26 import astropy.units
as u
30 import lsst.pex.config
as pexConfig
37 from lsst.pipe.tasks.colorterms
import ColortermLibrary
38 from lsst.verify
import Job, Measurement
43 from .dataIds
import PerTractCcdDataIdContainer
48 __all__ = [
"JointcalConfig",
"JointcalRunner",
"JointcalTask"]
50 Photometry = collections.namedtuple(
'Photometry', (
'fit',
'model'))
51 Astrometry = collections.namedtuple(
'Astrometry', (
'fit',
'model',
'sky_to_tan_projection'))
56 meas = Measurement(job.metrics[name], value)
57 job.measurements.insert(meas)
61 """Subclass of TaskRunner for jointcalTask
63 jointcalTask.runDataRef() takes a number of arguments, one of which is a list of dataRefs
64 extracted from the command line (whereas most CmdLineTasks' runDataRef methods take
65 single dataRef, are are called repeatedly). This class transforms the processed
66 arguments generated by the ArgumentParser into the arguments expected by
67 Jointcal.runDataRef().
69 See pipeBase.TaskRunner for more information.
75 Return a list of tuples per tract, each containing (dataRefs, kwargs).
77 Jointcal operates on lists of dataRefs simultaneously.
79 kwargs[
'profile_jointcal'] = parsedCmd.profile_jointcal
80 kwargs[
'butler'] = parsedCmd.butler
84 for ref
in parsedCmd.id.refList:
85 refListDict.setdefault(ref.dataId[
"tract"], []).append(ref)
87 result = [(refListDict[tract], kwargs)
for tract
in sorted(refListDict.keys())]
95 Arguments for Task.runDataRef()
100 if self.doReturnResults is False:
102 - ``exitStatus``: 0 if the task completed successfully, 1 otherwise.
104 if self.doReturnResults is True:
106 - ``result``: the result of calling jointcal.runDataRef()
107 - ``exitStatus``: 0 if the task completed successfully, 1 otherwise.
112 dataRefList, kwargs = args
113 butler = kwargs.pop(
'butler')
114 task = self.TaskClass(config=self.config, log=self.log, butler=butler)
117 result = task.runDataRef(dataRefList, **kwargs)
118 exitStatus = result.exitStatus
119 job_path = butler.get(
'verify_job_filename')
120 result.job.write(job_path[0])
121 except Exception
as e:
126 eName = type(e).__name__
127 tract = dataRefList[0].dataId[
'tract']
128 task.log.fatal(
"Failed processing tract %s, %s: %s", tract, eName, e)
131 kwargs[
'butler'] = butler
132 if self.doReturnResults:
133 return pipeBase.Struct(result=result, exitStatus=exitStatus)
135 return pipeBase.Struct(exitStatus=exitStatus)
139 """Configuration for JointcalTask"""
141 doAstrometry = pexConfig.Field(
142 doc=
"Fit astrometry and write the fitted result.",
146 doPhotometry = pexConfig.Field(
147 doc=
"Fit photometry and write the fitted result.",
151 coaddName = pexConfig.Field(
152 doc=
"Type of coadd, typically deep or goodSeeing",
156 positionErrorPedestal = pexConfig.Field(
157 doc=
"Systematic term to apply to the measured position error (pixels)",
161 photometryErrorPedestal = pexConfig.Field(
162 doc=
"Systematic term to apply to the measured error on flux or magnitude as a "
163 "fraction of source flux or magnitude delta (e.g. 0.05 is 5% of flux or +50 millimag).",
168 matchCut = pexConfig.Field(
169 doc=
"Matching radius between fitted and reference stars (arcseconds)",
173 minMeasurements = pexConfig.Field(
174 doc=
"Minimum number of associated measured stars for a fitted star to be included in the fit",
178 minMeasuredStarsPerCcd = pexConfig.Field(
179 doc=
"Minimum number of measuredStars per ccdImage before printing warnings",
183 minRefStarsPerCcd = pexConfig.Field(
184 doc=
"Minimum number of measuredStars per ccdImage before printing warnings",
188 allowLineSearch = pexConfig.Field(
189 doc=
"Allow a line search during minimization, if it is reasonable for the model"
190 " (models with a significant non-linear component, e.g. constrainedPhotometry).",
194 astrometrySimpleOrder = pexConfig.Field(
195 doc=
"Polynomial order for fitting the simple astrometry model.",
199 astrometryChipOrder = pexConfig.Field(
200 doc=
"Order of the per-chip transform for the constrained astrometry model.",
204 astrometryVisitOrder = pexConfig.Field(
205 doc=
"Order of the per-visit transform for the constrained astrometry model.",
209 useInputWcs = pexConfig.Field(
210 doc=
"Use the input calexp WCSs to initialize a SimpleAstrometryModel.",
214 astrometryModel = pexConfig.ChoiceField(
215 doc=
"Type of model to fit to astrometry",
217 default=
"constrained",
218 allowed={
"simple":
"One polynomial per ccd",
219 "constrained":
"One polynomial per ccd, and one polynomial per visit"}
221 photometryModel = pexConfig.ChoiceField(
222 doc=
"Type of model to fit to photometry",
224 default=
"constrainedMagnitude",
225 allowed={
"simpleFlux":
"One constant zeropoint per ccd and visit, fitting in flux space.",
226 "constrainedFlux":
"Constrained zeropoint per ccd, and one polynomial per visit,"
227 " fitting in flux space.",
228 "simpleMagnitude":
"One constant zeropoint per ccd and visit,"
229 " fitting in magnitude space.",
230 "constrainedMagnitude":
"Constrained zeropoint per ccd, and one polynomial per visit,"
231 " fitting in magnitude space.",
234 applyColorTerms = pexConfig.Field(
235 doc=
"Apply photometric color terms to reference stars?"
236 "Requires that colorterms be set to a ColortermLibrary",
240 colorterms = pexConfig.ConfigField(
241 doc=
"Library of photometric reference catalog name to color term dict.",
242 dtype=ColortermLibrary,
244 photometryVisitOrder = pexConfig.Field(
245 doc=
"Order of the per-visit polynomial transform for the constrained photometry model.",
249 photometryDoRankUpdate = pexConfig.Field(
250 doc=(
"Do the rank update step during minimization. "
251 "Skipping this can help deal with models that are too non-linear."),
255 astrometryDoRankUpdate = pexConfig.Field(
256 doc=(
"Do the rank update step during minimization (should not change the astrometry fit). "
257 "Skipping this can help deal with models that are too non-linear."),
261 outlierRejectSigma = pexConfig.Field(
262 doc=
"How many sigma to reject outliers at during minimization.",
266 maxPhotometrySteps = pexConfig.Field(
267 doc=
"Maximum number of minimize iterations to take when fitting photometry.",
271 maxAstrometrySteps = pexConfig.Field(
272 doc=
"Maximum number of minimize iterations to take when fitting photometry.",
276 astrometryRefObjLoader = pexConfig.ConfigurableField(
277 target=LoadIndexedReferenceObjectsTask,
278 doc=
"Reference object loader for astrometric fit",
280 photometryRefObjLoader = pexConfig.ConfigurableField(
281 target=LoadIndexedReferenceObjectsTask,
282 doc=
"Reference object loader for photometric fit",
284 sourceSelector = sourceSelectorRegistry.makeField(
285 doc=
"How to select sources for cross-matching",
288 astrometryReferenceSelector = pexConfig.ConfigurableField(
289 target=ReferenceSourceSelectorTask,
290 doc=
"How to down-select the loaded astrometry reference catalog.",
292 photometryReferenceSelector = pexConfig.ConfigurableField(
293 target=ReferenceSourceSelectorTask,
294 doc=
"How to down-select the loaded photometry reference catalog.",
296 astrometryReferenceErr = pexConfig.Field(
297 doc=(
"Uncertainty on reference catalog coordinates [mas] to use in place of the `coord_*Err` fields. "
298 "If None, then raise an exception if the reference catalog is missing coordinate errors. "
299 "If specified, overrides any existing `coord_*Err` values."),
304 writeInitMatrix = pexConfig.Field(
306 doc=(
"Write the pre/post-initialization Hessian and gradient to text files, for debugging. "
307 "The output files will be of the form 'astrometry_preinit-mat.txt', in the current directory. "
308 "Note that these files are the dense versions of the matrix, and so may be very large."),
311 writeChi2FilesInitialFinal = pexConfig.Field(
313 doc=
"Write .csv files containing the contributions to chi2 for the initialization and final fit.",
316 writeChi2FilesOuterLoop = pexConfig.Field(
318 doc=
"Write .csv files containing the contributions to chi2 for the outer fit loop.",
321 writeInitialModel = pexConfig.Field(
323 doc=(
"Write the pre-initialization model to text files, for debugging."
324 " Output is written to `initial[Astro|Photo]metryModel.txt` in the current working directory."),
327 debugOutputPath = pexConfig.Field(
330 doc=(
"Path to write debug output files to. Used by "
331 "`writeInitialModel`, `writeChi2Files*`, `writeInitMatrix`.")
333 sourceFluxType = pexConfig.Field(
335 doc=
"Source flux field to use in source selection and to get fluxes from the catalog.",
342 msg =
"applyColorTerms=True requires the `colorterms` field be set to a ColortermLibrary."
343 raise pexConfig.FieldValidationError(JointcalConfig.colorterms, self, msg)
345 msg = (
"Only doing astrometry, but Colorterms are not applied for astrometry;"
346 "applyColorTerms=True will be ignored.")
360 fluxField = f
"slot_{self.sourceFluxType}Flux_instFlux"
361 self.
sourceSelector[
'science'].signalToNoise.fluxField = fluxField
362 self.
sourceSelector[
'science'].signalToNoise.errField = fluxField +
"Err"
368 badFlags = [
'base_PixelFlags_flag_edge',
'base_PixelFlags_flag_saturated',
369 'base_PixelFlags_flag_interpolatedCenter',
'base_SdssCentroid_flag',
370 'base_PsfFlux_flag',
'base_PixelFlags_flag_suspectCenter']
375 """Write model to outfile."""
376 with open(filename,
"w")
as file:
377 file.write(repr(model))
378 log.info(
"Wrote %s to file: %s", model, filename)
382 """Jointly astrometrically and photometrically calibrate a group of images."""
384 ConfigClass = JointcalConfig
385 RunnerClass = JointcalRunner
386 _DefaultName =
"jointcal"
388 def __init__(self, butler=None, profile_jointcal=False, **kwargs):
390 Instantiate a JointcalTask.
394 butler : `lsst.daf.persistence.Butler`
395 The butler is passed to the refObjLoader constructor in case it is
396 needed. Ignored if the refObjLoader argument provides a loader directly.
397 Used to initialize the astrometry and photometry refObjLoaders.
398 profile_jointcal : `bool`
399 Set to True to profile different stages of this jointcal run.
401 pipeBase.CmdLineTask.__init__(self, **kwargs)
403 self.makeSubtask(
"sourceSelector")
404 if self.config.doAstrometry:
405 self.makeSubtask(
'astrometryRefObjLoader', butler=butler)
406 self.makeSubtask(
"astrometryReferenceSelector")
409 if self.config.doPhotometry:
410 self.makeSubtask(
'photometryRefObjLoader', butler=butler)
411 self.makeSubtask(
"photometryReferenceSelector")
416 self.
job = Job.load_metrics_package(subset=
'jointcal')
421 def _getMetadataName(self):
425 def _makeArgumentParser(cls):
426 """Create an argument parser"""
428 parser.add_argument(
"--profile_jointcal", default=
False, action=
"store_true",
429 help=
"Profile steps of jointcal separately.")
430 parser.add_id_argument(
"--id",
"calexp", help=
"data ID, e.g. --id visit=6789 ccd=0..9",
431 ContainerClass=PerTractCcdDataIdContainer)
434 def _build_ccdImage(self, dataRef, associations, jointcalControl):
436 Extract the necessary things from this dataRef to add a new ccdImage.
440 dataRef : `lsst.daf.persistence.ButlerDataRef`
441 DataRef to extract info from.
442 associations : `lsst.jointcal.Associations`
443 Object to add the info to, to construct a new CcdImage
444 jointcalControl : `jointcal.JointcalControl`
445 Control object for associations management
451 The TAN WCS of this image, read from the calexp
452 (`lsst.afw.geom.SkyWcs`).
454 A key to identify this dataRef by its visit and ccd ids
457 This calexp's filter (`str`).
459 if "visit" in dataRef.dataId.keys():
460 visit = dataRef.dataId[
"visit"]
462 visit = dataRef.getButler().queryMetadata(
"calexp", (
"visit"), dataRef.dataId)[0]
464 src = dataRef.get(
"src", flags=lsst.afw.table.SOURCE_IO_NO_FOOTPRINTS, immediate=
True)
466 visitInfo = dataRef.get(
'calexp_visitInfo')
467 detector = dataRef.get(
'calexp_detector')
468 ccdId = detector.getId()
469 photoCalib = dataRef.get(
'calexp_photoCalib')
470 tanWcs = dataRef.get(
'calexp_wcs')
471 bbox = dataRef.get(
'calexp_bbox')
472 filt = dataRef.get(
'calexp_filter')
473 filterName = filt.getName()
475 goodSrc = self.sourceSelector.run(src)
477 if len(goodSrc.sourceCat) == 0:
478 self.log.warn(
"No sources selected in visit %s ccd %s", visit, ccdId)
480 self.log.info(
"%d sources selected in visit %d ccd %d", len(goodSrc.sourceCat), visit, ccdId)
481 associations.createCcdImage(goodSrc.sourceCat,
492 Result = collections.namedtuple(
'Result_from_build_CcdImage', (
'wcs',
'key',
'filter'))
493 Key = collections.namedtuple(
'Key', (
'visit',
'ccd'))
494 return Result(tanWcs, Key(visit, ccdId), filterName)
496 def _getDebugPath(self, filename):
497 """Constructs a path to filename using the configured debug path.
499 return os.path.join(self.config.debugOutputPath, filename)
504 Jointly calibrate the astrometry and photometry across a set of images.
508 dataRefs : `list` of `lsst.daf.persistence.ButlerDataRef`
509 List of data references to the exposures to be fit.
510 profile_jointcal : `bool`
511 Profile the individual steps of jointcal.
515 result : `lsst.pipe.base.Struct`
516 Struct of metadata from the fit, containing:
519 The provided data references that were fit (with updated WCSs)
521 The original WCS from each dataRef
523 Dictionary of internally-computed metrics for testing/validation.
525 if len(dataRefs) == 0:
526 raise ValueError(
'Need a non-empty list of data references!')
530 sourceFluxField =
"slot_%sFlux" % (self.config.sourceFluxType,)
534 visit_ccd_to_dataRef = {}
537 load_cat_prof_file =
'jointcal_build_ccdImage.prof' if profile_jointcal
else ''
538 with pipeBase.cmdLineTask.profile(load_cat_prof_file):
541 camera = dataRefs[0].get(
'camera', immediate=
True)
545 oldWcsList.append(result.wcs)
546 visit_ccd_to_dataRef[result.key] = ref
547 filters.append(result.filter)
548 filters = collections.Counter(filters)
550 associations.computeCommonTangentPoint()
552 boundingCircle = associations.computeBoundingCircle()
554 radius =
lsst.geom.Angle(boundingCircle.getOpeningAngle().asRadians(), lsst.geom.radians)
556 self.log.info(f
"Data has center={center} with radius={radius.asDegrees()} degrees.")
559 defaultFilter = filters.most_common(1)[0][0]
560 self.log.debug(
"Using %s band for reference flux", defaultFilter)
563 tract = dataRefs[0].dataId[
'tract']
565 if self.config.doAstrometry:
569 referenceSelector=self.astrometryReferenceSelector,
571 profile_jointcal=profile_jointcal,
577 if self.config.doPhotometry:
581 referenceSelector=self.photometryReferenceSelector,
583 profile_jointcal=profile_jointcal,
586 reject_bad_fluxes=
True)
591 return pipeBase.Struct(dataRefs=dataRefs,
592 oldWcsList=oldWcsList,
596 defaultFilter=defaultFilter,
597 exitStatus=exitStatus)
599 def _do_load_refcat_and_fit(self, associations, defaultFilter, center, radius,
601 tract="", profile_jointcal=False, match_cut=3.0,
602 reject_bad_fluxes=False, *,
603 name="", refObjLoader=None, referenceSelector=None,
605 """Load reference catalog, perform the fit, and return the result.
609 associations : `lsst.jointcal.Associations`
610 The star/reference star associations to fit.
611 defaultFilter : `str`
612 filter to load from reference catalog.
613 center : `lsst.geom.SpherePoint`
614 ICRS center of field to load from reference catalog.
615 radius : `lsst.geom.Angle`
616 On-sky radius to load from reference catalog.
618 Name of thing being fit: "astrometry" or "photometry".
619 refObjLoader : `lsst.meas.algorithms.LoadReferenceObjectsTask`
620 Reference object loader to use to load a reference catalog.
621 referenceSelector : `lsst.meas.algorithms.ReferenceSourceSelectorTask`
622 Selector to use to pick objects from the loaded reference catalog.
623 fit_function : callable
624 Function to call to perform fit (takes Associations object).
625 filters : `list` [`str`], optional
626 List of filters to load from the reference catalog.
627 tract : `str`, optional
628 Name of tract currently being fit.
629 profile_jointcal : `bool`, optional
630 Separately profile the fitting step.
631 match_cut : `float`, optional
632 Radius in arcseconds to find cross-catalog matches to during
633 associations.associateCatalogs.
634 reject_bad_fluxes : `bool`, optional
635 Reject refCat sources with NaN/inf flux or NaN/0 fluxErr.
639 result : `Photometry` or `Astrometry`
640 Result of `fit_function()`
642 self.log.info(
"====== Now processing %s...", name)
645 associations.associateCatalogs(match_cut)
647 associations.fittedStarListSize())
649 applyColorterms =
False if name.lower() ==
"astrometry" else self.config.applyColorTerms
651 center, radius, defaultFilter,
652 applyColorterms=applyColorterms)
654 if self.config.astrometryReferenceErr
is None:
655 refCoordErr = float(
'nan')
657 refCoordErr = self.config.astrometryReferenceErr
659 associations.collectRefStars(refCat,
660 self.config.matchCut*lsst.geom.arcseconds,
662 refCoordinateErr=refCoordErr,
663 rejectBadFluxes=reject_bad_fluxes)
665 associations.refStarListSize())
667 associations.prepareFittedStars(self.config.minMeasurements)
671 associations.nFittedStarsWithAssociatedRefStar())
673 associations.fittedStarListSize())
675 associations.nCcdImagesValidForFit())
677 load_cat_prof_file =
'jointcal_fit_%s.prof'%name
if profile_jointcal
else ''
678 dataName =
"{}_{}".format(tract, defaultFilter)
679 with pipeBase.cmdLineTask.profile(load_cat_prof_file):
680 result = fit_function(associations, dataName)
683 if self.config.writeChi2FilesInitialFinal:
684 baseName = self.
_getDebugPath(f
"{name}_final_chi2-{dataName}")
685 result.fit.saveChi2Contributions(baseName+
"{type}")
686 self.log.info(
"Wrote chi2 contributions files: %s", baseName)
690 def _load_reference_catalog(self, refObjLoader, referenceSelector, center, radius, filterName,
691 applyColorterms=False):
692 """Load the necessary reference catalog sources, convert fluxes to
693 correct units, and apply color term corrections if requested.
697 refObjLoader : `lsst.meas.algorithms.LoadReferenceObjectsTask`
698 The reference catalog loader to use to get the data.
699 referenceSelector : `lsst.meas.algorithms.ReferenceSourceSelectorTask`
700 Source selector to apply to loaded reference catalog.
701 center : `lsst.geom.SpherePoint`
702 The center around which to load sources.
703 radius : `lsst.geom.Angle`
704 The radius around ``center`` to load sources in.
706 The name of the camera filter to load fluxes for.
707 applyColorterms : `bool`
708 Apply colorterm corrections to the refcat for ``filterName``?
712 refCat : `lsst.afw.table.SimpleCatalog`
713 The loaded reference catalog.
715 The name of the reference catalog flux field appropriate for ``filterName``.
717 skyCircle = refObjLoader.loadSkyCircle(center,
721 selected = referenceSelector.run(skyCircle.refCat)
723 if not selected.sourceCat.isContiguous():
724 refCat = selected.sourceCat.copy(deep=
True)
726 refCat = selected.sourceCat
728 if self.config.astrometryReferenceErr
is None and 'coord_raErr' not in refCat.schema:
729 msg = (
"Reference catalog does not contain coordinate errors, "
730 "and config.astrometryReferenceErr not supplied.")
731 raise pexConfig.FieldValidationError(JointcalConfig.astrometryReferenceErr,
735 if self.config.astrometryReferenceErr
is not None and 'coord_raErr' in refCat.schema:
736 self.log.warn(
"Overriding reference catalog coordinate errors with %f/coordinate [mas]",
737 self.config.astrometryReferenceErr)
741 refCatName = refObjLoader.ref_dataset_name
742 except AttributeError:
744 raise RuntimeError(
"Cannot perform colorterm corrections with a.net refcats.")
745 self.log.info(
"Applying color terms for filterName=%r reference catalog=%s",
746 filterName, refCatName)
747 colorterm = self.config.colorterms.getColorterm(
748 filterName=filterName, photoCatName=refCatName, doRaise=
True)
750 refMag, refMagErr = colorterm.getCorrectedMagnitudes(refCat, filterName)
751 refCat[skyCircle.fluxField] = u.Magnitude(refMag, u.ABmag).to_value(u.nJy)
753 refCat[skyCircle.fluxField+
'Err'] = fluxErrFromABMagErr(refMagErr, refMag) * 1e9
755 return refCat, skyCircle.fluxField
757 def _check_star_lists(self, associations, name):
759 if associations.nCcdImagesValidForFit() == 0:
760 raise RuntimeError(
'No images in the ccdImageList!')
761 if associations.fittedStarListSize() == 0:
762 raise RuntimeError(
'No stars in the {} fittedStarList!'.format(name))
763 if associations.refStarListSize() == 0:
764 raise RuntimeError(
'No stars in the {} reference star list!'.format(name))
766 def _logChi2AndValidate(self, associations, fit, model, chi2Label="Model",
768 """Compute chi2, log it, validate the model, and return chi2.
772 associations : `lsst.jointcal.Associations`
773 The star/reference star associations to fit.
774 fit : `lsst.jointcal.FitterBase`
775 The fitter to use for minimization.
776 model : `lsst.jointcal.Model`
778 chi2Label : str, optional
779 Label to describe the chi2 (e.g. "Initialized", "Final").
780 writeChi2Name : `str`, optional
781 Filename prefix to write the chi2 contributions to.
782 Do not supply an extension: an appropriate one will be added.
786 chi2: `lsst.jointcal.Chi2Accumulator`
787 The chi2 object for the current fitter and model.
792 Raised if chi2 is infinite or NaN.
794 Raised if the model is not valid.
796 if writeChi2Name
is not None:
798 fit.saveChi2Contributions(fullpath+
"{type}")
799 self.log.info(
"Wrote chi2 contributions files: %s", fullpath)
801 chi2 = fit.computeChi2()
802 self.log.info(
"%s %s", chi2Label, chi2)
804 if not np.isfinite(chi2.chi2):
805 raise FloatingPointError(f
'{chi2Label} chi2 is invalid: {chi2}')
806 if not model.validate(associations.getCcdImageList(), chi2.ndof):
807 raise ValueError(
"Model is not valid: check log messages for warnings.")
810 def _fit_photometry(self, associations, dataName=None):
812 Fit the photometric data.
816 associations : `lsst.jointcal.Associations`
817 The star/reference star associations to fit.
819 Name of the data being processed (e.g. "1234_HSC-Y"), for
820 identifying debugging files.
824 fit_result : `namedtuple`
825 fit : `lsst.jointcal.PhotometryFit`
826 The photometric fitter used to perform the fit.
827 model : `lsst.jointcal.PhotometryModel`
828 The photometric model that was fit.
830 self.log.info(
"=== Starting photometric fitting...")
833 if self.config.photometryModel ==
"constrainedFlux":
836 visitOrder=self.config.photometryVisitOrder,
837 errorPedestal=self.config.photometryErrorPedestal)
839 doLineSearch = self.config.allowLineSearch
840 elif self.config.photometryModel ==
"constrainedMagnitude":
843 visitOrder=self.config.photometryVisitOrder,
844 errorPedestal=self.config.photometryErrorPedestal)
846 doLineSearch = self.config.allowLineSearch
847 elif self.config.photometryModel ==
"simpleFlux":
849 errorPedestal=self.config.photometryErrorPedestal)
851 elif self.config.photometryModel ==
"simpleMagnitude":
853 errorPedestal=self.config.photometryErrorPedestal)
859 if self.config.writeChi2FilesInitialFinal:
860 baseName = f
"photometry_initial_chi2-{dataName}"
863 if self.config.writeInitialModel:
868 def getChi2Name(whatToFit):
869 if self.config.writeChi2FilesOuterLoop:
870 return f
"photometry_init-%s_chi2-{dataName}" % whatToFit
876 dumpMatrixFile = self.
_getDebugPath(
"photometry_preinit")
if self.config.writeInitMatrix
else ""
877 if self.config.photometryModel.startswith(
"constrained"):
880 fit.minimize(
"ModelVisit", dumpMatrixFile=dumpMatrixFile)
881 self.
_logChi2AndValidate(associations, fit, model, writeChi2Name=getChi2Name(
"ModelVisit"))
884 fit.minimize(
"Model", doLineSearch=doLineSearch, dumpMatrixFile=dumpMatrixFile)
887 fit.minimize(
"Fluxes")
890 fit.minimize(
"Model Fluxes", doLineSearch=doLineSearch)
892 writeChi2Name=getChi2Name(
"ModelFluxes"))
894 model.freezeErrorTransform()
895 self.log.debug(
"Photometry error scales are frozen.")
899 self.config.maxPhotometrySteps,
902 doRankUpdate=self.config.photometryDoRankUpdate,
903 doLineSearch=doLineSearch,
910 def _fit_astrometry(self, associations, dataName=None):
912 Fit the astrometric data.
916 associations : `lsst.jointcal.Associations`
917 The star/reference star associations to fit.
919 Name of the data being processed (e.g. "1234_HSC-Y"), for
920 identifying debugging files.
924 fit_result : `namedtuple`
925 fit : `lsst.jointcal.AstrometryFit`
926 The astrometric fitter used to perform the fit.
927 model : `lsst.jointcal.AstrometryModel`
928 The astrometric model that was fit.
929 sky_to_tan_projection : `lsst.jointcal.ProjectionHandler`
930 The model for the sky to tangent plane projection that was used in the fit.
933 self.log.info(
"=== Starting astrometric fitting...")
935 associations.deprojectFittedStars()
942 if self.config.astrometryModel ==
"constrained":
944 sky_to_tan_projection,
945 chipOrder=self.config.astrometryChipOrder,
946 visitOrder=self.config.astrometryVisitOrder)
947 elif self.config.astrometryModel ==
"simple":
949 sky_to_tan_projection,
950 self.config.useInputWcs,
952 order=self.config.astrometrySimpleOrder)
957 if self.config.writeChi2FilesInitialFinal:
958 baseName = f
"astrometry_initial_chi2-{dataName}"
961 if self.config.writeInitialModel:
966 def getChi2Name(whatToFit):
967 if self.config.writeChi2FilesOuterLoop:
968 return f
"astrometry_init-%s_chi2-{dataName}" % whatToFit
972 dumpMatrixFile = self.
_getDebugPath(
"astrometry_preinit")
if self.config.writeInitMatrix
else ""
975 if self.config.astrometryModel ==
"constrained":
976 fit.minimize(
"DistortionsVisit", dumpMatrixFile=dumpMatrixFile)
977 self.
_logChi2AndValidate(associations, fit, model, writeChi2Name=getChi2Name(
"DistortionsVisit"))
980 fit.minimize(
"Distortions", dumpMatrixFile=dumpMatrixFile)
981 self.
_logChi2AndValidate(associations, fit, model, writeChi2Name=getChi2Name(
"Distortions"))
983 fit.minimize(
"Positions")
986 fit.minimize(
"Distortions Positions")
988 writeChi2Name=getChi2Name(
"DistortionsPositions"))
992 self.config.maxAstrometrySteps,
994 "Distortions Positions",
995 doRankUpdate=self.config.astrometryDoRankUpdate,
1001 return Astrometry(fit, model, sky_to_tan_projection)
1003 def _check_stars(self, associations):
1004 """Count measured and reference stars per ccd and warn/log them."""
1005 for ccdImage
in associations.getCcdImageList():
1006 nMeasuredStars, nRefStars = ccdImage.countStars()
1007 self.log.debug(
"ccdImage %s has %s measured and %s reference stars",
1008 ccdImage.getName(), nMeasuredStars, nRefStars)
1009 if nMeasuredStars < self.config.minMeasuredStarsPerCcd:
1010 self.log.warn(
"ccdImage %s has only %s measuredStars (desired %s)",
1011 ccdImage.getName(), nMeasuredStars, self.config.minMeasuredStarsPerCcd)
1012 if nRefStars < self.config.minRefStarsPerCcd:
1013 self.log.warn(
"ccdImage %s has only %s RefStars (desired %s)",
1014 ccdImage.getName(), nRefStars, self.config.minRefStarsPerCcd)
1016 def _iterate_fit(self, associations, fitter, max_steps, name, whatToFit,
1019 doLineSearch=False):
1020 """Run fitter.minimize up to max_steps times, returning the final chi2.
1024 associations : `lsst.jointcal.Associations`
1025 The star/reference star associations to fit.
1026 fitter : `lsst.jointcal.FitterBase`
1027 The fitter to use for minimization.
1029 Maximum number of steps to run outlier rejection before declaring
1030 convergence failure.
1031 name : {'photometry' or 'astrometry'}
1032 What type of data are we fitting (for logs and debugging files).
1034 Passed to ``fitter.minimize()`` to define the parameters to fit.
1035 dataName : `str`, optional
1036 Descriptive name for this dataset (e.g. tract and filter),
1038 doRankUpdate : `bool`, optional
1039 Do an Eigen rank update during minimization, or recompute the full
1040 matrix and gradient?
1041 doLineSearch : `bool`, optional
1042 Do a line search for the optimum step during minimization?
1046 chi2: `lsst.jointcal.Chi2Statistic`
1047 The final chi2 after the fit converges, or is forced to end.
1052 Raised if the fitter fails with a non-finite value.
1054 Raised if the fitter fails for some other reason;
1055 log messages will provide further details.
1057 dumpMatrixFile = self.
_getDebugPath(f
"{name}_postinit")
if self.config.writeInitMatrix
else ""
1058 for i
in range(max_steps):
1059 if self.config.writeChi2FilesOuterLoop:
1060 writeChi2Name = f
"{name}_iterate_{i}_chi2-{dataName}"
1062 writeChi2Name =
None
1063 result = fitter.minimize(whatToFit,
1064 self.config.outlierRejectSigma,
1065 doRankUpdate=doRankUpdate,
1066 doLineSearch=doLineSearch,
1067 dumpMatrixFile=dumpMatrixFile)
1070 writeChi2Name=writeChi2Name)
1072 if result == MinimizeResult.Converged:
1074 self.log.debug(
"fit has converged - no more outliers - redo minimization "
1075 "one more time in case we have lost accuracy in rank update.")
1077 result = fitter.minimize(whatToFit, self.config.outlierRejectSigma)
1081 if chi2.chi2/chi2.ndof >= 4.0:
1082 self.log.error(
"Potentially bad fit: High chi-squared/ndof.")
1085 elif result == MinimizeResult.Chi2Increased:
1086 self.log.warn(
"still some outliers but chi2 increases - retry")
1087 elif result == MinimizeResult.NonFinite:
1088 filename = self.
_getDebugPath(
"{}_failure-nonfinite_chi2-{}.csv".format(name, dataName))
1090 fitter.saveChi2Contributions(filename+
"{type}")
1091 msg =
"Nonfinite value in chi2 minimization, cannot complete fit. Dumped star tables to: {}"
1092 raise FloatingPointError(msg.format(filename))
1093 elif result == MinimizeResult.Failed:
1094 raise RuntimeError(
"Chi2 minimization failure, cannot complete fit.")
1096 raise RuntimeError(
"Unxepected return code from minimize().")
1098 self.log.error(
"%s failed to converge after %d steps"%(name, max_steps))
1102 def _write_astrometry_results(self, associations, model, visit_ccd_to_dataRef):
1104 Write the fitted astrometric results to a new 'jointcal_wcs' dataRef.
1108 associations : `lsst.jointcal.Associations`
1109 The star/reference star associations to fit.
1110 model : `lsst.jointcal.AstrometryModel`
1111 The astrometric model that was fit.
1112 visit_ccd_to_dataRef : `dict` of Key: `lsst.daf.persistence.ButlerDataRef`
1113 Dict of ccdImage identifiers to dataRefs that were fit.
1116 ccdImageList = associations.getCcdImageList()
1117 for ccdImage
in ccdImageList:
1119 ccd = ccdImage.ccdId
1120 visit = ccdImage.visit
1121 dataRef = visit_ccd_to_dataRef[(visit, ccd)]
1122 self.log.info(
"Updating WCS for visit: %d, ccd: %d", visit, ccd)
1123 skyWcs = model.makeSkyWcs(ccdImage)
1125 dataRef.put(skyWcs,
'jointcal_wcs')
1126 except pexExceptions.Exception
as e:
1127 self.log.fatal(
'Failed to write updated Wcs: %s', str(e))
1130 def _write_photometry_results(self, associations, model, visit_ccd_to_dataRef):
1132 Write the fitted photometric results to a new 'jointcal_photoCalib' dataRef.
1136 associations : `lsst.jointcal.Associations`
1137 The star/reference star associations to fit.
1138 model : `lsst.jointcal.PhotometryModel`
1139 The photoometric model that was fit.
1140 visit_ccd_to_dataRef : `dict` of Key: `lsst.daf.persistence.ButlerDataRef`
1141 Dict of ccdImage identifiers to dataRefs that were fit.
1144 ccdImageList = associations.getCcdImageList()
1145 for ccdImage
in ccdImageList:
1147 ccd = ccdImage.ccdId
1148 visit = ccdImage.visit
1149 dataRef = visit_ccd_to_dataRef[(visit, ccd)]
1150 self.log.info(
"Updating PhotoCalib for visit: %d, ccd: %d", visit, ccd)
1151 photoCalib = model.toPhotoCalib(ccdImage)
1153 dataRef.put(photoCalib,
'jointcal_photoCalib')
1154 except pexExceptions.Exception
as e:
1155 self.log.fatal(
'Failed to write updated PhotoCalib: %s', str(e))