Coverage for python/lsst/pipe/tasks/calibrate.py: 20%
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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
10# the Free Software Foundation, either version 3 of the License, or
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#
18# You should have received a copy of the LSST License Statement and
19# the GNU General Public License along with this program. If not,
20# see <https://www.lsstcorp.org/LegalNotices/>.
21#
22import math
24from lsstDebug import getDebugFrame
25import lsst.pex.config as pexConfig
26import lsst.pipe.base as pipeBase
27import lsst.pipe.base.connectionTypes as cT
28import lsst.afw.table as afwTable
29from lsst.meas.astrom import AstrometryTask, displayAstrometry, denormalizeMatches
30from lsst.meas.algorithms import LoadIndexedReferenceObjectsTask, SkyObjectsTask
31from lsst.obs.base import ExposureIdInfo
32import lsst.daf.base as dafBase
33from lsst.afw.math import BackgroundList
34from lsst.afw.table import SourceTable
35from lsst.meas.algorithms import SourceDetectionTask, ReferenceObjectLoader
36from lsst.meas.base import (SingleFrameMeasurementTask,
37 ApplyApCorrTask,
38 CatalogCalculationTask)
39from lsst.meas.deblender import SourceDeblendTask
40from lsst.utils.timer import timeMethod
41from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask
42from .fakes import BaseFakeSourcesTask
43from .photoCal import PhotoCalTask
44from .computeExposureSummaryStats import ComputeExposureSummaryStatsTask
47__all__ = ["CalibrateConfig", "CalibrateTask"]
50class CalibrateConnections(pipeBase.PipelineTaskConnections, dimensions=("instrument", "visit", "detector"),
51 defaultTemplates={}):
53 icSourceSchema = cT.InitInput(
54 doc="Schema produced by characterize image task, used to initialize this task",
55 name="icSrc_schema",
56 storageClass="SourceCatalog",
57 )
59 outputSchema = cT.InitOutput(
60 doc="Schema after CalibrateTask has been initialized",
61 name="src_schema",
62 storageClass="SourceCatalog",
63 )
65 exposure = cT.Input(
66 doc="Input image to calibrate",
67 name="icExp",
68 storageClass="ExposureF",
69 dimensions=("instrument", "visit", "detector"),
70 )
72 background = cT.Input(
73 doc="Backgrounds determined by characterize task",
74 name="icExpBackground",
75 storageClass="Background",
76 dimensions=("instrument", "visit", "detector"),
77 )
79 icSourceCat = cT.Input(
80 doc="Source catalog created by characterize task",
81 name="icSrc",
82 storageClass="SourceCatalog",
83 dimensions=("instrument", "visit", "detector"),
84 )
86 astromRefCat = cT.PrerequisiteInput(
87 doc="Reference catalog to use for astrometry",
88 name="gaia_dr2_20200414",
89 storageClass="SimpleCatalog",
90 dimensions=("skypix",),
91 deferLoad=True,
92 multiple=True,
93 )
95 photoRefCat = cT.PrerequisiteInput(
96 doc="Reference catalog to use for photometric calibration",
97 name="ps1_pv3_3pi_20170110",
98 storageClass="SimpleCatalog",
99 dimensions=("skypix",),
100 deferLoad=True,
101 multiple=True
102 )
104 outputExposure = cT.Output(
105 doc="Exposure after running calibration task",
106 name="calexp",
107 storageClass="ExposureF",
108 dimensions=("instrument", "visit", "detector"),
109 )
111 outputCat = cT.Output(
112 doc="Source catalog produced in calibrate task",
113 name="src",
114 storageClass="SourceCatalog",
115 dimensions=("instrument", "visit", "detector"),
116 )
118 outputBackground = cT.Output(
119 doc="Background models estimated in calibration task",
120 name="calexpBackground",
121 storageClass="Background",
122 dimensions=("instrument", "visit", "detector"),
123 )
125 matches = cT.Output(
126 doc="Source/refObj matches from the astrometry solver",
127 name="srcMatch",
128 storageClass="Catalog",
129 dimensions=("instrument", "visit", "detector"),
130 )
132 matchesDenormalized = cT.Output(
133 doc="Denormalized matches from astrometry solver",
134 name="srcMatchFull",
135 storageClass="Catalog",
136 dimensions=("instrument", "visit", "detector"),
137 )
139 def __init__(self, *, config=None):
140 super().__init__(config=config)
142 if config.doAstrometry is False:
143 self.prerequisiteInputs.remove("astromRefCat")
144 if config.doPhotoCal is False:
145 self.prerequisiteInputs.remove("photoRefCat")
147 if config.doWriteMatches is False or config.doAstrometry is False:
148 self.outputs.remove("matches")
149 if config.doWriteMatchesDenormalized is False or config.doAstrometry is False:
150 self.outputs.remove("matchesDenormalized")
153class CalibrateConfig(pipeBase.PipelineTaskConfig, pipelineConnections=CalibrateConnections):
154 """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=False,
174 doc=("Write reference matches in denormalized format? "
175 "This format uses more disk space, but is more convenient to "
176 "read. 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.ConfigurableField(
184 target=LoadIndexedReferenceObjectsTask,
185 doc="reference object loader for astrometric calibration",
186 )
187 photoRefObjLoader = pexConfig.ConfigurableField(
188 target=LoadIndexedReferenceObjectsTask,
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 doInsertFakes = pexConfig.Field(
287 dtype=bool,
288 default=False,
289 doc="Run fake sources injection task",
290 deprecated=("doInsertFakes is no longer supported. This config will be removed after v24. "
291 "Please use ProcessCcdWithFakesTask instead.")
292 )
293 insertFakes = pexConfig.ConfigurableField(
294 target=BaseFakeSourcesTask,
295 doc="Injection of fake sources for testing purposes (must be "
296 "retargeted)",
297 deprecated=("insertFakes is no longer supported. This config will be removed after v24. "
298 "Please use ProcessCcdWithFakesTask instead.")
299 )
300 doComputeSummaryStats = pexConfig.Field(
301 dtype=bool,
302 default=True,
303 doc="Run subtask to measure exposure summary statistics?"
304 )
305 computeSummaryStats = pexConfig.ConfigurableField(
306 target=ComputeExposureSummaryStatsTask,
307 doc="Subtask to run computeSummaryStats on exposure"
308 )
309 doWriteExposure = pexConfig.Field(
310 dtype=bool,
311 default=True,
312 doc="Write the calexp? If fakes have been added then we do not want to write out the calexp as a "
313 "normal calexp but as a fakes_calexp."
314 )
316 def setDefaults(self):
317 super().setDefaults()
318 self.detection.doTempLocalBackground = False
319 self.deblend.maxFootprintSize = 2000
320 self.postCalibrationMeasurement.plugins.names = ["base_LocalPhotoCalib", "base_LocalWcs"]
321 self.postCalibrationMeasurement.doReplaceWithNoise = False
322 for key in self.postCalibrationMeasurement.slots:
323 setattr(self.postCalibrationMeasurement.slots, key, None)
324 self.astromRefObjLoader.anyFilterMapsToThis = "phot_g_mean"
325 # The photoRefCat connection is the name to use for the colorterms.
326 self.photoCal.photoCatName = self.connections.photoRefCat
328 # NOTE: these two lines are for gen2, and are only here for compatibility.
329 self.astromRefObjLoader.ref_dataset_name = "gaia_dr2_20200414"
330 self.photoRefObjLoader.ref_dataset_name = "ps1_pv3_3pi_20170110"
332 def validate(self):
333 super().validate()
334 astromRefCatGen2 = getattr(self.astromRefObjLoader, "ref_dataset_name", None)
335 if astromRefCatGen2 is not None and astromRefCatGen2 != self.connections.astromRefCat:
336 raise ValueError(
337 f"Gen2 ({astromRefCatGen2}) and Gen3 ({self.connections.astromRefCat}) astrometry reference "
338 f"catalogs are different. These options must be kept in sync until Gen2 is retired."
339 )
340 photoRefCatGen2 = getattr(self.photoRefObjLoader, "ref_dataset_name", None)
341 if photoRefCatGen2 is not None and photoRefCatGen2 != self.connections.photoRefCat:
342 raise ValueError(
343 f"Gen2 ({photoRefCatGen2}) and Gen3 ({self.connections.photoRefCat}) photometry reference "
344 f"catalogs are different. These options must be kept in sync until Gen2 is retired."
345 )
348## \addtogroup LSST_task_documentation
349## \{
350## \page page_CalibrateTask CalibrateTask
351## \ref CalibrateTask_ "CalibrateTask"
352## \copybrief CalibrateTask
353## \}
355class CalibrateTask(pipeBase.PipelineTask, pipeBase.CmdLineTask):
356 r"""!Calibrate an exposure: measure sources and perform astrometric and
357 photometric calibration
359 @anchor CalibrateTask_
361 @section pipe_tasks_calibrate_Contents Contents
363 - @ref pipe_tasks_calibrate_Purpose
364 - @ref pipe_tasks_calibrate_Initialize
365 - @ref pipe_tasks_calibrate_IO
366 - @ref pipe_tasks_calibrate_Config
367 - @ref pipe_tasks_calibrate_Metadata
368 - @ref pipe_tasks_calibrate_Debug
370 @section pipe_tasks_calibrate_Purpose Description
372 Given an exposure with a good PSF model and aperture correction map
373 (e.g. as provided by @ref characterizeImage::CharacterizeImageTask "CharacterizeImageTask"),
374 perform the following operations:
375 - Run detection and measurement
376 - Run astrometry subtask to fit an improved WCS
377 - Run photoCal subtask to fit the exposure's photometric zero-point
379 @section pipe_tasks_calibrate_Initialize Task initialisation
381 @copydoc \_\_init\_\_
383 @section pipe_tasks_calibrate_IO Invoking the Task
385 If you want this task to unpersist inputs or persist outputs, then call
386 the `runDataRef` method (a wrapper around the `run` method).
388 If you already have the inputs unpersisted and do not want to persist the
389 output then it is more direct to call the `run` method:
391 @section pipe_tasks_calibrate_Config Configuration parameters
393 See @ref CalibrateConfig
395 @section pipe_tasks_calibrate_Metadata Quantities set in exposure Metadata
397 Exposure metadata
398 <dl>
399 <dt>MAGZERO_RMS <dd>MAGZERO's RMS == sigma reported by photoCal task
400 <dt>MAGZERO_NOBJ <dd>Number of stars used == ngood reported by photoCal
401 task
402 <dt>COLORTERM1 <dd>?? (always 0.0)
403 <dt>COLORTERM2 <dd>?? (always 0.0)
404 <dt>COLORTERM3 <dd>?? (always 0.0)
405 </dl>
407 @section pipe_tasks_calibrate_Debug Debug variables
409 The command line task
410 interface supports a flag
411 `--debug` to import `debug.py` from your `$PYTHONPATH`; see
412 <a href="https://pipelines.lsst.io/modules/lsstDebug/">the lsstDebug documentation</a>
413 for more about `debug.py`.
415 CalibrateTask has a debug dictionary containing one key:
416 <dl>
417 <dt>calibrate
418 <dd>frame (an int; <= 0 to not display) in which to display the exposure,
419 sources and matches. See @ref lsst.meas.astrom.displayAstrometry for
420 the meaning of the various symbols.
421 </dl>
423 For example, put something like:
424 @code{.py}
425 import lsstDebug
426 def DebugInfo(name):
427 di = lsstDebug.getInfo(name) # N.b. lsstDebug.Info(name) would
428 # call us recursively
429 if name == "lsst.pipe.tasks.calibrate":
430 di.display = dict(
431 calibrate = 1,
432 )
434 return di
436 lsstDebug.Info = DebugInfo
437 @endcode
438 into your `debug.py` file and run `calibrateTask.py` with the `--debug`
439 flag.
441 Some subtasks may have their own debug variables; see individual Task
442 documentation.
443 """
445 # Example description used to live here, removed 2-20-2017 as per
446 # https://jira.lsstcorp.org/browse/DM-9520
448 ConfigClass = CalibrateConfig
449 _DefaultName = "calibrate"
450 RunnerClass = pipeBase.ButlerInitializedTaskRunner
452 def __init__(self, butler=None, astromRefObjLoader=None,
453 photoRefObjLoader=None, icSourceSchema=None,
454 initInputs=None, **kwargs):
455 """!Construct a CalibrateTask
457 @param[in] butler The butler is passed to the refObjLoader constructor
458 in case it is needed. Ignored if the refObjLoader argument
459 provides a loader directly.
460 @param[in] astromRefObjLoader An instance of LoadReferenceObjectsTasks
461 that supplies an external reference catalog for astrometric
462 calibration. May be None if the desired loader can be constructed
463 from the butler argument or all steps requiring a reference catalog
464 are disabled.
465 @param[in] photoRefObjLoader An instance of LoadReferenceObjectsTasks
466 that supplies an external reference catalog for photometric
467 calibration. May be None if the desired loader can be constructed
468 from the butler argument or all steps requiring a reference catalog
469 are disabled.
470 @param[in] icSourceSchema schema for icSource catalog, or None.
471 Schema values specified in config.icSourceFieldsToCopy will be
472 taken from this schema. If set to None, no values will be
473 propagated from the icSourceCatalog
474 @param[in,out] kwargs other keyword arguments for
475 lsst.pipe.base.CmdLineTask
476 """
477 super().__init__(**kwargs)
479 if icSourceSchema is None and butler is not None:
480 # Use butler to read icSourceSchema from disk.
481 icSourceSchema = butler.get("icSrc_schema", immediate=True).schema
483 if icSourceSchema is None and butler is None and initInputs is not None:
484 icSourceSchema = initInputs['icSourceSchema'].schema
486 if icSourceSchema is not None:
487 # use a schema mapper to avoid copying each field separately
488 self.schemaMapper = afwTable.SchemaMapper(icSourceSchema)
489 minimumSchema = afwTable.SourceTable.makeMinimalSchema()
490 self.schemaMapper.addMinimalSchema(minimumSchema, False)
492 # Add fields to copy from an icSource catalog
493 # and a field to indicate that the source matched a source in that
494 # catalog. If any fields are missing then raise an exception, but
495 # first find all missing fields in order to make the error message
496 # more useful.
497 self.calibSourceKey = self.schemaMapper.addOutputField(
498 afwTable.Field["Flag"]("calib_detected",
499 "Source was detected as an icSource"))
500 missingFieldNames = []
501 for fieldName in self.config.icSourceFieldsToCopy:
502 try:
503 schemaItem = icSourceSchema.find(fieldName)
504 except Exception:
505 missingFieldNames.append(fieldName)
506 else:
507 # field found; if addMapping fails then raise an exception
508 self.schemaMapper.addMapping(schemaItem.getKey())
510 if missingFieldNames:
511 raise RuntimeError("isSourceCat is missing fields {} "
512 "specified in icSourceFieldsToCopy"
513 .format(missingFieldNames))
515 # produce a temporary schema to pass to the subtasks; finalize it
516 # later
517 self.schema = self.schemaMapper.editOutputSchema()
518 else:
519 self.schemaMapper = None
520 self.schema = afwTable.SourceTable.makeMinimalSchema()
521 self.makeSubtask('detection', schema=self.schema)
523 self.algMetadata = dafBase.PropertyList()
525 if self.config.doDeblend:
526 self.makeSubtask("deblend", schema=self.schema)
527 if self.config.doSkySources:
528 self.makeSubtask("skySources")
529 self.skySourceKey = self.schema.addField("sky_source", type="Flag", doc="Sky objects.")
530 self.makeSubtask('measurement', schema=self.schema,
531 algMetadata=self.algMetadata)
532 self.makeSubtask('postCalibrationMeasurement', schema=self.schema,
533 algMetadata=self.algMetadata)
534 self.makeSubtask("setPrimaryFlags", schema=self.schema, isSingleFrame=True)
535 if self.config.doApCorr:
536 self.makeSubtask('applyApCorr', schema=self.schema)
537 self.makeSubtask('catalogCalculation', schema=self.schema)
539 if self.config.doAstrometry:
540 if astromRefObjLoader is None and butler is not None:
541 self.makeSubtask('astromRefObjLoader', butler=butler)
542 astromRefObjLoader = self.astromRefObjLoader
543 self.makeSubtask("astrometry", refObjLoader=astromRefObjLoader,
544 schema=self.schema)
545 if self.config.doPhotoCal:
546 if photoRefObjLoader is None and butler is not None:
547 self.makeSubtask('photoRefObjLoader', butler=butler)
548 photoRefObjLoader = self.photoRefObjLoader
549 self.makeSubtask("photoCal", refObjLoader=photoRefObjLoader,
550 schema=self.schema)
551 if self.config.doComputeSummaryStats:
552 self.makeSubtask('computeSummaryStats')
554 if initInputs is not None and (astromRefObjLoader is not None or photoRefObjLoader is not None):
555 raise RuntimeError("PipelineTask form of this task should not be initialized with "
556 "reference object loaders.")
558 if self.schemaMapper is not None:
559 # finalize the schema
560 self.schema = self.schemaMapper.getOutputSchema()
561 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
563 sourceCatSchema = afwTable.SourceCatalog(self.schema)
564 sourceCatSchema.getTable().setMetadata(self.algMetadata)
565 self.outputSchema = sourceCatSchema
567 @timeMethod
568 def runDataRef(self, dataRef, exposure=None, background=None, icSourceCat=None,
569 doUnpersist=True):
570 """!Calibrate an exposure, optionally unpersisting inputs and
571 persisting outputs.
573 This is a wrapper around the `run` method that unpersists inputs
574 (if `doUnpersist` true) and persists outputs (if `config.doWrite` true)
576 @param[in] dataRef butler data reference corresponding to a science
577 image
578 @param[in,out] exposure characterized exposure (an
579 lsst.afw.image.ExposureF or similar), or None to unpersist existing
580 icExp and icBackground. See `run` method for details of what is
581 read and written.
582 @param[in,out] background initial model of background already
583 subtracted from exposure (an lsst.afw.math.BackgroundList). May be
584 None if no background has been subtracted, though that is unusual
585 for calibration. A refined background model is output. Ignored if
586 exposure is None.
587 @param[in] icSourceCat catalog from which to copy the fields specified
588 by icSourceKeys, or None;
589 @param[in] doUnpersist unpersist data:
590 - if True, exposure, background and icSourceCat are read from
591 dataRef and those three arguments must all be None;
592 - if False the exposure must be provided; background and
593 icSourceCat are optional. True is intended for running as a
594 command-line task, False for running as a subtask
595 @return same data as the calibrate method
596 """
597 self.log.info("Processing %s", dataRef.dataId)
599 if doUnpersist:
600 if any(item is not None for item in (exposure, background,
601 icSourceCat)):
602 raise RuntimeError("doUnpersist true; exposure, background "
603 "and icSourceCat must all be None")
604 exposure = dataRef.get("icExp", immediate=True)
605 background = dataRef.get("icExpBackground", immediate=True)
606 icSourceCat = dataRef.get("icSrc", immediate=True)
607 elif exposure is None:
608 raise RuntimeError("doUnpersist false; exposure must be provided")
610 exposureIdInfo = dataRef.get("expIdInfo")
612 calRes = self.run(
613 exposure=exposure,
614 exposureIdInfo=exposureIdInfo,
615 background=background,
616 icSourceCat=icSourceCat,
617 )
619 if self.config.doWrite:
620 self.writeOutputs(
621 dataRef=dataRef,
622 exposure=calRes.exposure,
623 background=calRes.background,
624 sourceCat=calRes.sourceCat,
625 astromMatches=calRes.astromMatches,
626 matchMeta=calRes.matchMeta,
627 )
629 return calRes
631 def runQuantum(self, butlerQC, inputRefs, outputRefs):
632 inputs = butlerQC.get(inputRefs)
633 inputs['exposureIdInfo'] = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "visit_detector")
635 if self.config.doAstrometry:
636 refObjLoader = ReferenceObjectLoader(dataIds=[ref.datasetRef.dataId
637 for ref in inputRefs.astromRefCat],
638 refCats=inputs.pop('astromRefCat'),
639 config=self.config.astromRefObjLoader, log=self.log)
640 self.astrometry.setRefObjLoader(refObjLoader)
642 if self.config.doPhotoCal:
643 photoRefObjLoader = ReferenceObjectLoader(dataIds=[ref.datasetRef.dataId
644 for ref in inputRefs.photoRefCat],
645 refCats=inputs.pop('photoRefCat'),
646 config=self.config.photoRefObjLoader,
647 log=self.log)
648 self.photoCal.match.setRefObjLoader(photoRefObjLoader)
650 outputs = self.run(**inputs)
652 if self.config.doWriteMatches and self.config.doAstrometry:
653 normalizedMatches = afwTable.packMatches(outputs.astromMatches)
654 normalizedMatches.table.setMetadata(outputs.matchMeta)
655 if self.config.doWriteMatchesDenormalized:
656 denormMatches = denormalizeMatches(outputs.astromMatches, outputs.matchMeta)
657 outputs.matchesDenormalized = denormMatches
658 outputs.matches = normalizedMatches
659 butlerQC.put(outputs, outputRefs)
661 @timeMethod
662 def run(self, exposure, exposureIdInfo=None, background=None,
663 icSourceCat=None):
664 """!Calibrate an exposure (science image or coadd)
666 @param[in,out] exposure exposure to calibrate (an
667 lsst.afw.image.ExposureF or similar);
668 in:
669 - MaskedImage
670 - Psf
671 out:
672 - MaskedImage has background subtracted
673 - Wcs is replaced
674 - PhotoCalib is replaced
675 @param[in] exposureIdInfo ID info for exposure (an
676 lsst.obs.base.ExposureIdInfo) If not provided, returned
677 SourceCatalog IDs will not be globally unique.
678 @param[in,out] background background model already subtracted from
679 exposure (an lsst.afw.math.BackgroundList). May be None if no
680 background has been subtracted, though that is unusual for
681 calibration. A refined background model is output.
682 @param[in] icSourceCat A SourceCatalog from CharacterizeImageTask
683 from which we can copy some fields.
685 @return pipe_base Struct containing these fields:
686 - exposure calibrate science exposure with refined WCS and PhotoCalib
687 - background model of background subtracted from exposure (an
688 lsst.afw.math.BackgroundList)
689 - sourceCat catalog of measured sources
690 - astromMatches list of source/refObj matches from the astrometry
691 solver
692 """
693 # detect, deblend and measure sources
694 if exposureIdInfo is None:
695 exposureIdInfo = ExposureIdInfo()
697 if background is None:
698 background = BackgroundList()
699 sourceIdFactory = exposureIdInfo.makeSourceIdFactory()
700 table = SourceTable.make(self.schema, sourceIdFactory)
701 table.setMetadata(self.algMetadata)
703 detRes = self.detection.run(table=table, exposure=exposure,
704 doSmooth=True)
705 sourceCat = detRes.sources
706 if detRes.fpSets.background:
707 for bg in detRes.fpSets.background:
708 background.append(bg)
709 if self.config.doSkySources:
710 skySourceFootprints = self.skySources.run(mask=exposure.mask, seed=exposureIdInfo.expId)
711 if skySourceFootprints:
712 for foot in skySourceFootprints:
713 s = sourceCat.addNew()
714 s.setFootprint(foot)
715 s.set(self.skySourceKey, True)
716 if self.config.doDeblend:
717 self.deblend.run(exposure=exposure, sources=sourceCat)
718 self.measurement.run(
719 measCat=sourceCat,
720 exposure=exposure,
721 exposureId=exposureIdInfo.expId
722 )
723 if self.config.doApCorr:
724 self.applyApCorr.run(
725 catalog=sourceCat,
726 apCorrMap=exposure.getInfo().getApCorrMap()
727 )
728 self.catalogCalculation.run(sourceCat)
730 self.setPrimaryFlags.run(sourceCat)
732 if icSourceCat is not None and \
733 len(self.config.icSourceFieldsToCopy) > 0:
734 self.copyIcSourceFields(icSourceCat=icSourceCat,
735 sourceCat=sourceCat)
737 # TODO DM-11568: this contiguous check-and-copy could go away if we
738 # reserve enough space during SourceDetection and/or SourceDeblend.
739 # NOTE: sourceSelectors require contiguous catalogs, so ensure
740 # contiguity now, so views are preserved from here on.
741 if not sourceCat.isContiguous():
742 sourceCat = sourceCat.copy(deep=True)
744 # perform astrometry calibration:
745 # fit an improved WCS and update the exposure's WCS in place
746 astromMatches = None
747 matchMeta = None
748 if self.config.doAstrometry:
749 try:
750 astromRes = self.astrometry.run(
751 exposure=exposure,
752 sourceCat=sourceCat,
753 )
754 astromMatches = astromRes.matches
755 matchMeta = astromRes.matchMeta
756 except Exception as e:
757 if self.config.requireAstrometry:
758 raise
759 self.log.warning("Unable to perform astrometric calibration "
760 "(%s): attempting to proceed", e)
762 # compute photometric calibration
763 if self.config.doPhotoCal:
764 try:
765 photoRes = self.photoCal.run(exposure, sourceCat=sourceCat, expId=exposureIdInfo.expId)
766 exposure.setPhotoCalib(photoRes.photoCalib)
767 # TODO: reword this to phrase it in terms of the calibration factor?
768 self.log.info("Photometric zero-point: %f",
769 photoRes.photoCalib.instFluxToMagnitude(1.0))
770 self.setMetadata(exposure=exposure, photoRes=photoRes)
771 except Exception as e:
772 if self.config.requirePhotoCal:
773 raise
774 self.log.warning("Unable to perform photometric calibration "
775 "(%s): attempting to proceed", e)
776 self.setMetadata(exposure=exposure, photoRes=None)
778 self.postCalibrationMeasurement.run(
779 measCat=sourceCat,
780 exposure=exposure,
781 exposureId=exposureIdInfo.expId
782 )
784 if self.config.doComputeSummaryStats:
785 summary = self.computeSummaryStats.run(exposure=exposure,
786 sources=sourceCat,
787 background=background)
788 exposure.getInfo().setSummaryStats(summary)
790 frame = getDebugFrame(self._display, "calibrate")
791 if frame:
792 displayAstrometry(
793 sourceCat=sourceCat,
794 exposure=exposure,
795 matches=astromMatches,
796 frame=frame,
797 pause=False,
798 )
800 return pipeBase.Struct(
801 exposure=exposure,
802 background=background,
803 sourceCat=sourceCat,
804 astromMatches=astromMatches,
805 matchMeta=matchMeta,
806 # These are duplicate entries with different names for use with
807 # gen3 middleware
808 outputExposure=exposure,
809 outputCat=sourceCat,
810 outputBackground=background,
811 )
813 def writeOutputs(self, dataRef, exposure, background, sourceCat,
814 astromMatches, matchMeta):
815 """Write output data to the output repository
817 @param[in] dataRef butler data reference corresponding to a science
818 image
819 @param[in] exposure exposure to write
820 @param[in] background background model for exposure
821 @param[in] sourceCat catalog of measured sources
822 @param[in] astromMatches list of source/refObj matches from the
823 astrometry solver
824 """
825 dataRef.put(sourceCat, "src")
826 if self.config.doWriteMatches and astromMatches is not None:
827 normalizedMatches = afwTable.packMatches(astromMatches)
828 normalizedMatches.table.setMetadata(matchMeta)
829 dataRef.put(normalizedMatches, "srcMatch")
830 if self.config.doWriteMatchesDenormalized:
831 denormMatches = denormalizeMatches(astromMatches, matchMeta)
832 dataRef.put(denormMatches, "srcMatchFull")
833 if self.config.doWriteExposure:
834 dataRef.put(exposure, "calexp")
835 dataRef.put(background, "calexpBackground")
837 def getSchemaCatalogs(self):
838 """Return a dict of empty catalogs for each catalog dataset produced
839 by this task.
840 """
841 sourceCat = afwTable.SourceCatalog(self.schema)
842 sourceCat.getTable().setMetadata(self.algMetadata)
843 return {"src": sourceCat}
845 def setMetadata(self, exposure, photoRes=None):
846 """!Set task and exposure metadata
848 Logs a warning and continues if needed data is missing.
850 @param[in,out] exposure exposure whose metadata is to be set
851 @param[in] photoRes results of running photoCal; if None then it was
852 not run
853 """
854 if photoRes is None:
855 return
857 metadata = exposure.getMetadata()
859 # convert zero-point to (mag/sec/adu) for task MAGZERO metadata
860 try:
861 exposureTime = exposure.getInfo().getVisitInfo().getExposureTime()
862 magZero = photoRes.zp - 2.5*math.log10(exposureTime)
863 except Exception:
864 self.log.warning("Could not set normalized MAGZERO in header: no "
865 "exposure time")
866 magZero = math.nan
868 try:
869 metadata.set('MAGZERO', magZero)
870 metadata.set('MAGZERO_RMS', photoRes.sigma)
871 metadata.set('MAGZERO_NOBJ', photoRes.ngood)
872 metadata.set('COLORTERM1', 0.0)
873 metadata.set('COLORTERM2', 0.0)
874 metadata.set('COLORTERM3', 0.0)
875 except Exception as e:
876 self.log.warning("Could not set exposure metadata: %s", e)
878 def copyIcSourceFields(self, icSourceCat, sourceCat):
879 """!Match sources in icSourceCat and sourceCat and copy the specified fields
881 @param[in] icSourceCat catalog from which to copy fields
882 @param[in,out] sourceCat catalog to which to copy fields
884 The fields copied are those specified by `config.icSourceFieldsToCopy`
885 that actually exist in the schema. This was set up by the constructor
886 using self.schemaMapper.
887 """
888 if self.schemaMapper is None:
889 raise RuntimeError("To copy icSource fields you must specify "
890 "icSourceSchema nd icSourceKeys when "
891 "constructing this task")
892 if icSourceCat is None or sourceCat is None:
893 raise RuntimeError("icSourceCat and sourceCat must both be "
894 "specified")
895 if len(self.config.icSourceFieldsToCopy) == 0:
896 self.log.warning("copyIcSourceFields doing nothing because "
897 "icSourceFieldsToCopy is empty")
898 return
900 mc = afwTable.MatchControl()
901 mc.findOnlyClosest = False # return all matched objects
902 matches = afwTable.matchXy(icSourceCat, sourceCat,
903 self.config.matchRadiusPix, mc)
904 if self.config.doDeblend:
905 deblendKey = sourceCat.schema["deblend_nChild"].asKey()
906 # if deblended, keep children
907 matches = [m for m in matches if m[1].get(deblendKey) == 0]
909 # Because we had to allow multiple matches to handle parents, we now
910 # need to prune to the best matches
911 # closest matches as a dict of icSourceCat source ID:
912 # (icSourceCat source, sourceCat source, distance in pixels)
913 bestMatches = {}
914 for m0, m1, d in matches:
915 id0 = m0.getId()
916 match = bestMatches.get(id0)
917 if match is None or d <= match[2]:
918 bestMatches[id0] = (m0, m1, d)
919 matches = list(bestMatches.values())
921 # Check that no sourceCat sources are listed twice (we already know
922 # that each match has a unique icSourceCat source ID, due to using
923 # that ID as the key in bestMatches)
924 numMatches = len(matches)
925 numUniqueSources = len(set(m[1].getId() for m in matches))
926 if numUniqueSources != numMatches:
927 self.log.warning("%d icSourceCat sources matched only %d sourceCat "
928 "sources", numMatches, numUniqueSources)
930 self.log.info("Copying flags from icSourceCat to sourceCat for "
931 "%d sources", numMatches)
933 # For each match: set the calibSourceKey flag and copy the desired
934 # fields
935 for icSrc, src, d in matches:
936 src.setFlag(self.calibSourceKey, True)
937 # src.assign copies the footprint from icSrc, which we don't want
938 # (DM-407)
939 # so set icSrc's footprint to src's footprint before src.assign,
940 # then restore it
941 icSrcFootprint = icSrc.getFootprint()
942 try:
943 icSrc.setFootprint(src.getFootprint())
944 src.assign(icSrc, self.schemaMapper)
945 finally:
946 icSrc.setFootprint(icSrcFootprint)