24 __all__ = [
"getRefFluxField",
"getRefFluxKeys",
"LoadReferenceObjectsTask",
"LoadReferenceObjectsConfig",
25 "ReferenceObjectLoader"]
42 from lsst
import sphgeom
47 """Return True if this name/units combination corresponds to an
48 "old-style" reference catalog flux field.
50 unitsCheck = units !=
'nJy'
51 isFlux = name.endswith(
'_flux')
52 isFluxSigma = name.endswith(
'_fluxSigma')
53 isFluxErr = name.endswith(
'_fluxErr')
54 return (isFlux
or isFluxSigma
or isFluxErr)
and unitsCheck
58 """Return True if the units of all flux and fluxErr are correct (nJy).
67 """"Return the format version stored in a reference catalog header.
71 refCat : `lsst.afw.table.SimpleCatalog`
72 Reference catalog to inspect.
76 version : `int` or `None`
77 Format version integer, or `None` if the catalog has no metadata
78 or the metadata does not include a "REFCAT_FORMAT_VERSION" key.
80 md = refCat.getMetadata()
84 return md.getScalar(
"REFCAT_FORMAT_VERSION")
90 """Convert fluxes in a catalog from jansky to nanojansky.
94 catalog : `lsst.afw.table.SimpleCatalog`
95 The catalog to convert.
97 Log to send messages to.
98 doConvert : `bool`, optional
99 Return a converted catalog, or just identify the fields that need to be converted?
100 This supports the "write=False" mode of `bin/convert_to_nJy.py`.
104 catalog : `lsst.afw.table.SimpleCatalog` or None
105 The converted catalog, or None if ``doConvert`` is False.
109 Support for old units in reference catalogs will be removed after the
110 release of late calendar year 2019.
111 Use `meas_algorithms/bin/convert_to_nJy.py` to update your reference catalog.
119 for field
in catalog.schema:
120 oldName = field.field.getName()
121 oldUnits = field.field.getUnits()
125 if oldName.endswith(
'_fluxSigma'):
126 name = oldName.replace(
'_fluxSigma',
'_fluxErr')
130 mapper.addMapping(field.getKey(), newField)
131 input_fields.append(field.field)
132 output_fields.append(newField)
134 mapper.addMapping(field.getKey())
136 fluxFieldsStr =
'; '.join(
"(%s, '%s')" % (field.getName(), field.getUnits())
for field
in input_fields)
139 newSchema = mapper.getOutputSchema()
141 output.extend(catalog, mapper=mapper)
142 for field
in output_fields:
143 output[field.getName()] *= 1e9
144 log.info(f
"Converted refcat flux fields to nJy (name, units): {fluxFieldsStr}")
147 log.info(f
"Found old-style refcat flux fields (name, units): {fluxFieldsStr}")
152 """This is a private helper class which filters catalogs by
153 row based on the row being inside the region used to initialize
158 region : `lsst.sphgeom.Region`
159 The spatial region which all objects should lie within
165 """This call method on an instance of this class takes in a reference
166 catalog, and the region from which the catalog was generated.
168 If the catalog region is entirely contained within the region used to
169 initialize this class, then all the entries in the catalog must be
170 within the region and so the whole catalog is returned.
172 If the catalog region is not entirely contained, then the location for
173 each record is tested against the region used to initialize the class.
174 Records which fall inside this region are added to a new catalog, and
175 this catalog is then returned.
179 refCat : `lsst.afw.table.SourceCatalog`
180 SourceCatalog to be filtered.
181 catRegion : `lsst.sphgeom.Region`
182 Region in which the catalog was created
184 if catRegion.isWithin(self.
regionregion):
188 filteredRefCat = type(refCat)(refCat.table)
189 for record
in refCat:
190 if self.
regionregion.contains(record.getCoord().getVector()):
191 filteredRefCat.append(record)
192 return filteredRefCat
196 """ This class facilitates loading reference catalogs with gen 3 middleware
198 The middleware preflight solver will create a list of datarefs that may
199 possibly overlap a given region. These datarefs are then used to construct
200 and instance of this class. The class instance should then be passed into
201 a task which needs reference catalogs. These tasks should then determine
202 the exact region of the sky reference catalogs will be loaded for, and
203 call a corresponding method to load the reference objects.
205 def __init__(self, dataIds, refCats, config, log=None):
206 """ Constructs an instance of ReferenceObjectLoader
210 dataIds : iterable of `lsst.daf.butler.DataIds`
211 An iterable object of DataSetRefs which point to reference catalogs
212 in a gen 3 repository
213 refCats : Iterable of `lsst.daf.butler.DeferedDatasetHandle`
214 Handles to load refCats on demand
216 Logger object used to write out messages. If `None` (default) the default
217 lsst logger will be used
226 def _makeBoxRegion(BBox, wcs, BBoxPadding):
233 outerLocalBBox.grow(BBoxPadding)
234 innerLocalBBox.grow(-1*BBoxPadding)
242 innerBoxCorners = innerLocalBBox.getCorners()
243 innerSphCorners = [wcs.pixelToSky(corner).getVector()
for corner
in innerBoxCorners]
248 outerBoxCorners = outerLocalBBox.getCorners()
249 outerSphCorners = [wcs.pixelToSky(corner).getVector()
for corner
in outerBoxCorners]
253 return innerSkyRegion, outerSkyRegion, innerSphCorners, outerSphCorners
255 def loadPixelBox(self, bbox, wcs, filterName=None, epoch=None, photoCalib=None, bboxPadding=100):
256 """Load reference objects that are within a pixel-based rectangular region
258 This algorithm works by creating a spherical box whose corners correspond
259 to the WCS converted corners of the input bounding box (possibly padded).
260 It then defines a filtering function which will look at a reference
261 objects pixel position and accept objects that lie within the specified
264 The spherical box region and filtering function are passed to the generic
265 loadRegion method which will load and filter the reference objects from
266 the datastore and return a single catalog containing all reference objects
270 bbox : `lsst.geom.box2I`
271 Box which bounds a region in pixel space
272 wcs : `lsst.afw.geom.SkyWcs`
273 Wcs object defining the pixel to sky (and inverse) transform for the space
274 of pixels of the supplied bbox
276 Name of camera filter, or None or blank for the default filter
277 epoch : `astropy.time.Time` (optional)
278 Epoch to which to correct proper motion and parallax,
279 or None to not apply such corrections.
281 Deprecated and ignored, only included for api compatibility
283 Number describing how much to pad the input bbox by (in pixels), defaults
284 to 100. This parameter is necessary because optical distortions in telescopes
285 can cause a rectangular pixel grid to map into a non "rectangular" spherical
286 region in sky coordinates. This padding is used to create a spherical
287 "rectangle", which will for sure enclose the input box. This padding is only
288 used to determine if the reference catalog for a sky patch will be loaded from
289 the data store, this function will filter out objects which lie within the
290 padded region but fall outside the input bounding box region.
294 referenceCatalog : `lsst.afw.table.SimpleCatalog`
295 Catalog containing reference objects inside the specified bounding box
299 `lsst.pex.exception.RuntimeError`
300 Raised if no reference catalogs could be found for the specified region
302 `lsst.pex.exception.TypeError`
303 Raised if the loaded reference catalogs do not have matching schemas
305 innerSkyRegion, outerSkyRegion, _, _ = self.
_makeBoxRegion_makeBoxRegion(bbox, wcs, bboxPadding)
307 def _filterFunction(refCat, region):
311 afwTable.updateRefCentroids(wcs, refCat)
314 if innerSkyRegion.contains(region):
317 filteredRefCat = type(refCat)(refCat.table)
318 centroidKey = afwTable.Point2DKey(refCat.schema[
'centroid'])
319 for record
in refCat:
320 pixCoords = record[centroidKey]
322 filteredRefCat.append(record)
323 return filteredRefCat
324 return self.
loadRegionloadRegion(outerSkyRegion, filtFunc=_filterFunction, epoch=epoch, filterName=filterName)
326 def loadRegion(self, region, filtFunc=None, filterName=None, epoch=None):
327 """ Load reference objects within a specified region
329 This function loads the DataIds used to construct an instance of this class
330 which intersect or are contained within the specified region. The reference
331 catalogs which intersect but are not fully contained within the input region are
332 further filtered by the specified filter function. This function will return a
333 single source catalog containing all reference objects inside the specified region.
337 region : `lsst.sphgeom.Region`
338 This can be any type that is derived from `lsst.sphgeom.region` and should
339 define the spatial region for which reference objects are to be loaded.
341 This optional parameter should be a callable object that takes a reference
342 catalog and its corresponding region as parameters, filters the catalog by
343 some criteria and returns the filtered reference catalog. If the value is
344 left as the default (None) than an internal filter function is used which
345 filters according to if a reference object falls within the input region.
347 Name of camera filter, or None or blank for the default filter
348 epoch : `astropy.time.Time` (optional)
349 Epoch to which to correct proper motion and parallax,
350 or None to not apply such corrections.
354 referenceCatalog : `lsst.afw.table.SourceCatalog`
355 Catalog containing reference objects which intersect the input region,
356 filtered by the specified filter function
360 `lsst.pex.exception.RuntimeError`
361 Raised if no reference catalogs could be found for the specified region
363 `lsst.pex.exception.TypeError`
364 Raised if the loaded reference catalogs do not have matching schemas
367 regionBounding = region.getBoundingBox()
368 self.
loglog.info(
"Loading reference objects from region bounded by {}, {} lat lon".format(
369 regionBounding.getLat(), regionBounding.getLon()))
374 for dataId, refCat
in zip(self.
dataIdsdataIds, self.
refCatsrefCats):
378 intersects = dataId.region.intersects(region)
380 intersects = region.intersects(dataId.region)
383 overlapList.append((dataId, refCat))
385 if len(overlapList) == 0:
386 raise pexExceptions.RuntimeError(
"No reference tables could be found for input region")
388 firstCat = overlapList[0][1].get()
389 refCat = filtFunc(firstCat, overlapList[0][0].region)
390 trimmedAmount = len(firstCat) - len(refCat)
393 for dataId, inputRefCat
in overlapList[1:]:
394 tmpCat = inputRefCat.get()
396 if tmpCat.schema != firstCat.schema:
397 raise pexExceptions.TypeError(
"Reference catalogs have mismatching schemas")
399 filteredCat = filtFunc(tmpCat, dataId.region)
400 refCat.extend(filteredCat)
401 trimmedAmount += len(tmpCat) - len(filteredCat)
403 self.
loglog.debug(f
"Trimmed {trimmedAmount} out of region objects, leaving {len(refCat)}")
404 self.
loglog.info(f
"Loaded {len(refCat)} reference objects")
407 if not refCat.isContiguous():
408 refCat = refCat.copy(deep=
True)
410 if epoch
is not None and "pm_ra" in refCat.schema:
412 if isinstance(refCat.schema[
"pm_ra"].asKey(), lsst.afw.table.KeyAngle):
415 self.
loglog.warn(
"Catalog pm_ra field is not an Angle; not applying proper motion")
420 self.
loglog.warn(
"Found version 0 reference catalog with old style units in schema.")
421 self.
loglog.warn(
"run `meas_algorithms/bin/convert_refcat_to_nJy.py` to convert fluxes to nJy.")
422 self.
loglog.warn(
"See RFC-575 for more details.")
431 if not expandedCat.isContiguous():
432 expandedCat = expandedCat.copy(deep=
True)
434 fluxField =
getRefFluxField(schema=expandedCat.schema, filterName=filterName)
435 return pipeBase.Struct(refCat=expandedCat, fluxField=fluxField)
438 """Load reference objects that lie within a circular region on the sky
440 This method constructs a circular region from an input center and angular radius,
441 loads reference catalogs which are contained in or intersect the circle, and
442 filters reference catalogs which intersect down to objects which lie within
447 ctrCoord : `lsst.geom.SpherePoint`
448 Point defining the center of the circular region
449 radius : `lsst.geom.Angle`
450 Defines the angular radius of the circular region
452 Name of camera filter, or None or blank for the default filter
453 epoch : `astropy.time.Time` (optional)
454 Epoch to which to correct proper motion and parallax,
455 or None to not apply such corrections.
459 referenceCatalog : `lsst.afw.table.SourceCatalog`
460 Catalog containing reference objects inside the specified bounding box
464 `lsst.pex.exception.RuntimeError`
465 Raised if no reference catalogs could be found for the specified region
467 `lsst.pex.exception.TypeError`
468 Raised if the loaded reference catalogs do not have matching schemas
471 centerVector = ctrCoord.getVector()
474 return self.
loadRegionloadRegion(circularRegion, filterName=filterName, epoch=epoch)
477 """Relink an unpersisted match list to sources and reference
480 A match list is persisted and unpersisted as a catalog of IDs
481 produced by afw.table.packMatches(), with match metadata
482 (as returned by the astrometry tasks) in the catalog's metadata
483 attribute. This method converts such a match catalog into a match
484 list, with links to source records and reference object records.
488 matchCat : `lsst.afw.table.BaseCatalog`
489 Unpersisted packed match list.
490 ``matchCat.table.getMetadata()`` must contain match metadata,
491 as returned by the astrometry tasks.
492 sourceCat : `lsst.afw.table.SourceCatalog`
493 Source catalog. As a side effect, the catalog will be sorted
498 matchList : `lsst.afw.table.ReferenceMatchVector`
504 def getMetadataBox(cls, bbox, wcs, filterName=None, photoCalib=None, epoch=None, bboxPadding=100):
505 """Return metadata about the load
507 This metadata is used for reloading the catalog (e.g., for
508 reconstituting a normalised match list.)
512 bbox : `lsst.geom.Box2I`
513 Bounding bos for the pixels
514 wcs : `lsst.afw.geom.SkyWcs
516 filterName : `str` or None
517 filterName of the camera filter, or None or blank for the default filter
519 Deprecated, only included for api compatibility
520 epoch : `astropy.time.Time` (optional)
521 Epoch to which to correct proper motion and parallax,
522 or None to not apply such corrections.
524 Number describing how much to pad the input bbox by (in pixels), defaults
525 to 100. This parameter is necessary because optical distortions in telescopes
526 can cause a rectangular pixel grid to map into a non "rectangular" spherical
527 region in sky coordinates. This padding is used to create a spherical
528 "rectangle", which will for sure enclose the input box. This padding is only
529 used to determine if the reference catalog for a sky patch will be loaded from
530 the data store, this function will filter out objects which lie within the
531 padded region but fall outside the input bounding box region.
534 md : `lsst.daf.base.PropertyList`
536 _, _, innerCorners, outerCorners = cls.
_makeBoxRegion_makeBoxRegion(bbox, wcs, bboxPadding)
538 for box, corners
in zip((
"INNER",
"OUTER"), (innerCorners, outerCorners)):
539 for (name, corner)
in zip((
"UPPER_LEFT",
"UPPER_RIGHT",
"LOWER_LEFT",
"LOWER_RIGHT"),
541 md.add(f
"{box}_{name}_RA",
geom.SpherePoint(corner).getRa().asDegrees(), f
"{box}_corner")
542 md.add(f
"{box}_{name}_DEC",
geom.SpherePoint(corner).getDec().asDegrees(), f
"{box}_corner")
543 md.add(
"SMATCHV", 1,
'SourceMatchVector version number')
544 filterName =
"UNKNOWN" if filterName
is None else str(filterName)
545 md.add(
'FILTER', filterName,
'filter name for photometric data')
546 md.add(
'EPOCH',
"NONE" if epoch
is None else epoch.mjd,
'Epoch (TAI MJD) for catalog')
551 """Return metadata about the load
553 This metadata is used for reloading the catalog (e.g. for reconstituting
554 a normalized match list.)
558 coord : `lsst.geom.SpherePoint`
559 ICRS center of a circle
560 radius : `lsst.geom.angle`
562 filterName : `str` or None
563 filterName of the camera filter, or None or blank for the default filter
565 Deprecated, only included for api compatibility
566 epoch : `astropy.time.Time` (optional)
567 Epoch to which to correct proper motion and parallax,
568 or None to not apply such corrections.
572 md : `lsst.daf.base.PropertyList`
575 md.add(
'RA', coord.getRa().asDegrees(),
'field center in degrees')
576 md.add(
'DEC', coord.getDec().asDegrees(),
'field center in degrees')
577 md.add(
'RADIUS', radius.asDegrees(),
'field radius in degrees, minimum')
578 md.add(
'SMATCHV', 1,
'SourceMatchVector version number')
579 filterName =
"UNKNOWN" if filterName
is None else str(filterName)
580 md.add(
'FILTER', filterName,
'filter name for photometric data')
581 md.add(
'EPOCH',
"NONE" if epoch
is None else epoch.mjd,
'Epoch (TAI MJD) for catalog')
586 """This function creates a new catalog containing the information of the input refCat
587 as well as added flux columns and aliases between camera and reference flux.
591 refCat : `lsst.afw.table.SimpleCatalog`
592 Catalog of reference objects
593 defaultFilter : `str`
594 Name of the default reference filter
595 filterReferenceMap : `dict` of `str`
596 Dictionary with keys corresponding to a filter name, and values which
597 correspond to the name of the reference filter.
601 refCat : `lsst.afw.table.SimpleCatalog`
602 Reference catalog with columns added to track reference filters
607 If specified reference filter name is not a filter specifed as a key in the
608 reference filter map.
610 refCat = ReferenceObjectLoader.remapReferenceCatalogSchema(refCat,
611 filterNameList=filterReferenceMap.keys())
612 aliasMap = refCat.schema.getAliasMap()
613 if filterReferenceMap
is None:
614 filterReferenceMap = {}
615 for filterName, refFilterName
in itertools.chain([(
None, defaultFilter)],
616 filterReferenceMap.items()):
618 camFluxName = filterName +
"_camFlux" if filterName
is not None else "camFlux"
619 refFluxName = refFilterName +
"_flux"
620 if refFluxName
not in refCat.schema:
621 raise RuntimeError(
"Unknown reference filter %s" % (refFluxName,))
622 aliasMap.set(camFluxName, refFluxName)
624 refFluxErrName = refFluxName +
"Err"
625 camFluxErrName = camFluxName +
"Err"
626 aliasMap.set(camFluxErrName, refFluxErrName)
632 """This function takes in a reference catalog and creates a new catalog with additional
633 columns defined the remaining function arguments.
637 refCat : `lsst.afw.table.SimpleCatalog`
638 Reference catalog to map to new catalog
642 expandedCat : `lsst.afw.table.SimpleCatalog`
643 Deep copy of input reference catalog with additional columns added
645 mapper = afwTable.SchemaMapper(refCat.schema,
True)
646 mapper.addMinimalSchema(refCat.schema,
True)
647 mapper.editOutputSchema().disconnectAliases()
649 for filterName
in filterNameList:
650 mapper.editOutputSchema().addField(f
"{filterName}_flux",
652 doc=f
"flux in filter {filterName}",
655 mapper.editOutputSchema().addField(f
"{filterName}_fluxErr",
657 doc=f
"flux uncertanty in filter {filterName}",
662 mapper.editOutputSchema().addField(
"centroid_x", type=float, doReplace=
True)
663 mapper.editOutputSchema().addField(
"centroid_y", type=float, doReplace=
True)
664 mapper.editOutputSchema().addField(
"hasCentroid", type=
"Flag", doReplace=
True)
665 mapper.editOutputSchema().getAliasMap().set(
"slot_Centroid",
"centroid")
668 mapper.editOutputSchema().addField(
"photometric",
670 doc=
"set if the object can be used for photometric"
673 mapper.editOutputSchema().addField(
"resolved",
675 doc=
"set if the object is spatially resolved"
677 mapper.editOutputSchema().addField(
"variable",
679 doc=
"set if the object has variable brightness"
682 expandedCat = afwTable.SimpleCatalog(mapper.getOutputSchema())
683 expandedCat.setMetadata(refCat.getMetadata())
684 expandedCat.extend(refCat, mapper=mapper)
690 """Get the name of a flux field from a schema.
692 return the alias of "anyFilterMapsToThis", if present
693 else if filterName is specified:
694 return "*filterName*_camFlux" if present
695 else return "*filterName*_flux" if present (camera filter name
696 matches reference filter name)
697 else throw RuntimeError
699 return "camFlux", if present,
700 else throw RuntimeError
704 schema : `lsst.afw.table.Schema`
705 Reference catalog schema.
706 filterName : `str`, optional
707 Name of camera filter. If not specified, ``defaultFilter`` needs to be
708 set in the refcat loader config.
712 fluxFieldName : `str`
718 If an appropriate field is not found.
720 if not isinstance(schema, afwTable.Schema):
721 raise RuntimeError(
"schema=%s is not a schema" % (schema,))
723 return schema.getAliasMap().get(
"anyFilterMapsToThis")
728 fluxFieldList = [filterName +
"_camFlux", filterName +
"_flux"]
730 fluxFieldList = [
"camFlux"]
731 for fluxField
in fluxFieldList:
732 if fluxField
in schema:
735 raise RuntimeError(
"Could not find flux field(s) %s" % (
", ".join(fluxFieldList)))
739 """Return keys for flux and flux error.
743 schema : `lsst.afw.table.Schema`
744 Reference catalog schema.
746 Name of camera filter.
750 keys : `tuple` of (`lsst.afw.table.Key`, `lsst.afw.table.Key`)
754 - flux error key, if present, else None
759 If flux field not found.
762 fluxErrField = fluxField +
"Err"
763 fluxKey = schema[fluxField].asKey()
765 fluxErrKey = schema[fluxErrField].asKey()
768 return (fluxKey, fluxErrKey)
772 pixelMargin = pexConfig.RangeField(
773 doc=
"Padding to add to 4 all edges of the bounding box (pixels)",
778 defaultFilter = pexConfig.Field(
779 doc=(
"Default reference catalog filter to use if filter not specified in exposure;"
780 " if blank then filter must be specified in exposure."),
784 anyFilterMapsToThis = pexConfig.Field(
785 doc=(
"Always use this reference catalog filter, no matter whether or what filter name is "
786 "supplied to the loader. Effectively a trivial filterMap: map all filter names to this filter."
787 " This can be set for purely-astrometric catalogs (e.g. Gaia DR2) where there is only one "
788 "reasonable choice for every camera filter->refcat mapping, but not for refcats used for "
789 "photometry, which need a filterMap and/or colorterms/transmission corrections."),
794 filterMap = pexConfig.DictField(
795 doc=(
"Mapping of camera filter name: reference catalog filter name; "
796 "each reference filter must exist in the refcat."
797 " Note that this does not perform any bandpass corrections: it is just a lookup."),
802 requireProperMotion = pexConfig.Field(
803 doc=
"Require that the fields needed to correct proper motion "
804 "(epoch, pm_ra and pm_dec) are present?",
812 msg =
"`filterMap` and `anyFilterMapsToThis` are mutually exclusive"
813 raise pexConfig.FieldValidationError(LoadReferenceObjectsConfig.anyFilterMapsToThis,
818 r"""Abstract base class to load objects from reference catalogs
820 ConfigClass = LoadReferenceObjectsConfig
821 _DefaultName =
"LoadReferenceObjects"
824 """Construct a LoadReferenceObjectsTask
828 butler : `lsst.daf.persistence.Butler`
829 Data butler, for access reference catalogs.
831 pipeBase.Task.__init__(self, *args, **kwargs)
835 def loadPixelBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
836 """Load reference objects that overlap a rectangular pixel region.
840 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
841 Bounding box for pixels.
842 wcs : `lsst.afw.geom.SkyWcs`
843 WCS; used to convert pixel positions to sky coordinates
846 Name of filter, or `None` or `""` for the default filter.
847 This is used for flux values in case we have flux limits
848 (which are not yet implemented).
849 photoCalib : `lsst.afw.image.PhotoCalib` (optional)
850 Calibration, or `None` if unknown.
851 epoch : `astropy.time.Time` (optional)
852 Epoch to which to correct proper motion and parallax,
853 or None to not apply such corrections.
857 results : `lsst.pipe.base.Struct`
858 A Struct containing the following fields:
859 refCat : `lsst.afw.catalog.SimpleCatalog`
860 A catalog of reference objects with the standard
861 schema, as documented in the main doc string for
862 `LoadReferenceObjects`.
863 The catalog is guaranteed to be contiguous.
865 Name of flux field for specified `filterName`.
869 The search algorithm works by searching in a region in sky
870 coordinates whose center is the center of the bbox and radius
871 is large enough to just include all 4 corners of the bbox.
872 Stars that lie outside the bbox are then trimmed from the list.
877 self.log.info(
"Loading reference objects using center %s and radius %s deg" %
878 (circle.coord, circle.radius.asDegrees()))
879 loadRes = self.
loadSkyCircleloadSkyCircle(circle.coord, circle.radius, filterName=filterName, epoch=epoch,
881 refCat = loadRes.refCat
882 numFound = len(refCat)
885 refCat = self.
_trimToBBox_trimToBBox(refCat=refCat, bbox=circle.bbox, wcs=wcs)
886 numTrimmed = numFound - len(refCat)
887 self.log.debug(
"trimmed %d out-of-bbox objects, leaving %d", numTrimmed, len(refCat))
888 self.log.info(
"Loaded %d reference objects", len(refCat))
891 if not refCat.isContiguous():
892 loadRes.refCat = refCat.copy(deep=
True)
897 def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None, centroids=False):
898 """Load reference objects that overlap a circular sky region.
902 ctrCoord : `lsst.geom.SpherePoint`
903 ICRS center of search region.
904 radius : `lsst.geom.Angle`
905 Radius of search region.
906 filterName : `str` (optional)
907 Name of filter, or `None` or `""` for the default filter.
908 This is used for flux values in case we have flux limits
909 (which are not yet implemented).
910 epoch : `astropy.time.Time` (optional)
911 Epoch to which to correct proper motion and parallax,
912 or None to not apply such corrections.
913 centroids : `bool` (optional)
914 Add centroid fields to the loaded Schema. ``loadPixelBox`` expects
915 these fields to exist.
919 results : `lsst.pipe.base.Struct`
920 A Struct containing the following fields:
921 refCat : `lsst.afw.catalog.SimpleCatalog`
922 A catalog of reference objects with the standard
923 schema, as documented in the main doc string for
924 `LoadReferenceObjects`.
925 The catalog is guaranteed to be contiguous.
927 Name of flux field for specified `filterName`.
931 Note that subclasses are responsible for performing the proper motion
932 correction, since this is the lowest-level interface for retrieving
938 def _trimToBBox(refCat, bbox, wcs):
939 """Remove objects outside a given pixel bounding box and set
940 centroid and hasCentroid fields.
944 refCat : `lsst.afw.table.SimpleCatalog`
945 A catalog of objects. The schema must include fields
946 "coord", "centroid" and "hasCentroid".
947 The "coord" field is read.
948 The "centroid" and "hasCentroid" fields are set.
949 bbox : `lsst.geom.Box2D`
951 wcs : `lsst.afw.geom.SkyWcs`
952 WCS; used to convert sky coordinates to pixel positions.
956 catalog : `lsst.afw.table.SimpleCatalog`
957 Reference objects in the bbox, with centroid and
958 hasCentroid fields set.
960 afwTable.updateRefCentroids(wcs, refCat)
961 centroidKey = afwTable.Point2DKey(refCat.schema[
"centroid"])
962 retStarCat = type(refCat)(refCat.table)
964 point = star.get(centroidKey)
965 if bbox.contains(point):
966 retStarCat.append(star)
969 def _addFluxAliases(self, schema):
970 """Add aliases for camera filter fluxes to the schema.
972 If self.config.defaultFilter then adds these aliases:
973 camFlux: <defaultFilter>_flux
974 camFluxErr: <defaultFilter>_fluxErr, if the latter exists
976 For each camFilter: refFilter in self.config.filterMap adds these aliases:
977 <camFilter>_camFlux: <refFilter>_flux
978 <camFilter>_camFluxErr: <refFilter>_fluxErr, if the latter exists
982 schema : `lsst.afw.table.Schema`
983 Schema for reference catalog.
988 If any reference flux field is missing from the schema.
990 aliasMap = schema.getAliasMap()
992 if self.config.anyFilterMapsToThis
is not None:
993 refFluxName = self.config.anyFilterMapsToThis +
"_flux"
994 if refFluxName
not in schema:
995 msg = f
"Unknown reference filter for anyFilterMapsToThis='{refFluxName}'"
996 raise RuntimeError(msg)
997 aliasMap.set(
"anyFilterMapsToThis", refFluxName)
1000 def addAliasesForOneFilter(filterName, refFilterName):
1001 """Add aliases for a single filter
1005 filterName : `str` (optional)
1006 Camera filter name. The resulting alias name is
1007 <filterName>_camFlux, or simply "camFlux" if `filterName`
1009 refFilterName : `str`
1010 Reference catalog filter name; the field
1011 <refFilterName>_flux must exist.
1013 camFluxName = filterName +
"_camFlux" if filterName
is not None else "camFlux"
1014 refFluxName = refFilterName +
"_flux"
1015 if refFluxName
not in schema:
1016 raise RuntimeError(
"Unknown reference filter %s" % (refFluxName,))
1017 aliasMap.set(camFluxName, refFluxName)
1018 refFluxErrName = refFluxName +
"Err"
1019 if refFluxErrName
in schema:
1020 camFluxErrName = camFluxName +
"Err"
1021 aliasMap.set(camFluxErrName, refFluxErrName)
1023 if self.config.defaultFilter:
1024 addAliasesForOneFilter(
None, self.config.defaultFilter)
1026 for filterName, refFilterName
in self.config.filterMap.items():
1027 addAliasesForOneFilter(filterName, refFilterName)
1031 addIsPhotometric=False, addIsResolved=False,
1032 addIsVariable=False, coordErrDim=2,
1033 addProperMotion=False, properMotionErrDim=2,
1035 """Make a standard schema for reference object catalogs.
1039 filterNameList : `list` of `str`
1040 List of filter names. Used to create <filterName>_flux fields.
1041 addIsPhotometric : `bool`
1042 If True then add field "photometric".
1043 addIsResolved : `bool`
1044 If True then add field "resolved".
1045 addIsVariable : `bool`
1046 If True then add field "variable".
1048 Number of coord error fields; must be one of 0, 2, 3:
1050 - If 2 or 3: add fields "coord_raErr" and "coord_decErr".
1051 - If 3: also add field "coord_radecErr".
1052 addProperMotion : `bool`
1053 If True add fields "epoch", "pm_ra", "pm_dec" and "pm_flag".
1054 properMotionErrDim : `int`
1055 Number of proper motion error fields; must be one of 0, 2, 3;
1056 ignored if addProperMotion false:
1057 - If 2 or 3: add fields "pm_raErr" and "pm_decErr".
1058 - If 3: also add field "pm_radecErr".
1059 addParallax : `bool`
1060 If True add fields "epoch", "parallax", "parallaxErr"
1061 and "parallax_flag".
1065 schema : `lsst.afw.table.Schema`
1066 Schema for reference catalog, an
1067 `lsst.afw.table.SimpleCatalog`.
1071 Reference catalogs support additional covariances, such as
1072 covariance between RA and proper motion in declination,
1073 that are not supported by this method, but can be added after
1074 calling this method.
1076 schema = afwTable.SimpleTable.makeMinimalSchema()
1078 afwTable.Point2DKey.addFields(
1081 "centroid on an exposure, if relevant",
1085 field=
"hasCentroid",
1087 doc=
"is position known?",
1089 for filterName
in filterNameList:
1091 field=
"%s_flux" % (filterName,),
1093 doc=
"flux in filter %s" % (filterName,),
1096 for filterName
in filterNameList:
1098 field=
"%s_fluxErr" % (filterName,),
1100 doc=
"flux uncertainty in filter %s" % (filterName,),
1103 if addIsPhotometric:
1105 field=
"photometric",
1107 doc=
"set if the object can be used for photometric calibration",
1113 doc=
"set if the object is spatially resolved",
1119 doc=
"set if the object has variable brightness",
1121 if coordErrDim
not in (0, 2, 3):
1122 raise ValueError(
"coordErrDim={}; must be (0, 2, 3)".format(coordErrDim))
1124 afwTable.CovarianceMatrix2fKey.addFields(
1127 names=[
"ra",
"dec"],
1128 units=[
"rad",
"rad"],
1129 diagonalOnly=(coordErrDim == 2),
1132 if addProperMotion
or addParallax:
1136 doc=
"date of observation (TAI, MJD)",
1144 doc=
"proper motion in the right ascension direction = dra/dt * cos(dec)",
1150 doc=
"proper motion in the declination direction",
1153 if properMotionErrDim
not in (0, 2, 3):
1154 raise ValueError(
"properMotionErrDim={}; must be (0, 2, 3)".format(properMotionErrDim))
1155 if properMotionErrDim > 0:
1156 afwTable.CovarianceMatrix2fKey.addFields(
1159 names=[
"ra",
"dec"],
1160 units=[
"rad/year",
"rad/year"],
1161 diagonalOnly=(properMotionErrDim == 2),
1166 doc=
"Set if proper motion or proper motion error is bad",
1177 field=
"parallaxErr",
1179 doc=
"uncertainty in parallax",
1183 field=
"parallax_flag",
1185 doc=
"Set if parallax or parallax error is bad",
1189 def _calculateCircle(self, bbox, wcs):
1190 """Compute on-sky center and radius of search region.
1194 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1196 wcs : `lsst.afw.geom.SkyWcs`
1197 WCS; used to convert pixel positions to sky coordinates.
1201 results : `lsst.pipe.base.Struct`
1202 A Struct containing:
1204 - coord : `lsst.geom.SpherePoint`
1205 ICRS center of the search region.
1206 - radius : `lsst.geom.Angle`
1207 Radius of the search region.
1208 - bbox : `lsst.geom.Box2D`
1209 Bounding box used to compute the circle.
1212 bbox.grow(self.config.pixelMargin)
1213 coord = wcs.pixelToSky(bbox.getCenter())
1214 radius = max(coord.separation(wcs.pixelToSky(pp))
for pp
in bbox.getCorners())
1215 return pipeBase.Struct(coord=coord, radius=radius, bbox=bbox)
1218 """Return metadata about the load.
1220 This metadata is used for reloading the catalog (e.g., for
1221 reconstituting a normalised match list.
1225 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1227 wcs : `lsst.afw.geom.SkyWcs`
1228 WCS; used to convert pixel positions to sky coordinates.
1230 Name of camera filter, or `None` or `""` for the default
1232 photoCalib : `lsst.afw.image.PhotoCalib` (optional)
1233 Calibration, or `None` if unknown.
1234 epoch : `astropy.time.Time` (optional)
1235 Epoch to which to correct proper motion and parallax,
1236 or None to not apply such corrections.
1240 metadata : lsst.daf.base.PropertyList
1241 Metadata about the load.
1244 return self.
getMetadataCirclegetMetadataCircle(circle.coord, circle.radius, filterName, photoCalib=photoCalib,
1248 """Return metadata about the load.
1250 This metadata is used for reloading the catalog (e.g., for
1251 reconstituting a normalised match list.
1255 coord : `lsst.geom.SpherePoint`
1256 ICRS center of the search region.
1257 radius : `lsst.geom.Angle`
1258 Radius of the search region.
1260 Name of camera filter, or `None` or `""` for the default
1262 photoCalib : `lsst.afw.image.PhotoCalib` (optional)
1263 Calibration, or `None` if unknown.
1264 epoch : `astropy.time.Time` (optional)
1265 Epoch to which to correct proper motion and parallax,
1266 or None to not apply such corrections.
1270 metadata : lsst.daf.base.PropertyList
1271 Metadata about the load
1274 md.add(
'RA', coord.getRa().asDegrees(),
'field center in degrees')
1275 md.add(
'DEC', coord.getDec().asDegrees(),
'field center in degrees')
1276 md.add(
'RADIUS', radius.asDegrees(),
'field radius in degrees, minimum')
1277 md.add(
'SMATCHV', 1,
'SourceMatchVector version number')
1278 filterName =
"UNKNOWN" if filterName
is None else str(filterName)
1279 md.add(
'FILTER', filterName,
'filter name for photometric data')
1280 md.add(
'EPOCH',
"NONE" if epoch
is None else epoch.mjd,
'Epoch (TAI MJD) for catalog')
1284 """Relink an unpersisted match list to sources and reference
1287 A match list is persisted and unpersisted as a catalog of IDs
1288 produced by afw.table.packMatches(), with match metadata
1289 (as returned by the astrometry tasks) in the catalog's metadata
1290 attribute. This method converts such a match catalog into a match
1291 list, with links to source records and reference object records.
1295 matchCat : `lsst.afw.table.BaseCatalog`
1296 Unperisted packed match list.
1297 ``matchCat.table.getMetadata()`` must contain match metadata,
1298 as returned by the astrometry tasks.
1299 sourceCat : `lsst.afw.table.SourceCatalog`
1300 Source catalog. As a side effect, the catalog will be sorted
1305 matchList : `lsst.afw.table.ReferenceMatchVector`
1311 """Apply proper motion correction to a reference catalog.
1313 Adjust position and position error in the ``catalog``
1314 for proper motion to the specified ``epoch``,
1315 modifying the catalog in place.
1319 catalog : `lsst.afw.table.SimpleCatalog`
1320 Catalog of positions, containing:
1322 - Coordinates, retrieved by the table's coordinate key.
1323 - ``coord_raErr`` : Error in Right Ascension (rad).
1324 - ``coord_decErr`` : Error in Declination (rad).
1325 - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
1327 - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
1328 - ``pm_dec`` : Proper motion in Declination (rad/yr,
1330 - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
1331 - ``epoch`` : Mean epoch of object (an astropy.time.Time)
1332 epoch : `astropy.time.Time`
1333 Epoch to which to correct proper motion,
1335 if (
"epoch" not in catalog.schema
or "pm_ra" not in catalog.schema
or "pm_dec" not in catalog.schema):
1336 if self.config.requireProperMotion:
1337 raise RuntimeError(
"Proper motion correction required but not available from catalog")
1338 self.log.warn(
"Proper motion correction not available from catalog")
1344 """Relink an unpersisted match list to sources and reference
1347 A match list is persisted and unpersisted as a catalog of IDs
1348 produced by afw.table.packMatches(), with match metadata
1349 (as returned by the astrometry tasks) in the catalog's metadata
1350 attribute. This method converts such a match catalog into a match
1351 list, with links to source records and reference object records.
1356 Reference object loader to use in getting reference objects
1357 matchCat : `lsst.afw.table.BaseCatalog`
1358 Unperisted packed match list.
1359 ``matchCat.table.getMetadata()`` must contain match metadata,
1360 as returned by the astrometry tasks.
1361 sourceCat : `lsst.afw.table.SourceCatalog`
1362 Source catalog. As a side effect, the catalog will be sorted
1367 matchList : `lsst.afw.table.ReferenceMatchVector`
1370 matchmeta = matchCat.table.getMetadata()
1371 version = matchmeta.getInt(
'SMATCHV')
1373 raise ValueError(
'SourceMatchVector version number is %i, not 1.' % version)
1374 filterName = matchmeta.getString(
'FILTER').strip()
1376 epoch = matchmeta.getDouble(
'EPOCH')
1377 except (pexExcept.NotFoundError, pexExcept.TypeError):
1379 if 'RADIUS' in matchmeta:
1382 matchmeta.getDouble(
'DEC'), lsst.geom.degrees)
1383 rad = matchmeta.getDouble(
'RADIUS') * lsst.geom.degrees
1384 refCat = refObjLoader.loadSkyCircle(ctrCoord, rad, filterName, epoch=epoch).refCat
1385 elif "INNER_UPPER_LEFT_RA" in matchmeta:
1391 for place
in (
"UPPER_LEFT",
"UPPER_RIGHT",
"LOWER_LEFT",
"LOWER_RIGHT"):
1393 matchmeta.getDouble(f
"OUTER_{place}_DEC"),
1394 lsst.geom.degrees).getVector()
1397 refCat = refObjLoader.loadRegion(outerBox, filterName=filterName, epoch=epoch).refCat
1401 return afwTable.unpackMatches(matchCat, refCat, sourceCat)
1405 """Apply proper motion correction to a reference catalog.
1407 Adjust position and position error in the ``catalog``
1408 for proper motion to the specified ``epoch``,
1409 modifying the catalog in place.
1413 log : `lsst.log.Log`
1414 Log object to write to.
1415 catalog : `lsst.afw.table.SimpleCatalog`
1416 Catalog of positions, containing:
1418 - Coordinates, retrieved by the table's coordinate key.
1419 - ``coord_raErr`` : Error in Right Ascension (rad).
1420 - ``coord_decErr`` : Error in Declination (rad).
1421 - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
1423 - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
1424 - ``pm_dec`` : Proper motion in Declination (rad/yr,
1426 - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
1427 - ``epoch`` : Mean epoch of object (an astropy.time.Time)
1428 epoch : `astropy.time.Time`
1429 Epoch to which to correct proper motion.
1431 if "epoch" not in catalog.schema
or "pm_ra" not in catalog.schema
or "pm_dec" not in catalog.schema:
1432 log.warn(
"Proper motion correction not available from catalog")
1434 if not catalog.isContiguous():
1435 raise RuntimeError(
"Catalog must be contiguous")
1436 catEpoch = astropy.time.Time(catalog[
"epoch"], scale=
"tai", format=
"mjd")
1437 log.info(
"Correcting reference catalog for proper motion to %r", epoch)
1439 timeDiffsYears = (epoch.tai - catEpoch).to(astropy.units.yr).value
1440 coordKey = catalog.table.getCoordKey()
1443 pmRaRad = catalog[
"pm_ra"]
1444 pmDecRad = catalog[
"pm_dec"]
1445 offsetsRaRad = pmRaRad*timeDiffsYears
1446 offsetsDecRad = pmDecRad*timeDiffsYears
1454 offsetBearingsRad = numpy.arctan2(pmDecRad*1e6, pmRaRad*1e6)
1455 offsetAmountsRad = numpy.hypot(offsetsRaRad, offsetsDecRad)
1456 for record, bearingRad, amountRad
in zip(catalog, offsetBearingsRad, offsetAmountsRad):
1457 record.set(coordKey,
1458 record.get(coordKey).offset(bearing=bearingRad*lsst.geom.radians,
1459 amount=amountRad*lsst.geom.radians))
1461 if "coord_raErr" in catalog.schema:
1462 catalog[
"coord_raErr"] = numpy.hypot(catalog[
"coord_raErr"],
1463 catalog[
"pm_raErr"]*timeDiffsYears)
1464 if "coord_decErr" in catalog.schema:
1465 catalog[
"coord_decErr"] = numpy.hypot(catalog[
"coord_decErr"],
1466 catalog[
"pm_decErr"]*timeDiffsYears)
static Schema makeMinimalSchema()
static Log getDefaultLogger()
def __call__(self, refCat, catRegion)
def __init__(self, region)
def _trimToBBox(refCat, bbox, wcs)
def joinMatchListWithCatalog(self, matchCat, sourceCat)
def makeMinimalSchema(filterNameList, *addCentroid=False, addIsPhotometric=False, addIsResolved=False, addIsVariable=False, coordErrDim=2, addProperMotion=False, properMotionErrDim=2, addParallax=False)
def getMetadataCircle(self, coord, radius, filterName, photoCalib=None, epoch=None)
def applyProperMotions(self, catalog, epoch)
def __init__(self, butler=None, *args, **kwargs)
def _calculateCircle(self, bbox, wcs)
def loadPixelBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None)
def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None, centroids=False)
def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None)
def loadRegion(self, region, filtFunc=None, filterName=None, epoch=None)
def getMetadataCircle(coord, radius, filterName, photoCalib=None, epoch=None)
def _makeBoxRegion(BBox, wcs, BBoxPadding)
def remapReferenceCatalogSchema(refCat, *filterNameList=None, position=False, photometric=False)
def getMetadataBox(cls, bbox, wcs, filterName=None, photoCalib=None, epoch=None, bboxPadding=100)
def addFluxAliases(refCat, defaultFilter, filterReferenceMap)
def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None)
def joinMatchListWithCatalog(self, matchCat, sourceCat)
def __init__(self, dataIds, refCats, config, log=None)
def loadPixelBox(self, bbox, wcs, filterName=None, epoch=None, photoCalib=None, bboxPadding=100)
def getRefFluxKeys(schema, filterName=None)
def hasNanojanskyFluxUnits(schema)
def getRefFluxField(schema, filterName=None)
def convertToNanojansky(catalog, log, doConvert=True)
def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat)
def isOldFluxField(name, units)
def getFormatVersionFromRefCat(refCat)
def applyProperMotionsImpl(log, catalog, epoch)