28 import astropy.units
as u
40 from lsst.pipe.tasks.colorterms
import ColortermLibrary
41 from lsst.verify
import Job, Measurement
46 from .dataIds
import PerTractCcdDataIdContainer
51 __all__ = [
"JointcalConfig",
"JointcalRunner",
"JointcalTask"]
53 Photometry = collections.namedtuple(
'Photometry', (
'fit',
'model'))
54 Astrometry = collections.namedtuple(
'Astrometry', (
'fit',
'model',
'sky_to_tan_projection'))
59 meas = Measurement(job.metrics[name], value)
60 job.measurements.insert(meas)
64 """Subclass of TaskRunner for jointcalTask
66 jointcalTask.runDataRef() takes a number of arguments, one of which is a list of dataRefs
67 extracted from the command line (whereas most CmdLineTasks' runDataRef methods take
68 single dataRef, are are called repeatedly). This class transforms the processed
69 arguments generated by the ArgumentParser into the arguments expected by
70 Jointcal.runDataRef().
72 See pipeBase.TaskRunner for more information.
78 Return a list of tuples per tract, each containing (dataRefs, kwargs).
80 Jointcal operates on lists of dataRefs simultaneously.
82 kwargs[
'profile_jointcal'] = parsedCmd.profile_jointcal
83 kwargs[
'butler'] = parsedCmd.butler
87 for ref
in parsedCmd.id.refList:
88 refListDict.setdefault(ref.dataId[
"tract"], []).append(ref)
90 result = [(refListDict[tract], kwargs)
for tract
in sorted(refListDict.keys())]
98 Arguments for Task.runDataRef()
103 if self.doReturnResults is False:
105 - ``exitStatus``: 0 if the task completed successfully, 1 otherwise.
107 if self.doReturnResults is True:
109 - ``result``: the result of calling jointcal.runDataRef()
110 - ``exitStatus``: 0 if the task completed successfully, 1 otherwise.
115 dataRefList, kwargs = args
116 butler = kwargs.pop(
'butler')
117 task = self.TaskClass(config=self.config, log=self.log, butler=butler)
120 result = task.runDataRef(dataRefList, **kwargs)
121 exitStatus = result.exitStatus
122 job_path = butler.get(
'verify_job_filename')
123 result.job.write(job_path[0])
124 except Exception
as e:
129 eName = type(e).__name__
130 tract = dataRefList[0].dataId[
'tract']
131 task.log.fatal(
"Failed processing tract %s, %s: %s", tract, eName, e)
134 kwargs[
'butler'] = butler
135 if self.doReturnResults:
136 return pipeBase.Struct(result=result, exitStatus=exitStatus)
138 return pipeBase.Struct(exitStatus=exitStatus)
142 """Configuration for JointcalTask"""
144 doAstrometry = pexConfig.Field(
145 doc=
"Fit astrometry and write the fitted result.",
149 doPhotometry = pexConfig.Field(
150 doc=
"Fit photometry and write the fitted result.",
154 coaddName = pexConfig.Field(
155 doc=
"Type of coadd, typically deep or goodSeeing",
159 positionErrorPedestal = pexConfig.Field(
160 doc=
"Systematic term to apply to the measured position error (pixels)",
164 photometryErrorPedestal = pexConfig.Field(
165 doc=
"Systematic term to apply to the measured error on flux or magnitude as a "
166 "fraction of source flux or magnitude delta (e.g. 0.05 is 5% of flux or +50 millimag).",
171 matchCut = pexConfig.Field(
172 doc=
"Matching radius between fitted and reference stars (arcseconds)",
176 minMeasurements = pexConfig.Field(
177 doc=
"Minimum number of associated measured stars for a fitted star to be included in the fit",
181 minMeasuredStarsPerCcd = pexConfig.Field(
182 doc=
"Minimum number of measuredStars per ccdImage before printing warnings",
186 minRefStarsPerCcd = pexConfig.Field(
187 doc=
"Minimum number of measuredStars per ccdImage before printing warnings",
191 allowLineSearch = pexConfig.Field(
192 doc=
"Allow a line search during minimization, if it is reasonable for the model"
193 " (models with a significant non-linear component, e.g. constrainedPhotometry).",
197 astrometrySimpleOrder = pexConfig.Field(
198 doc=
"Polynomial order for fitting the simple astrometry model.",
202 astrometryChipOrder = pexConfig.Field(
203 doc=
"Order of the per-chip transform for the constrained astrometry model.",
207 astrometryVisitOrder = pexConfig.Field(
208 doc=
"Order of the per-visit transform for the constrained astrometry model.",
212 useInputWcs = pexConfig.Field(
213 doc=
"Use the input calexp WCSs to initialize a SimpleAstrometryModel.",
217 astrometryModel = pexConfig.ChoiceField(
218 doc=
"Type of model to fit to astrometry",
220 default=
"constrained",
221 allowed={
"simple":
"One polynomial per ccd",
222 "constrained":
"One polynomial per ccd, and one polynomial per visit"}
224 photometryModel = pexConfig.ChoiceField(
225 doc=
"Type of model to fit to photometry",
227 default=
"constrainedMagnitude",
228 allowed={
"simpleFlux":
"One constant zeropoint per ccd and visit, fitting in flux space.",
229 "constrainedFlux":
"Constrained zeropoint per ccd, and one polynomial per visit,"
230 " fitting in flux space.",
231 "simpleMagnitude":
"One constant zeropoint per ccd and visit,"
232 " fitting in magnitude space.",
233 "constrainedMagnitude":
"Constrained zeropoint per ccd, and one polynomial per visit,"
234 " fitting in magnitude space.",
237 applyColorTerms = pexConfig.Field(
238 doc=
"Apply photometric color terms to reference stars?"
239 "Requires that colorterms be set to a ColortermLibrary",
243 colorterms = pexConfig.ConfigField(
244 doc=
"Library of photometric reference catalog name to color term dict.",
245 dtype=ColortermLibrary,
247 photometryVisitOrder = pexConfig.Field(
248 doc=
"Order of the per-visit polynomial transform for the constrained photometry model.",
252 photometryDoRankUpdate = pexConfig.Field(
253 doc=(
"Do the rank update step during minimization. "
254 "Skipping this can help deal with models that are too non-linear."),
258 astrometryDoRankUpdate = pexConfig.Field(
259 doc=(
"Do the rank update step during minimization (should not change the astrometry fit). "
260 "Skipping this can help deal with models that are too non-linear."),
264 outlierRejectSigma = pexConfig.Field(
265 doc=
"How many sigma to reject outliers at during minimization.",
269 maxPhotometrySteps = pexConfig.Field(
270 doc=
"Maximum number of minimize iterations to take when fitting photometry.",
274 maxAstrometrySteps = pexConfig.Field(
275 doc=
"Maximum number of minimize iterations to take when fitting photometry.",
279 astrometryRefObjLoader = pexConfig.ConfigurableField(
280 target=LoadIndexedReferenceObjectsTask,
281 doc=
"Reference object loader for astrometric fit",
283 photometryRefObjLoader = pexConfig.ConfigurableField(
284 target=LoadIndexedReferenceObjectsTask,
285 doc=
"Reference object loader for photometric fit",
287 sourceSelector = sourceSelectorRegistry.makeField(
288 doc=
"How to select sources for cross-matching",
291 astrometryReferenceSelector = pexConfig.ConfigurableField(
292 target=ReferenceSourceSelectorTask,
293 doc=
"How to down-select the loaded astrometry reference catalog.",
295 photometryReferenceSelector = pexConfig.ConfigurableField(
296 target=ReferenceSourceSelectorTask,
297 doc=
"How to down-select the loaded photometry reference catalog.",
299 astrometryReferenceErr = pexConfig.Field(
300 doc=(
"Uncertainty on reference catalog coordinates [mas] to use in place of the `coord_*Err` fields. "
301 "If None, then raise an exception if the reference catalog is missing coordinate errors. "
302 "If specified, overrides any existing `coord_*Err` values."),
307 writeInitMatrix = pexConfig.Field(
309 doc=(
"Write the pre/post-initialization Hessian and gradient to text files, for debugging. "
310 "The output files will be of the form 'astrometry_preinit-mat.txt', in the current directory. "
311 "Note that these files are the dense versions of the matrix, and so may be very large."),
314 writeChi2FilesInitialFinal = pexConfig.Field(
316 doc=
"Write .csv files containing the contributions to chi2 for the initialization and final fit.",
319 writeChi2FilesOuterLoop = pexConfig.Field(
321 doc=
"Write .csv files containing the contributions to chi2 for the outer fit loop.",
324 writeInitialModel = pexConfig.Field(
326 doc=(
"Write the pre-initialization model to text files, for debugging."
327 " Output is written to `initial[Astro|Photo]metryModel.txt` in the current working directory."),
330 debugOutputPath = pexConfig.Field(
333 doc=(
"Path to write debug output files to. Used by "
334 "`writeInitialModel`, `writeChi2Files*`, `writeInitMatrix`.")
336 sourceFluxType = pexConfig.Field(
338 doc=
"Source flux field to use in source selection and to get fluxes from the catalog.",
345 msg =
"applyColorTerms=True requires the `colorterms` field be set to a ColortermLibrary."
346 raise pexConfig.FieldValidationError(JointcalConfig.colorterms, self, msg)
348 msg = (
"Only doing astrometry, but Colorterms are not applied for astrometry;"
349 "applyColorTerms=True will be ignored.")
363 fluxField = f
"slot_{self.sourceFluxType}Flux_instFlux"
364 self.
sourceSelector[
'science'].signalToNoise.fluxField = fluxField
365 self.
sourceSelector[
'science'].signalToNoise.errField = fluxField +
"Err"
371 badFlags = [
'base_PixelFlags_flag_edge',
'base_PixelFlags_flag_saturated',
372 'base_PixelFlags_flag_interpolatedCenter',
'base_SdssCentroid_flag',
373 'base_PsfFlux_flag',
'base_PixelFlags_flag_suspectCenter']
385 """Write model to outfile."""
386 with open(filename,
"w")
as file:
387 file.write(repr(model))
388 log.info(
"Wrote %s to file: %s", model, filename)
391 @dataclasses.dataclass
393 """The input data jointcal needs for each detector/visit."""
395 """The visit identifier of this exposure."""
397 """The catalog derived from this exposure."""
399 """The VisitInfo of this exposure."""
401 """The detector of this exposure."""
403 """The photometric calibration of this exposure."""
405 """The WCS of this exposure."""
407 """The bounding box of this exposure."""
409 """The filter of this exposure."""
413 """Astrometricly and photometricly calibrate across multiple visits of the
418 butler : `lsst.daf.persistence.Butler`
419 The butler is passed to the refObjLoader constructor in case it is
420 needed. Ignored if the refObjLoader argument provides a loader directly.
421 Used to initialize the astrometry and photometry refObjLoaders.
422 profile_jointcal : `bool`
423 Set to True to profile different stages of this jointcal run.
426 ConfigClass = JointcalConfig
427 RunnerClass = JointcalRunner
428 _DefaultName =
"jointcal"
430 def __init__(self, butler=None, profile_jointcal=False, **kwargs):
433 self.makeSubtask(
"sourceSelector")
434 if self.config.doAstrometry:
435 self.makeSubtask(
'astrometryRefObjLoader', butler=butler)
436 self.makeSubtask(
"astrometryReferenceSelector")
439 if self.config.doPhotometry:
440 self.makeSubtask(
'photometryRefObjLoader', butler=butler)
441 self.makeSubtask(
"photometryReferenceSelector")
446 self.
job = Job.load_metrics_package(subset=
'jointcal')
451 def _getMetadataName(self):
455 def _makeArgumentParser(cls):
456 """Create an argument parser"""
458 parser.add_argument(
"--profile_jointcal", default=
False, action=
"store_true",
459 help=
"Profile steps of jointcal separately.")
460 parser.add_id_argument(
"--id",
"calexp", help=
"data ID, e.g. --id visit=6789 ccd=0..9",
461 ContainerClass=PerTractCcdDataIdContainer)
464 def _build_ccdImage(self, data, associations, jointcalControl):
466 Extract the necessary things from this dataRef to add a new ccdImage.
470 data : `JointcalInputData`
471 The loaded input data.
472 associations : `lsst.jointcal.Associations`
473 Object to add the info to, to construct a new CcdImage
474 jointcalControl : `jointcal.JointcalControl`
475 Control object for associations management
481 The TAN WCS of this image, read from the calexp
482 (`lsst.afw.geom.SkyWcs`).
484 A key to identify this dataRef by its visit and ccd ids
487 This calexp's filter (`str`).
489 goodSrc = self.sourceSelector.run(data.catalog)
491 if len(goodSrc.sourceCat) == 0:
492 self.log.warn(
"No sources selected in visit %s ccd %s", data.visit, data.detector.getId())
494 self.log.info(
"%d sources selected in visit %d ccd %d", len(goodSrc.sourceCat),
496 data.detector.getId())
497 associations.createCcdImage(goodSrc.sourceCat,
501 data.filter.getName(),
505 data.detector.getId(),
508 Result = collections.namedtuple(
'Result_from_build_CcdImage', (
'wcs',
'key',
'filter'))
509 Key = collections.namedtuple(
'Key', (
'visit',
'ccd'))
510 return Result(data.wcs, Key(data.visit, data.detector.getId()), data.filter.getName())
512 def _readDataId(self, butler, dataId):
513 """Read all of the data for one dataId from the butler. (gen2 version)"""
515 if "visit" in dataId.keys():
516 visit = dataId[
"visit"]
518 visit = butler.getButler().queryMetadata(
"calexp", (
"visit"), butler.dataId)[0]
520 catalog = butler.get(
'src',
521 flags=lsst.afw.table.SOURCE_IO_NO_FOOTPRINTS,
525 visitInfo=butler.get(
'calexp_visitInfo', dataId=dataId),
526 detector=butler.get(
'calexp_detector', dataId=dataId),
527 photoCalib=butler.get(
'calexp_photoCalib', dataId=dataId),
528 wcs=butler.get(
'calexp_wcs', dataId=dataId),
529 bbox=butler.get(
'calexp_bbox', dataId=dataId),
530 filter=butler.get(
'calexp_filter', dataId=dataId))
532 def loadData(self, dataRefs, associations, jointcalControl, profile_jointcal=False):
533 """Read the data that jointcal needs to run. (Gen2 version)"""
534 visit_ccd_to_dataRef = {}
537 load_cat_prof_file =
'jointcal_loadData.prof' if profile_jointcal
else ''
538 with pipeBase.cmdLineTask.profile(load_cat_prof_file):
540 camera = dataRefs[0].get(
'camera', immediate=
True)
542 for dataRef
in dataRefs:
543 data = self.
_readDataId(dataRef.getButler(), dataRef.dataId)
545 oldWcsList.append(result.wcs)
546 visit_ccd_to_dataRef[result.key] = dataRef
547 filters.append(result.filter)
548 filters = collections.Counter(filters)
550 return oldWcsList, filters, visit_ccd_to_dataRef
552 def _getDebugPath(self, filename):
553 """Constructs a path to filename using the configured debug path.
555 return os.path.join(self.config.debugOutputPath, filename)
557 def _prep_sky(self, associations, filters):
558 """Prepare on-sky and other data that must be computed after data has
561 associations.computeCommonTangentPoint()
563 boundingCircle = associations.computeBoundingCircle()
565 radius =
lsst.geom.Angle(boundingCircle.getOpeningAngle().asRadians(), lsst.geom.radians)
567 self.log.info(f
"Data has center={center} with radius={radius.asDegrees()} degrees.")
570 defaultFilter = filters.most_common(1)[0][0]
571 self.log.debug(
"Using %s band for reference flux", defaultFilter)
573 return boundingCircle, center, radius, defaultFilter
578 Jointly calibrate the astrometry and photometry across a set of images.
580 NOTE: this is for gen2 middleware only.
584 dataRefs : `list` of `lsst.daf.persistence.ButlerDataRef`
585 List of data references to the exposures to be fit.
586 profile_jointcal : `bool`
587 Profile the individual steps of jointcal.
591 result : `lsst.pipe.base.Struct`
592 Struct of metadata from the fit, containing:
595 The provided data references that were fit (with updated WCSs)
597 The original WCS from each dataRef
599 Dictionary of internally-computed metrics for testing/validation.
601 if len(dataRefs) == 0:
602 raise ValueError(
'Need a non-empty list of data references!')
606 sourceFluxField =
"slot_%sFlux" % (self.config.sourceFluxType,)
610 oldWcsList, filters, visit_ccd_to_dataRef = self.
loadData(dataRefs,
613 profile_jointcal=profile_jointcal)
615 boundingCircle, center, radius, defaultFilter = self.
_prep_sky(associations, filters)
617 tract = dataRefs[0].dataId[
'tract']
619 if self.config.doAstrometry:
623 referenceSelector=self.astrometryReferenceSelector,
625 profile_jointcal=profile_jointcal,
631 if self.config.doPhotometry:
635 referenceSelector=self.photometryReferenceSelector,
637 profile_jointcal=profile_jointcal,
640 reject_bad_fluxes=
True)
645 return pipeBase.Struct(dataRefs=dataRefs,
646 oldWcsList=oldWcsList,
650 defaultFilter=defaultFilter,
651 exitStatus=exitStatus)
653 def _get_refcat_coordinate_error_override(self, refCat, name):
654 """Check whether we should override the refcat coordinate errors, and
655 return the overridden error if necessary.
659 refCat : `lsst.afw.table.SimpleCatalog`
660 The reference catalog to check for a ``coord_raErr`` field.
662 Whether we are doing "astrometry" or "photometry".
666 refCoordErr : `float`
667 The refcat coordinate error to use, or NaN if we are not overriding
672 lsst.pex.config.FieldValidationError
673 Raised if the refcat does not contain coordinate errors and
674 ``config.astrometryReferenceErr`` is not set.
678 if name.lower() ==
"photometry":
679 if 'coord_raErr' not in refCat.schema:
684 if self.config.astrometryReferenceErr
is None and 'coord_raErr' not in refCat.schema:
685 msg = (
"Reference catalog does not contain coordinate errors, "
686 "and config.astrometryReferenceErr not supplied.")
687 raise pexConfig.FieldValidationError(JointcalConfig.astrometryReferenceErr,
691 if self.config.astrometryReferenceErr
is not None and 'coord_raErr' in refCat.schema:
692 self.log.warn(
"Overriding reference catalog coordinate errors with %f/coordinate [mas]",
693 self.config.astrometryReferenceErr)
695 if self.config.astrometryReferenceErr
is None:
698 return self.config.astrometryReferenceErr
700 def _compute_proper_motion_epoch(self, ccdImageList):
701 """Return the proper motion correction epoch of the provided images.
705 ccdImageList : `list` [`lsst.jointcal.CcdImage`]
706 The images to compute the appropriate epoch for.
710 epoch : `astropy.time.Time`
711 The date to use for proper motion corrections.
713 mjds = [ccdImage.getMjd()
for ccdImage
in ccdImageList]
714 return astropy.time.Time(np.mean(mjds), format=
'mjd', scale=
"tai")
716 def _do_load_refcat_and_fit(self, associations, defaultFilter, center, radius,
718 tract="", profile_jointcal=False, match_cut=3.0,
719 reject_bad_fluxes=False, *,
720 name="", refObjLoader=None, referenceSelector=None,
722 """Load reference catalog, perform the fit, and return the result.
726 associations : `lsst.jointcal.Associations`
727 The star/reference star associations to fit.
728 defaultFilter : `str`
729 filter to load from reference catalog.
730 center : `lsst.geom.SpherePoint`
731 ICRS center of field to load from reference catalog.
732 radius : `lsst.geom.Angle`
733 On-sky radius to load from reference catalog.
735 Name of thing being fit: "astrometry" or "photometry".
736 refObjLoader : `lsst.meas.algorithms.LoadReferenceObjectsTask`
737 Reference object loader to use to load a reference catalog.
738 referenceSelector : `lsst.meas.algorithms.ReferenceSourceSelectorTask`
739 Selector to use to pick objects from the loaded reference catalog.
740 fit_function : callable
741 Function to call to perform fit (takes Associations object).
742 filters : `list` [`str`], optional
743 List of filters to load from the reference catalog.
744 tract : `str`, optional
745 Name of tract currently being fit.
746 profile_jointcal : `bool`, optional
747 Separately profile the fitting step.
748 match_cut : `float`, optional
749 Radius in arcseconds to find cross-catalog matches to during
750 associations.associateCatalogs.
751 reject_bad_fluxes : `bool`, optional
752 Reject refCat sources with NaN/inf flux or NaN/0 fluxErr.
756 result : `Photometry` or `Astrometry`
757 Result of `fit_function()`
759 self.log.info(
"====== Now processing %s...", name)
762 associations.associateCatalogs(match_cut)
764 associations.fittedStarListSize())
766 applyColorterms =
False if name.lower() ==
"astrometry" else self.config.applyColorTerms
769 center, radius, defaultFilter,
770 applyColorterms=applyColorterms,
774 associations.collectRefStars(refCat,
775 self.config.matchCut*lsst.geom.arcseconds,
777 refCoordinateErr=refCoordErr,
778 rejectBadFluxes=reject_bad_fluxes)
780 associations.refStarListSize())
782 associations.prepareFittedStars(self.config.minMeasurements)
786 associations.nFittedStarsWithAssociatedRefStar())
788 associations.fittedStarListSize())
790 associations.nCcdImagesValidForFit())
792 load_cat_prof_file =
'jointcal_fit_%s.prof'%name
if profile_jointcal
else ''
793 dataName =
"{}_{}".format(tract, defaultFilter)
794 with pipeBase.cmdLineTask.profile(load_cat_prof_file):
795 result = fit_function(associations, dataName)
798 if self.config.writeChi2FilesInitialFinal:
799 baseName = self.
_getDebugPath(f
"{name}_final_chi2-{dataName}")
800 result.fit.saveChi2Contributions(baseName+
"{type}")
801 self.log.info(
"Wrote chi2 contributions files: %s", baseName)
805 def _load_reference_catalog(self, refObjLoader, referenceSelector, center, radius, filterName,
806 applyColorterms=False, epoch=None):
807 """Load the necessary reference catalog sources, convert fluxes to
808 correct units, and apply color term corrections if requested.
812 refObjLoader : `lsst.meas.algorithms.LoadReferenceObjectsTask`
813 The reference catalog loader to use to get the data.
814 referenceSelector : `lsst.meas.algorithms.ReferenceSourceSelectorTask`
815 Source selector to apply to loaded reference catalog.
816 center : `lsst.geom.SpherePoint`
817 The center around which to load sources.
818 radius : `lsst.geom.Angle`
819 The radius around ``center`` to load sources in.
821 The name of the camera filter to load fluxes for.
822 applyColorterms : `bool`
823 Apply colorterm corrections to the refcat for ``filterName``?
824 epoch : `astropy.time.Time`, optional
825 Epoch to which to correct refcat proper motion and parallax,
826 or `None` to not apply such corrections.
830 refCat : `lsst.afw.table.SimpleCatalog`
831 The loaded reference catalog.
833 The name of the reference catalog flux field appropriate for ``filterName``.
835 skyCircle = refObjLoader.loadSkyCircle(center,
840 selected = referenceSelector.run(skyCircle.refCat)
842 if not selected.sourceCat.isContiguous():
843 refCat = selected.sourceCat.copy(deep=
True)
845 refCat = selected.sourceCat
848 refCatName = refObjLoader.ref_dataset_name
849 self.log.info(
"Applying color terms for filterName=%r reference catalog=%s",
850 filterName, refCatName)
851 colorterm = self.config.colorterms.getColorterm(
852 filterName=filterName, photoCatName=refCatName, doRaise=
True)
854 refMag, refMagErr = colorterm.getCorrectedMagnitudes(refCat, filterName)
855 refCat[skyCircle.fluxField] = u.Magnitude(refMag, u.ABmag).to_value(u.nJy)
857 refCat[skyCircle.fluxField+
'Err'] = fluxErrFromABMagErr(refMagErr, refMag) * 1e9
859 return refCat, skyCircle.fluxField
861 def _check_star_lists(self, associations, name):
863 if associations.nCcdImagesValidForFit() == 0:
864 raise RuntimeError(
'No images in the ccdImageList!')
865 if associations.fittedStarListSize() == 0:
866 raise RuntimeError(
'No stars in the {} fittedStarList!'.format(name))
867 if associations.refStarListSize() == 0:
868 raise RuntimeError(
'No stars in the {} reference star list!'.format(name))
870 def _logChi2AndValidate(self, associations, fit, model, chi2Label, writeChi2Name=None):
871 """Compute chi2, log it, validate the model, and return chi2.
875 associations : `lsst.jointcal.Associations`
876 The star/reference star associations to fit.
877 fit : `lsst.jointcal.FitterBase`
878 The fitter to use for minimization.
879 model : `lsst.jointcal.Model`
882 Label to describe the chi2 (e.g. "Initialized", "Final").
883 writeChi2Name : `str`, optional
884 Filename prefix to write the chi2 contributions to.
885 Do not supply an extension: an appropriate one will be added.
889 chi2: `lsst.jointcal.Chi2Accumulator`
890 The chi2 object for the current fitter and model.
895 Raised if chi2 is infinite or NaN.
897 Raised if the model is not valid.
899 if writeChi2Name
is not None:
901 fit.saveChi2Contributions(fullpath+
"{type}")
902 self.log.info(
"Wrote chi2 contributions files: %s", fullpath)
904 chi2 = fit.computeChi2()
905 self.log.info(
"%s %s", chi2Label, chi2)
907 if not np.isfinite(chi2.chi2):
908 raise FloatingPointError(f
'{chi2Label} chi2 is invalid: {chi2}')
909 if not model.validate(associations.getCcdImageList(), chi2.ndof):
910 raise ValueError(
"Model is not valid: check log messages for warnings.")
913 def _fit_photometry(self, associations, dataName=None):
915 Fit the photometric data.
919 associations : `lsst.jointcal.Associations`
920 The star/reference star associations to fit.
922 Name of the data being processed (e.g. "1234_HSC-Y"), for
923 identifying debugging files.
927 fit_result : `namedtuple`
928 fit : `lsst.jointcal.PhotometryFit`
929 The photometric fitter used to perform the fit.
930 model : `lsst.jointcal.PhotometryModel`
931 The photometric model that was fit.
933 self.log.info(
"=== Starting photometric fitting...")
936 if self.config.photometryModel ==
"constrainedFlux":
939 visitOrder=self.config.photometryVisitOrder,
940 errorPedestal=self.config.photometryErrorPedestal)
942 doLineSearch = self.config.allowLineSearch
943 elif self.config.photometryModel ==
"constrainedMagnitude":
946 visitOrder=self.config.photometryVisitOrder,
947 errorPedestal=self.config.photometryErrorPedestal)
949 doLineSearch = self.config.allowLineSearch
950 elif self.config.photometryModel ==
"simpleFlux":
952 errorPedestal=self.config.photometryErrorPedestal)
954 elif self.config.photometryModel ==
"simpleMagnitude":
956 errorPedestal=self.config.photometryErrorPedestal)
962 if self.config.writeChi2FilesInitialFinal:
963 baseName = f
"photometry_initial_chi2-{dataName}"
966 if self.config.writeInitialModel:
971 def getChi2Name(whatToFit):
972 if self.config.writeChi2FilesOuterLoop:
973 return f
"photometry_init-%s_chi2-{dataName}" % whatToFit
979 dumpMatrixFile = self.
_getDebugPath(
"photometry_preinit")
if self.config.writeInitMatrix
else ""
980 if self.config.photometryModel.startswith(
"constrained"):
983 fit.minimize(
"ModelVisit", dumpMatrixFile=dumpMatrixFile)
985 writeChi2Name=getChi2Name(
"ModelVisit"))
988 fit.minimize(
"Model", doLineSearch=doLineSearch, dumpMatrixFile=dumpMatrixFile)
990 writeChi2Name=getChi2Name(
"Model"))
992 fit.minimize(
"Fluxes")
994 writeChi2Name=getChi2Name(
"Fluxes"))
996 fit.minimize(
"Model Fluxes", doLineSearch=doLineSearch)
998 writeChi2Name=getChi2Name(
"ModelFluxes"))
1000 model.freezeErrorTransform()
1001 self.log.debug(
"Photometry error scales are frozen.")
1005 self.config.maxPhotometrySteps,
1008 doRankUpdate=self.config.photometryDoRankUpdate,
1009 doLineSearch=doLineSearch,
1016 def _fit_astrometry(self, associations, dataName=None):
1018 Fit the astrometric data.
1022 associations : `lsst.jointcal.Associations`
1023 The star/reference star associations to fit.
1025 Name of the data being processed (e.g. "1234_HSC-Y"), for
1026 identifying debugging files.
1030 fit_result : `namedtuple`
1031 fit : `lsst.jointcal.AstrometryFit`
1032 The astrometric fitter used to perform the fit.
1033 model : `lsst.jointcal.AstrometryModel`
1034 The astrometric model that was fit.
1035 sky_to_tan_projection : `lsst.jointcal.ProjectionHandler`
1036 The model for the sky to tangent plane projection that was used in the fit.
1039 self.log.info(
"=== Starting astrometric fitting...")
1041 associations.deprojectFittedStars()
1048 if self.config.astrometryModel ==
"constrained":
1050 sky_to_tan_projection,
1051 chipOrder=self.config.astrometryChipOrder,
1052 visitOrder=self.config.astrometryVisitOrder)
1053 elif self.config.astrometryModel ==
"simple":
1055 sky_to_tan_projection,
1056 self.config.useInputWcs,
1058 order=self.config.astrometrySimpleOrder)
1063 if self.config.writeChi2FilesInitialFinal:
1064 baseName = f
"astrometry_initial_chi2-{dataName}"
1067 if self.config.writeInitialModel:
1072 def getChi2Name(whatToFit):
1073 if self.config.writeChi2FilesOuterLoop:
1074 return f
"astrometry_init-%s_chi2-{dataName}" % whatToFit
1078 dumpMatrixFile = self.
_getDebugPath(
"astrometry_preinit")
if self.config.writeInitMatrix
else ""
1081 if self.config.astrometryModel ==
"constrained":
1082 fit.minimize(
"DistortionsVisit", dumpMatrixFile=dumpMatrixFile)
1084 writeChi2Name=getChi2Name(
"DistortionsVisit"))
1087 fit.minimize(
"Distortions", dumpMatrixFile=dumpMatrixFile)
1089 writeChi2Name=getChi2Name(
"Distortions"))
1091 fit.minimize(
"Positions")
1093 writeChi2Name=getChi2Name(
"Positions"))
1095 fit.minimize(
"Distortions Positions")
1097 writeChi2Name=getChi2Name(
"DistortionsPositions"))
1101 self.config.maxAstrometrySteps,
1103 "Distortions Positions",
1104 doRankUpdate=self.config.astrometryDoRankUpdate,
1110 return Astrometry(fit, model, sky_to_tan_projection)
1112 def _check_stars(self, associations):
1113 """Count measured and reference stars per ccd and warn/log them."""
1114 for ccdImage
in associations.getCcdImageList():
1115 nMeasuredStars, nRefStars = ccdImage.countStars()
1116 self.log.debug(
"ccdImage %s has %s measured and %s reference stars",
1117 ccdImage.getName(), nMeasuredStars, nRefStars)
1118 if nMeasuredStars < self.config.minMeasuredStarsPerCcd:
1119 self.log.warn(
"ccdImage %s has only %s measuredStars (desired %s)",
1120 ccdImage.getName(), nMeasuredStars, self.config.minMeasuredStarsPerCcd)
1121 if nRefStars < self.config.minRefStarsPerCcd:
1122 self.log.warn(
"ccdImage %s has only %s RefStars (desired %s)",
1123 ccdImage.getName(), nRefStars, self.config.minRefStarsPerCcd)
1125 def _iterate_fit(self, associations, fitter, max_steps, name, whatToFit,
1128 doLineSearch=False):
1129 """Run fitter.minimize up to max_steps times, returning the final chi2.
1133 associations : `lsst.jointcal.Associations`
1134 The star/reference star associations to fit.
1135 fitter : `lsst.jointcal.FitterBase`
1136 The fitter to use for minimization.
1138 Maximum number of steps to run outlier rejection before declaring
1139 convergence failure.
1140 name : {'photometry' or 'astrometry'}
1141 What type of data are we fitting (for logs and debugging files).
1143 Passed to ``fitter.minimize()`` to define the parameters to fit.
1144 dataName : `str`, optional
1145 Descriptive name for this dataset (e.g. tract and filter),
1147 doRankUpdate : `bool`, optional
1148 Do an Eigen rank update during minimization, or recompute the full
1149 matrix and gradient?
1150 doLineSearch : `bool`, optional
1151 Do a line search for the optimum step during minimization?
1155 chi2: `lsst.jointcal.Chi2Statistic`
1156 The final chi2 after the fit converges, or is forced to end.
1161 Raised if the fitter fails with a non-finite value.
1163 Raised if the fitter fails for some other reason;
1164 log messages will provide further details.
1166 dumpMatrixFile = self.
_getDebugPath(f
"{name}_postinit")
if self.config.writeInitMatrix
else ""
1168 oldChi2.chi2 = float(
"inf")
1169 for i
in range(max_steps):
1170 if self.config.writeChi2FilesOuterLoop:
1171 writeChi2Name = f
"{name}_iterate_{i}_chi2-{dataName}"
1173 writeChi2Name =
None
1174 result = fitter.minimize(whatToFit,
1175 self.config.outlierRejectSigma,
1176 doRankUpdate=doRankUpdate,
1177 doLineSearch=doLineSearch,
1178 dumpMatrixFile=dumpMatrixFile)
1181 f
"Fit iteration {i}", writeChi2Name=writeChi2Name)
1183 if result == MinimizeResult.Converged:
1185 self.log.debug(
"fit has converged - no more outliers - redo minimization "
1186 "one more time in case we have lost accuracy in rank update.")
1188 result = fitter.minimize(whatToFit, self.config.outlierRejectSigma)
1192 if chi2.chi2/chi2.ndof >= 4.0:
1193 self.log.error(
"Potentially bad fit: High chi-squared/ndof.")
1196 elif result == MinimizeResult.Chi2Increased:
1197 self.log.warn(
"Still some outliers remaining but chi2 increased - retry")
1199 chi2Ratio = chi2.chi2 / oldChi2.chi2
1201 self.log.warn(
'Significant chi2 increase by a factor of %.4g / %.4g = %.4g',
1202 chi2.chi2, oldChi2.chi2, chi2Ratio)
1209 msg = (
"Large chi2 increase between steps: fit likely cannot converge."
1210 " Try setting one or more of the `writeChi2*` config fields and looking"
1211 " at how individual star chi2-values evolve during the fit.")
1212 raise RuntimeError(msg)
1214 elif result == MinimizeResult.NonFinite:
1215 filename = self.
_getDebugPath(
"{}_failure-nonfinite_chi2-{}.csv".format(name, dataName))
1217 fitter.saveChi2Contributions(filename+
"{type}")
1218 msg =
"Nonfinite value in chi2 minimization, cannot complete fit. Dumped star tables to: {}"
1219 raise FloatingPointError(msg.format(filename))
1220 elif result == MinimizeResult.Failed:
1221 raise RuntimeError(
"Chi2 minimization failure, cannot complete fit.")
1223 raise RuntimeError(
"Unxepected return code from minimize().")
1225 self.log.error(
"%s failed to converge after %d steps"%(name, max_steps))
1229 def _write_astrometry_results(self, associations, model, visit_ccd_to_dataRef):
1231 Write the fitted astrometric results to a new 'jointcal_wcs' dataRef.
1235 associations : `lsst.jointcal.Associations`
1236 The star/reference star associations to fit.
1237 model : `lsst.jointcal.AstrometryModel`
1238 The astrometric model that was fit.
1239 visit_ccd_to_dataRef : `dict` of Key: `lsst.daf.persistence.ButlerDataRef`
1240 Dict of ccdImage identifiers to dataRefs that were fit.
1243 ccdImageList = associations.getCcdImageList()
1244 for ccdImage
in ccdImageList:
1246 ccd = ccdImage.ccdId
1247 visit = ccdImage.visit
1248 dataRef = visit_ccd_to_dataRef[(visit, ccd)]
1249 self.log.info(
"Updating WCS for visit: %d, ccd: %d", visit, ccd)
1250 skyWcs = model.makeSkyWcs(ccdImage)
1252 dataRef.put(skyWcs,
'jointcal_wcs')
1253 except pexExceptions.Exception
as e:
1254 self.log.fatal(
'Failed to write updated Wcs: %s', str(e))
1257 def _write_photometry_results(self, associations, model, visit_ccd_to_dataRef):
1259 Write the fitted photometric results to a new 'jointcal_photoCalib' dataRef.
1263 associations : `lsst.jointcal.Associations`
1264 The star/reference star associations to fit.
1265 model : `lsst.jointcal.PhotometryModel`
1266 The photoometric model that was fit.
1267 visit_ccd_to_dataRef : `dict` of Key: `lsst.daf.persistence.ButlerDataRef`
1268 Dict of ccdImage identifiers to dataRefs that were fit.
1271 ccdImageList = associations.getCcdImageList()
1272 for ccdImage
in ccdImageList:
1274 ccd = ccdImage.ccdId
1275 visit = ccdImage.visit
1276 dataRef = visit_ccd_to_dataRef[(visit, ccd)]
1277 self.log.info(
"Updating PhotoCalib for visit: %d, ccd: %d", visit, ccd)
1278 photoCalib = model.toPhotoCalib(ccdImage)
1280 dataRef.put(photoCalib,
'jointcal_photoCalib')
1281 except pexExceptions.Exception
as e:
1282 self.log.fatal(
'Failed to write updated PhotoCalib: %s', str(e))