)
662 metadata.set('MAGZERO_NOBJ', photoRes.ngood)
663 metadata.set('COLORTERM1', 0.0)
664 metadata.set('COLORTERM2', 0.0)
665 metadata.set('COLORTERM3', 0.0)
666 except Exception as e:
667 self.log.warning("Could not set exposure metadata: %s", e)
669 def copyIcSourceFields(self, icSourceCat, sourceCat):
670 """Match sources in an icSourceCat and a sourceCat and copy fields.
672 The fields copied are those specified by ``config.icSourceFieldsToCopy``.
674 Parameters
675 ----------
676 icSourceCat : `lsst.afw.table.SourceCatalog`
677 Catalog from which to copy fields.
678 sourceCat : `lsst.afw.table.SourceCatalog`
679 Catalog to which to copy fields.
680 """
681 if self.schemaMapper is None:
682 raise RuntimeError("To copy icSource fields you must specify "
683 "icSourceSchema nd icSourceKeys when "
684 "constructing this task")
685 if icSourceCat is None or sourceCat is None:
686 raise RuntimeError("icSourceCat and sourceCat must both be "
687 "specified")
688 if len(self.config.icSourceFieldsToCopy) == 0:
689 self.log.warning("copyIcSourceFields doing nothing because "
690 "icSourceFieldsToCopy is empty")
691 return
693 mc = afwTable.MatchControl()
694 mc.findOnlyClosest = False # return all matched objects
695 matches = afwTable.matchXy(icSourceCat, sourceCat,
696 self.config.matchRadiusPix, mc)
697 if self.config.doDeblend:
698 deblendKey = sourceCat.schema["deblend_nChild"].asKey()
699 # if deblended, keep children
700 matches = [m for m in matches if m[1].get(deblendKey) == 0]
702 # Because we had to allow multiple matches to handle parents, we now
703 # need to prune to the best matches
704 # closest matches as a dict of icSourceCat source ID:
705 # (icSourceCat source, sourceCat source, distance in pixels)
706 bestMatches = {}
707 for m0, m1, d in matches:
708 id0 = m0.getId()
709 match = bestMatches.get(id0)
710 if match is None or d <= match[2]:
711 bestMatches[id0] = (m0, m1, d)
712 matches = list(bestMatches.values())
714 # Check that no sourceCat sources are listed twice (we already know
715 # that each match has a unique icSourceCat source ID, due to using
716 # that ID as the key in bestMatches)
717 numMatches = len(matches)
718 numUniqueSources = len(set(m[1].getId() for m in matches))
719 if numUniqueSources != numMatches:
720 self.log.warning("%d icSourceCat sources matched only %d sourceCat "
721 "sources", numMatches, numUniqueSources)
723 self.log.info("Copying flags from icSourceCat to sourceCat for "
724 "%d sources", numMatches)
726 # For each match: set the calibSourceKey flag and copy the desired
727 # fields
728 for icSrc, src, d in matches:
729 src.setFlag(self.calibSourceKey, True)
730 # src.assign copies the footprint from icSrc, which we don't want
731 # (DM-407)
732 # so set icSrc's footprint to src's footprint before src.assign,
733 # then restore it
734 icSrcFootprint = icSrc.getFootprint()
735 try:
736 icSrc.setFootprint(src.getFootprint())
737 src.assign(icSrc, self.schemaMapper)
738 finally:
739 icSrc.setFootprint(icSrcFootprint)