Coverage for python/lsst/pipe/tasks/calibrate.py: 19%
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1# This file is part of pipe_tasks.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
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 GNU General Public License
20# along with this program. If not, see <https://www.gnu.org/licenses/>.
22__all__ = ["CalibrateConfig", "CalibrateTask"]
24import math
25import numpy as np
27from lsstDebug import getDebugFrame
28import lsst.pex.config as pexConfig
29import lsst.pipe.base as pipeBase
30import lsst.pipe.base.connectionTypes as cT
31import lsst.afw.table as afwTable
32from lsst.meas.astrom import AstrometryTask, displayAstrometry, denormalizeMatches
33from lsst.meas.algorithms import LoadReferenceObjectsConfig, SkyObjectsTask
34import lsst.daf.base as dafBase
35from lsst.afw.math import BackgroundList
36from lsst.afw.table import SourceTable
37from lsst.meas.algorithms import SourceDetectionTask, ReferenceObjectLoader, SetPrimaryFlagsTask
38from lsst.meas.base import (SingleFrameMeasurementTask,
39 ApplyApCorrTask,
40 CatalogCalculationTask,
41 IdGenerator,
42 DetectorVisitIdGeneratorConfig)
43from lsst.meas.deblender import SourceDeblendTask
44from lsst.utils.timer import timeMethod
45from .photoCal import PhotoCalTask
46from .computeExposureSummaryStats import ComputeExposureSummaryStatsTask
49class CalibrateConnections(pipeBase.PipelineTaskConnections, dimensions=("instrument", "visit", "detector"),
50 defaultTemplates={}):
52 icSourceSchema = cT.InitInput(
53 doc="Schema produced by characterize image task, used to initialize this task",
54 name="icSrc_schema",
55 storageClass="SourceCatalog",
56 )
58 outputSchema = cT.InitOutput(
59 doc="Schema after CalibrateTask has been initialized",
60 name="src_schema",
61 storageClass="SourceCatalog",
62 )
64 exposure = cT.Input(
65 doc="Input image to calibrate",
66 name="icExp",
67 storageClass="ExposureF",
68 dimensions=("instrument", "visit", "detector"),
69 )
71 background = cT.Input(
72 doc="Backgrounds determined by characterize task",
73 name="icExpBackground",
74 storageClass="Background",
75 dimensions=("instrument", "visit", "detector"),
76 )
78 icSourceCat = cT.Input(
79 doc="Source catalog created by characterize task",
80 name="icSrc",
81 storageClass="SourceCatalog",
82 dimensions=("instrument", "visit", "detector"),
83 )
85 astromRefCat = cT.PrerequisiteInput(
86 doc="Reference catalog to use for astrometry",
87 name="gaia_dr3_20230707",
88 storageClass="SimpleCatalog",
89 dimensions=("skypix",),
90 deferLoad=True,
91 multiple=True,
92 )
94 photoRefCat = cT.PrerequisiteInput(
95 doc="Reference catalog to use for photometric calibration",
96 name="ps1_pv3_3pi_20170110",
97 storageClass="SimpleCatalog",
98 dimensions=("skypix",),
99 deferLoad=True,
100 multiple=True
101 )
103 outputExposure = cT.Output(
104 doc="Exposure after running calibration task",
105 name="calexp",
106 storageClass="ExposureF",
107 dimensions=("instrument", "visit", "detector"),
108 )
110 outputCat = cT.Output(
111 doc="Source catalog produced in calibrate task",
112 name="src",
113 storageClass="SourceCatalog",
114 dimensions=("instrument", "visit", "detector"),
115 )
117 outputBackground = cT.Output(
118 doc="Background models estimated in calibration task",
119 name="calexpBackground",
120 storageClass="Background",
121 dimensions=("instrument", "visit", "detector"),
122 )
124 matches = cT.Output(
125 doc="Source/refObj matches from the astrometry solver",
126 name="srcMatch",
127 storageClass="Catalog",
128 dimensions=("instrument", "visit", "detector"),
129 )
131 matchesDenormalized = cT.Output(
132 doc="Denormalized matches from astrometry solver",
133 name="srcMatchFull",
134 storageClass="Catalog",
135 dimensions=("instrument", "visit", "detector"),
136 )
138 def __init__(self, *, config=None):
139 super().__init__(config=config)
141 if config.doAstrometry is False:
142 self.prerequisiteInputs.remove("astromRefCat")
143 if config.doPhotoCal is False:
144 self.prerequisiteInputs.remove("photoRefCat")
146 if config.doWriteMatches is False or config.doAstrometry is False:
147 self.outputs.remove("matches")
148 if config.doWriteMatchesDenormalized is False or config.doAstrometry is False:
149 self.outputs.remove("matchesDenormalized")
152class CalibrateConfig(pipeBase.PipelineTaskConfig, pipelineConnections=CalibrateConnections):
153 """Config for CalibrateTask."""
155 doWrite = pexConfig.Field(
156 dtype=bool,
157 default=True,
158 doc="Save calibration results?",
159 )
160 doWriteHeavyFootprintsInSources = pexConfig.Field(
161 dtype=bool,
162 default=True,
163 doc="Include HeavyFootprint data in source table? If false then heavy "
164 "footprints are saved as normal footprints, which saves some space"
165 )
166 doWriteMatches = pexConfig.Field(
167 dtype=bool,
168 default=True,
169 doc="Write reference matches (ignored if doWrite or doAstrometry false)?",
170 )
171 doWriteMatchesDenormalized = pexConfig.Field(
172 dtype=bool,
173 default=True,
174 doc=("Write reference matches in denormalized format? "
175 "This format uses more disk space, but is more convenient to "
176 "read for debugging. Ignored if doWriteMatches=False or doWrite=False."),
177 )
178 doAstrometry = pexConfig.Field(
179 dtype=bool,
180 default=True,
181 doc="Perform astrometric calibration?",
182 )
183 astromRefObjLoader = pexConfig.ConfigField(
184 dtype=LoadReferenceObjectsConfig,
185 doc="reference object loader for astrometric calibration",
186 )
187 photoRefObjLoader = pexConfig.ConfigField(
188 dtype=LoadReferenceObjectsConfig,
189 doc="reference object loader for photometric calibration",
190 )
191 astrometry = pexConfig.ConfigurableField(
192 target=AstrometryTask,
193 doc="Perform astrometric calibration to refine the WCS",
194 )
195 requireAstrometry = pexConfig.Field(
196 dtype=bool,
197 default=True,
198 doc=("Raise an exception if astrometry fails? Ignored if doAstrometry "
199 "false."),
200 )
201 doPhotoCal = pexConfig.Field(
202 dtype=bool,
203 default=True,
204 doc="Perform phometric calibration?",
205 )
206 requirePhotoCal = pexConfig.Field(
207 dtype=bool,
208 default=True,
209 doc=("Raise an exception if photoCal fails? Ignored if doPhotoCal "
210 "false."),
211 )
212 photoCal = pexConfig.ConfigurableField(
213 target=PhotoCalTask,
214 doc="Perform photometric calibration",
215 )
216 icSourceFieldsToCopy = pexConfig.ListField(
217 dtype=str,
218 default=("calib_psf_candidate", "calib_psf_used", "calib_psf_reserved"),
219 doc=("Fields to copy from the icSource catalog to the output catalog "
220 "for matching sources Any missing fields will trigger a "
221 "RuntimeError exception. Ignored if icSourceCat is not provided.")
222 )
223 matchRadiusPix = pexConfig.Field(
224 dtype=float,
225 default=3,
226 doc=("Match radius for matching icSourceCat objects to sourceCat "
227 "objects (pixels)"),
228 )
229 checkUnitsParseStrict = pexConfig.Field(
230 doc=("Strictness of Astropy unit compatibility check, can be 'raise', "
231 "'warn' or 'silent'"),
232 dtype=str,
233 default="raise",
234 )
235 detection = pexConfig.ConfigurableField(
236 target=SourceDetectionTask,
237 doc="Detect sources"
238 )
239 doDeblend = pexConfig.Field(
240 dtype=bool,
241 default=True,
242 doc="Run deblender input exposure"
243 )
244 deblend = pexConfig.ConfigurableField(
245 target=SourceDeblendTask,
246 doc="Split blended sources into their components"
247 )
248 doSkySources = pexConfig.Field(
249 dtype=bool,
250 default=True,
251 doc="Generate sky sources?",
252 )
253 skySources = pexConfig.ConfigurableField(
254 target=SkyObjectsTask,
255 doc="Generate sky sources",
256 )
257 measurement = pexConfig.ConfigurableField(
258 target=SingleFrameMeasurementTask,
259 doc="Measure sources"
260 )
261 postCalibrationMeasurement = pexConfig.ConfigurableField(
262 target=SingleFrameMeasurementTask,
263 doc="Second round of measurement for plugins that need to be run after photocal"
264 )
265 setPrimaryFlags = pexConfig.ConfigurableField(
266 target=SetPrimaryFlagsTask,
267 doc=("Set flags for primary source classification in single frame "
268 "processing. True if sources are not sky sources and not a parent.")
269 )
270 doApCorr = pexConfig.Field(
271 dtype=bool,
272 default=True,
273 doc="Run subtask to apply aperture correction"
274 )
275 applyApCorr = pexConfig.ConfigurableField(
276 target=ApplyApCorrTask,
277 doc="Subtask to apply aperture corrections"
278 )
279 # If doApCorr is False, and the exposure does not have apcorrections
280 # already applied, the active plugins in catalogCalculation almost
281 # certainly should not contain the characterization plugin
282 catalogCalculation = pexConfig.ConfigurableField(
283 target=CatalogCalculationTask,
284 doc="Subtask to run catalogCalculation plugins on catalog"
285 )
286 doComputeSummaryStats = pexConfig.Field(
287 dtype=bool,
288 default=True,
289 doc="Run subtask to measure exposure summary statistics?"
290 )
291 computeSummaryStats = pexConfig.ConfigurableField(
292 target=ComputeExposureSummaryStatsTask,
293 doc="Subtask to run computeSummaryStats on exposure"
294 )
295 doWriteExposure = pexConfig.Field(
296 dtype=bool,
297 default=True,
298 doc="Write the calexp? If fakes have been added then we do not want to write out the calexp as a "
299 "normal calexp but as a fakes_calexp."
300 )
301 idGenerator = DetectorVisitIdGeneratorConfig.make_field()
303 def setDefaults(self):
304 super().setDefaults()
305 self.postCalibrationMeasurement.plugins.names = ["base_LocalPhotoCalib", "base_LocalWcs"]
306 self.postCalibrationMeasurement.doReplaceWithNoise = False
307 for key in self.postCalibrationMeasurement.slots:
308 setattr(self.postCalibrationMeasurement.slots, key, None)
309 self.astromRefObjLoader.anyFilterMapsToThis = "phot_g_mean"
310 # The photoRefCat connection is the name to use for the colorterms.
311 self.photoCal.photoCatName = self.connections.photoRefCat
313 # Keep track of which footprints contain streaks
314 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['STREAK']
315 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['STREAK']
318class CalibrateTask(pipeBase.PipelineTask):
319 """Calibrate an exposure: measure sources and perform astrometric and
320 photometric calibration.
322 Given an exposure with a good PSF model and aperture correction map(e.g. as
323 provided by `~lsst.pipe.tasks.characterizeImage.CharacterizeImageTask`),
324 perform the following operations:
325 - Run detection and measurement
326 - Run astrometry subtask to fit an improved WCS
327 - Run photoCal subtask to fit the exposure's photometric zero-point
329 Parameters
330 ----------
331 butler : `None`
332 Compatibility parameter. Should always be `None`.
333 astromRefObjLoader : `lsst.meas.algorithms.ReferenceObjectLoader`, optional
334 Unused in gen3: must be `None`.
335 photoRefObjLoader : `lsst.meas.algorithms.ReferenceObjectLoader`, optional
336 Unused in gen3: must be `None`.
337 icSourceSchema : `lsst.afw.table.Schema`, optional
338 Schema for the icSource catalog.
339 initInputs : `dict`, optional
340 Dictionary that can contain a key ``icSourceSchema`` containing the
341 input schema. If present will override the value of ``icSourceSchema``.
343 Raises
344 ------
345 RuntimeError
346 Raised if any of the following occur:
347 - isSourceCat is missing fields specified in icSourceFieldsToCopy.
348 - PipelineTask form of this task is initialized with reference object
349 loaders.
351 Notes
352 -----
353 Quantities set in exposure Metadata:
355 MAGZERO_RMS
356 MAGZERO's RMS == sigma reported by photoCal task
357 MAGZERO_NOBJ
358 Number of stars used == ngood reported by photoCal task
359 COLORTERM1
360 ?? (always 0.0)
361 COLORTERM2
362 ?? (always 0.0)
363 COLORTERM3
364 ?? (always 0.0)
366 Debugging:
367 CalibrateTask has a debug dictionary containing one key:
369 calibrate
370 frame (an int; <= 0 to not display) in which to display the exposure,
371 sources and matches. See @ref lsst.meas.astrom.displayAstrometry for
372 the meaning of the various symbols.
373 """
375 ConfigClass = CalibrateConfig
376 _DefaultName = "calibrate"
378 def __init__(self, astromRefObjLoader=None,
379 photoRefObjLoader=None, icSourceSchema=None,
380 initInputs=None, **kwargs):
381 super().__init__(**kwargs)
383 if initInputs is not None:
384 icSourceSchema = initInputs['icSourceSchema'].schema
386 if icSourceSchema is not None:
387 # use a schema mapper to avoid copying each field separately
388 self.schemaMapper = afwTable.SchemaMapper(icSourceSchema)
389 minimumSchema = afwTable.SourceTable.makeMinimalSchema()
390 self.schemaMapper.addMinimalSchema(minimumSchema, False)
392 # Add fields to copy from an icSource catalog
393 # and a field to indicate that the source matched a source in that
394 # catalog. If any fields are missing then raise an exception, but
395 # first find all missing fields in order to make the error message
396 # more useful.
397 self.calibSourceKey = self.schemaMapper.addOutputField(
398 afwTable.Field["Flag"]("calib_detected",
399 "Source was detected as an icSource"))
400 missingFieldNames = []
401 for fieldName in self.config.icSourceFieldsToCopy:
402 try:
403 schemaItem = icSourceSchema.find(fieldName)
404 except Exception:
405 missingFieldNames.append(fieldName)
406 else:
407 # field found; if addMapping fails then raise an exception
408 self.schemaMapper.addMapping(schemaItem.getKey())
410 if missingFieldNames:
411 raise RuntimeError("isSourceCat is missing fields {} "
412 "specified in icSourceFieldsToCopy"
413 .format(missingFieldNames))
415 # produce a temporary schema to pass to the subtasks; finalize it
416 # later
417 self.schema = self.schemaMapper.editOutputSchema()
418 else:
419 self.schemaMapper = None
420 self.schema = afwTable.SourceTable.makeMinimalSchema()
421 afwTable.CoordKey.addErrorFields(self.schema)
422 self.makeSubtask('detection', schema=self.schema)
424 self.algMetadata = dafBase.PropertyList()
426 if self.config.doDeblend:
427 self.makeSubtask("deblend", schema=self.schema)
428 if self.config.doSkySources:
429 self.makeSubtask("skySources")
430 self.skySourceKey = self.schema.addField("sky_source", type="Flag", doc="Sky objects.")
431 self.makeSubtask('measurement', schema=self.schema,
432 algMetadata=self.algMetadata)
433 self.makeSubtask('postCalibrationMeasurement', schema=self.schema,
434 algMetadata=self.algMetadata)
435 self.makeSubtask("setPrimaryFlags", schema=self.schema, isSingleFrame=True)
436 if self.config.doApCorr:
437 self.makeSubtask('applyApCorr', schema=self.schema)
438 self.makeSubtask('catalogCalculation', schema=self.schema)
440 if self.config.doAstrometry:
441 self.makeSubtask("astrometry", refObjLoader=astromRefObjLoader,
442 schema=self.schema)
443 if self.config.doPhotoCal:
444 self.makeSubtask("photoCal", refObjLoader=photoRefObjLoader,
445 schema=self.schema)
446 if self.config.doComputeSummaryStats:
447 self.makeSubtask('computeSummaryStats')
449 if initInputs is not None and (astromRefObjLoader is not None or photoRefObjLoader is not None):
450 raise RuntimeError("PipelineTask form of this task should not be initialized with "
451 "reference object loaders.")
453 if self.schemaMapper is not None:
454 # finalize the schema
455 self.schema = self.schemaMapper.getOutputSchema()
456 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
458 sourceCatSchema = afwTable.SourceCatalog(self.schema)
459 sourceCatSchema.getTable().setMetadata(self.algMetadata)
460 self.outputSchema = sourceCatSchema
462 def runQuantum(self, butlerQC, inputRefs, outputRefs):
463 inputs = butlerQC.get(inputRefs)
464 inputs['idGenerator'] = self.config.idGenerator.apply(butlerQC.quantum.dataId)
466 if self.config.doAstrometry:
467 refObjLoader = ReferenceObjectLoader(dataIds=[ref.datasetRef.dataId
468 for ref in inputRefs.astromRefCat],
469 refCats=inputs.pop('astromRefCat'),
470 name=self.config.connections.astromRefCat,
471 config=self.config.astromRefObjLoader, log=self.log)
472 self.astrometry.setRefObjLoader(refObjLoader)
474 if self.config.doPhotoCal:
475 photoRefObjLoader = ReferenceObjectLoader(dataIds=[ref.datasetRef.dataId
476 for ref in inputRefs.photoRefCat],
477 refCats=inputs.pop('photoRefCat'),
478 name=self.config.connections.photoRefCat,
479 config=self.config.photoRefObjLoader,
480 log=self.log)
481 self.photoCal.match.setRefObjLoader(photoRefObjLoader)
483 outputs = self.run(**inputs)
485 if self.config.doWriteMatches and self.config.doAstrometry:
486 if outputs.astromMatches is not None:
487 normalizedMatches = afwTable.packMatches(outputs.astromMatches)
488 normalizedMatches.table.setMetadata(outputs.matchMeta)
489 if self.config.doWriteMatchesDenormalized:
490 denormMatches = denormalizeMatches(outputs.astromMatches, outputs.matchMeta)
491 outputs.matchesDenormalized = denormMatches
492 outputs.matches = normalizedMatches
493 else:
494 del outputRefs.matches
495 if self.config.doWriteMatchesDenormalized:
496 del outputRefs.matchesDenormalized
497 butlerQC.put(outputs, outputRefs)
499 @timeMethod
500 def run(self, exposure, background=None,
501 icSourceCat=None, idGenerator=None):
502 """Calibrate an exposure.
504 Parameters
505 ----------
506 exposure : `lsst.afw.image.ExposureF`
507 Exposure to calibrate.
508 background : `lsst.afw.math.BackgroundList`, optional
509 Initial model of background already subtracted from exposure.
510 icSourceCat : `lsst.afw.image.SourceCatalog`, optional
511 SourceCatalog from CharacterizeImageTask from which we can copy
512 some fields.
513 idGenerator : `lsst.meas.base.IdGenerator`, optional
514 Object that generates source IDs and provides RNG seeds.
516 Returns
517 -------
518 result : `lsst.pipe.base.Struct`
519 Results as a struct with attributes:
521 ``exposure``
522 Characterized exposure (`lsst.afw.image.ExposureF`).
523 ``sourceCat``
524 Detected sources (`lsst.afw.table.SourceCatalog`).
525 ``outputBackground``
526 Model of subtracted background (`lsst.afw.math.BackgroundList`).
527 ``astromMatches``
528 List of source/ref matches from astrometry solver.
529 ``matchMeta``
530 Metadata from astrometry matches.
531 ``outputExposure``
532 Another reference to ``exposure`` for compatibility.
533 ``outputCat``
534 Another reference to ``sourceCat`` for compatibility.
535 """
536 # detect, deblend and measure sources
537 if idGenerator is None:
538 idGenerator = IdGenerator()
540 if background is None:
541 background = BackgroundList()
542 table = SourceTable.make(self.schema, idGenerator.make_table_id_factory())
543 table.setMetadata(self.algMetadata)
545 detRes = self.detection.run(table=table, exposure=exposure,
546 doSmooth=True)
547 sourceCat = detRes.sources
548 if detRes.background:
549 for bg in detRes.background:
550 background.append(bg)
551 if self.config.doSkySources:
552 skySourceFootprints = self.skySources.run(mask=exposure.mask, seed=idGenerator.catalog_id)
553 if skySourceFootprints:
554 for foot in skySourceFootprints:
555 s = sourceCat.addNew()
556 s.setFootprint(foot)
557 s.set(self.skySourceKey, True)
558 if self.config.doDeblend:
559 self.deblend.run(exposure=exposure, sources=sourceCat)
560 self.measurement.run(
561 measCat=sourceCat,
562 exposure=exposure,
563 exposureId=idGenerator.catalog_id,
564 )
565 if self.config.doApCorr:
566 apCorrMap = exposure.getInfo().getApCorrMap()
567 if apCorrMap is None:
568 self.log.warning("Image does not have valid aperture correction map for %r; "
569 "skipping aperture correction", idGenerator)
570 else:
571 self.applyApCorr.run(
572 catalog=sourceCat,
573 apCorrMap=apCorrMap,
574 )
575 self.catalogCalculation.run(sourceCat)
577 self.setPrimaryFlags.run(sourceCat)
579 if icSourceCat is not None and \
580 len(self.config.icSourceFieldsToCopy) > 0:
581 self.copyIcSourceFields(icSourceCat=icSourceCat,
582 sourceCat=sourceCat)
584 # TODO DM-11568: this contiguous check-and-copy could go away if we
585 # reserve enough space during SourceDetection and/or SourceDeblend.
586 # NOTE: sourceSelectors require contiguous catalogs, so ensure
587 # contiguity now, so views are preserved from here on.
588 if not sourceCat.isContiguous():
589 sourceCat = sourceCat.copy(deep=True)
591 # perform astrometry calibration:
592 # fit an improved WCS and update the exposure's WCS in place
593 astromMatches = None
594 matchMeta = None
595 if self.config.doAstrometry:
596 astromRes = self.astrometry.run(
597 exposure=exposure,
598 sourceCat=sourceCat,
599 )
600 astromMatches = astromRes.matches
601 matchMeta = astromRes.matchMeta
602 if exposure.getWcs() is None:
603 if self.config.requireAstrometry:
604 raise RuntimeError(f"WCS fit failed for {idGenerator} and requireAstrometry "
605 "is True.")
606 else:
607 self.log.warning("Unable to perform astrometric calibration for %r but "
608 "requireAstrometry is False: attempting to proceed...",
609 idGenerator)
611 # compute photometric calibration
612 if self.config.doPhotoCal:
613 if np.all(np.isnan(sourceCat["coord_ra"])) or np.all(np.isnan(sourceCat["coord_dec"])):
614 if self.config.requirePhotoCal:
615 raise RuntimeError(f"Astrometry failed for {idGenerator}, so cannot do "
616 "photoCal, but requirePhotoCal is True.")
617 self.log.warning("Astrometry failed for %r, so cannot do photoCal. requirePhotoCal "
618 "is False, so skipping photometric calibration and setting photoCalib "
619 "to None. Attempting to proceed...", idGenerator)
620 exposure.setPhotoCalib(None)
621 self.setMetadata(exposure=exposure, photoRes=None)
622 else:
623 try:
624 photoRes = self.photoCal.run(
625 exposure, sourceCat=sourceCat, expId=idGenerator.catalog_id
626 )
627 exposure.setPhotoCalib(photoRes.photoCalib)
628 # TODO: reword this to phrase it in terms of the
629 # calibration factor?
630 self.log.info("Photometric zero-point: %f",
631 photoRes.photoCalib.instFluxToMagnitude(1.0))
632 self.setMetadata(exposure=exposure, photoRes=photoRes)
633 except Exception as e:
634 if self.config.requirePhotoCal:
635 raise
636 self.log.warning("Unable to perform photometric calibration "
637 "(%s): attempting to proceed", e)
638 self.setMetadata(exposure=exposure, photoRes=None)
640 self.postCalibrationMeasurement.run(
641 measCat=sourceCat,
642 exposure=exposure,
643 exposureId=idGenerator.catalog_id,
644 )
646 if self.config.doComputeSummaryStats:
647 summary = self.computeSummaryStats.run(exposure=exposure,
648 sources=sourceCat,
649 background=background)
650 exposure.getInfo().setSummaryStats(summary)
652 frame = getDebugFrame(self._display, "calibrate")
653 if frame:
654 displayAstrometry(
655 sourceCat=sourceCat,
656 exposure=exposure,
657 matches=astromMatches,
658 frame=frame,
659 pause=False,
660 )
662 return pipeBase.Struct(
663 sourceCat=sourceCat,
664 astromMatches=astromMatches,
665 matchMeta=matchMeta,
666 outputExposure=exposure,
667 outputCat=sourceCat,
668 outputBackground=background,
669 )
671 def setMetadata(self, exposure, photoRes=None):
672 """Set task and exposure metadata.
674 Logs a warning continues if needed data is missing.
676 Parameters
677 ----------
678 exposure : `lsst.afw.image.ExposureF`
679 Exposure to set metadata on.
680 photoRes : `lsst.pipe.base.Struct`, optional
681 Result of running photoCal task.
682 """
683 if photoRes is None:
684 return
686 metadata = exposure.getMetadata()
688 # convert zero-point to (mag/sec/adu) for task MAGZERO metadata
689 try:
690 exposureTime = exposure.getInfo().getVisitInfo().getExposureTime()
691 magZero = photoRes.zp - 2.5*math.log10(exposureTime)
692 except Exception:
693 self.log.warning("Could not set normalized MAGZERO in header: no "
694 "exposure time")
695 magZero = math.nan
697 try:
698 metadata.set('MAGZERO', magZero)
699 metadata.set('MAGZERO_RMS', photoRes.sigma)
700 metadata.set('MAGZERO_NOBJ', photoRes.ngood)
701 metadata.set('COLORTERM1', 0.0)
702 metadata.set('COLORTERM2', 0.0)
703 metadata.set('COLORTERM3', 0.0)
704 except Exception as e:
705 self.log.warning("Could not set exposure metadata: %s", e)
707 def copyIcSourceFields(self, icSourceCat, sourceCat):
708 """Match sources in an icSourceCat and a sourceCat and copy fields.
710 The fields copied are those specified by
711 ``config.icSourceFieldsToCopy``.
713 Parameters
714 ----------
715 icSourceCat : `lsst.afw.table.SourceCatalog`
716 Catalog from which to copy fields.
717 sourceCat : `lsst.afw.table.SourceCatalog`
718 Catalog to which to copy fields.
720 Raises
721 ------
722 RuntimeError
723 Raised if any of the following occur:
724 - icSourceSchema and icSourceKeys are not specified.
725 - icSourceCat and sourceCat are not specified.
726 - icSourceFieldsToCopy is empty.
727 """
728 if self.schemaMapper is None:
729 raise RuntimeError("To copy icSource fields you must specify "
730 "icSourceSchema and icSourceKeys when "
731 "constructing this task")
732 if icSourceCat is None or sourceCat is None:
733 raise RuntimeError("icSourceCat and sourceCat must both be "
734 "specified")
735 if len(self.config.icSourceFieldsToCopy) == 0:
736 self.log.warning("copyIcSourceFields doing nothing because "
737 "icSourceFieldsToCopy is empty")
738 return
740 mc = afwTable.MatchControl()
741 mc.findOnlyClosest = False # return all matched objects
742 matches = afwTable.matchXy(icSourceCat, sourceCat,
743 self.config.matchRadiusPix, mc)
744 if self.config.doDeblend:
745 deblendKey = sourceCat.schema["deblend_nChild"].asKey()
746 # if deblended, keep children
747 matches = [m for m in matches if m[1].get(deblendKey) == 0]
749 # Because we had to allow multiple matches to handle parents, we now
750 # need to prune to the best matches
751 # closest matches as a dict of icSourceCat source ID:
752 # (icSourceCat source, sourceCat source, distance in pixels)
753 bestMatches = {}
754 for m0, m1, d in matches:
755 id0 = m0.getId()
756 match = bestMatches.get(id0)
757 if match is None or d <= match[2]:
758 bestMatches[id0] = (m0, m1, d)
759 matches = list(bestMatches.values())
761 # Check that no sourceCat sources are listed twice (we already know
762 # that each match has a unique icSourceCat source ID, due to using
763 # that ID as the key in bestMatches)
764 numMatches = len(matches)
765 numUniqueSources = len(set(m[1].getId() for m in matches))
766 if numUniqueSources != numMatches:
767 self.log.warning("%d icSourceCat sources matched only %d sourceCat "
768 "sources", numMatches, numUniqueSources)
770 self.log.info("Copying flags from icSourceCat to sourceCat for "
771 "%d sources", numMatches)
773 # For each match: set the calibSourceKey flag and copy the desired
774 # fields
775 for icSrc, src, d in matches:
776 src.setFlag(self.calibSourceKey, True)
777 # src.assign copies the footprint from icSrc, which we don't want
778 # (DM-407)
779 # so set icSrc's footprint to src's footprint before src.assign,
780 # then restore it
781 icSrcFootprint = icSrc.getFootprint()
782 try:
783 icSrc.setFootprint(src.getFootprint())
784 src.assign(icSrc, self.schemaMapper)
785 finally:
786 icSrc.setFootprint(icSrcFootprint)