lsst.meas.algorithms 22.0.1-33-g638f941b+010569f7a8
loadReferenceObjects.py
Go to the documentation of this file.
2# LSST Data Management System
3#
4# Copyright 2008-2017 AURA/LSST.
5#
6# This product includes software developed by the
7# LSST Project (http://www.lsst.org/).
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the LSST License Statement and
20# the GNU General Public License along with this program. If not,
21# see <https://www.lsstcorp.org/LegalNotices/>.
22#
23
24__all__ = ["getRefFluxField", "getRefFluxKeys", "LoadReferenceObjectsTask", "LoadReferenceObjectsConfig",
25 "ReferenceObjectLoader"]
26
27import abc
28import itertools
29import logging
30
31import astropy.time
32import astropy.units
33import numpy
34
35import lsst.geom as geom
36import lsst.afw.table as afwTable
37import lsst.pex.config as pexConfig
38import lsst.pipe.base as pipeBase
39from lsst import sphgeom
40from lsst.daf.base import PropertyList
41from lsst.utils.timer import timeMethod
42
43
44def isOldFluxField(name, units):
45 """Return True if this name/units combination corresponds to an
46 "old-style" reference catalog flux field.
47 """
48 unitsCheck = units != 'nJy' # (units == 'Jy' or units == '' or units == '?')
49 isFlux = name.endswith('_flux')
50 isFluxSigma = name.endswith('_fluxSigma')
51 isFluxErr = name.endswith('_fluxErr')
52 return (isFlux or isFluxSigma or isFluxErr) and unitsCheck
53
54
56 """Return True if the units of all flux and fluxErr are correct (nJy).
57 """
58 for field in schema:
59 if isOldFluxField(field.field.getName(), field.field.getUnits()):
60 return False
61 return True
62
63
65 """"Return the format version stored in a reference catalog header.
66
67 Parameters
68 ----------
70 Reference catalog to inspect.
71
72 Returns
73 -------
74 version : `int`
75 Format verison integer. Returns `0` if the catalog has no metadata
76 or the metadata does not include a "REFCAT_FORMAT_VERSION" key.
77 """
78 md = refCat.getMetadata()
79 if md is None:
80 return 0
81 try:
82 return md.getScalar("REFCAT_FORMAT_VERSION")
83 except KeyError:
84 return 0
85
86
87def convertToNanojansky(catalog, log, doConvert=True):
88 """Convert fluxes in a catalog from jansky to nanojansky.
89
90 Parameters
91 ----------
93 The catalog to convert.
94 log : `lsst.log.Log` or `logging.Logger`
95 Log to send messages to.
96 doConvert : `bool`, optional
97 Return a converted catalog, or just identify the fields that need to be converted?
98 This supports the "write=False" mode of `bin/convert_to_nJy.py`.
99
100 Returns
101 -------
102 catalog : `lsst.afw.table.SimpleCatalog` or None
103 The converted catalog, or None if ``doConvert`` is False.
104
105 Notes
106 -----
107 Support for old units in reference catalogs will be removed after the
108 release of late calendar year 2019.
109 Use `meas_algorithms/bin/convert_to_nJy.py` to update your reference catalog.
110 """
111 # Do not share the AliasMap: for refcats, that gets created when the
112 # catalog is read from disk and should not be propagated.
113 mapper = afwTable.SchemaMapper(catalog.schema, shareAliasMap=False)
114 mapper.addMinimalSchema(afwTable.SimpleTable.makeMinimalSchema())
115 input_fields = []
116 output_fields = []
117 for field in catalog.schema:
118 oldName = field.field.getName()
119 oldUnits = field.field.getUnits()
120 if isOldFluxField(oldName, oldUnits):
121 units = 'nJy'
122 # remap Sigma flux fields to Err, so we can drop the alias
123 if oldName.endswith('_fluxSigma'):
124 name = oldName.replace('_fluxSigma', '_fluxErr')
125 else:
126 name = oldName
127 newField = afwTable.Field[field.dtype](name, field.field.getDoc(), units)
128 mapper.addMapping(field.getKey(), newField)
129 input_fields.append(field.field)
130 output_fields.append(newField)
131 else:
132 mapper.addMapping(field.getKey())
133
134 fluxFieldsStr = '; '.join("(%s, '%s')" % (field.getName(), field.getUnits()) for field in input_fields)
135
136 if doConvert:
137 newSchema = mapper.getOutputSchema()
138 output = afwTable.SimpleCatalog(newSchema)
139 output.extend(catalog, mapper=mapper)
140 for field in output_fields:
141 output[field.getName()] *= 1e9
142 log.info("Converted refcat flux fields to nJy (name, units): %s", fluxFieldsStr)
143 return output
144 else:
145 log.info("Found old-style refcat flux fields (name, units): %s", fluxFieldsStr)
146 return None
147
148
150 """This is a private helper class which filters catalogs by
151 row based on the row being inside the region used to initialize
152 the class.
153
154 Parameters
155 ----------
156 region : `lsst.sphgeom.Region`
157 The spatial region which all objects should lie within
158 """
159 def __init__(self, region):
160 self.regionregion = region
161
162 def __call__(self, refCat, catRegion):
163 """This call method on an instance of this class takes in a reference
164 catalog, and the region from which the catalog was generated.
165
166 If the catalog region is entirely contained within the region used to
167 initialize this class, then all the entries in the catalog must be
168 within the region and so the whole catalog is returned.
169
170 If the catalog region is not entirely contained, then the location for
171 each record is tested against the region used to initialize the class.
172 Records which fall inside this region are added to a new catalog, and
173 this catalog is then returned.
174
175 Parameters
176 ---------
178 SourceCatalog to be filtered.
179 catRegion : `lsst.sphgeom.Region`
180 Region in which the catalog was created
181 """
182 if catRegion.isWithin(self.regionregion):
183 # no filtering needed, region completely contains refcat
184 return refCat
185
186 filteredRefCat = type(refCat)(refCat.table)
187 for record in refCat:
188 if self.regionregion.contains(record.getCoord().getVector()):
189 filteredRefCat.append(record)
190 return filteredRefCat
191
192
194 """Base class for reference object loaders, to facilitate gen2/gen3 code
195 sharing.
196 """
197 def applyProperMotions(self, catalog, epoch):
198 """Apply proper motion correction to a reference catalog.
199
200 Adjust position and position error in the ``catalog``
201 for proper motion to the specified ``epoch``,
202 modifying the catalog in place.
203
204 Parameters
205 ----------
207 Catalog of positions, containing at least these fields:
208
209 - Coordinates, retrieved by the table's coordinate key.
210 - ``coord_raErr`` : Error in Right Ascension (rad).
211 - ``coord_decErr`` : Error in Declination (rad).
212 - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
213 East positive)
214 - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
215 - ``pm_dec`` : Proper motion in Declination (rad/yr,
216 North positive)
217 - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
218 - ``epoch`` : Mean epoch of object (an astropy.time.Time)
219 epoch : `astropy.time.Time`
220 Epoch to which to correct proper motion.
221 If None, do not apply PM corrections or raise if
222 ``config.requireProperMotion`` is True.
223
224 Raises
225 ------
226 RuntimeError
227 Raised if ``config.requireProperMotion`` is set but we cannot
228 apply the proper motion correction for some reason.
229 """
230 if epoch is None:
231 if self.config.requireProperMotion:
232 raise RuntimeError("requireProperMotion=True but epoch not provided to loader.")
233 else:
234 self.log.debug("No epoch provided: not applying proper motion corrections to refcat.")
235 return
236
237 # Warn/raise for a catalog in an incorrect format, if epoch was specified.
238 if ("pm_ra" in catalog.schema
239 and not isinstance(catalog.schema["pm_ra"].asKey(), afwTable.KeyAngle)):
240 if self.config.requireProperMotion:
241 raise RuntimeError("requireProperMotion=True but refcat pm_ra field is not an Angle.")
242 else:
243 self.log.warning("Reference catalog pm_ra field is not an Angle; cannot apply proper motion.")
244 return
245
246 if ("epoch" not in catalog.schema or "pm_ra" not in catalog.schema):
247 if self.config.requireProperMotion:
248 raise RuntimeError("requireProperMotion=True but PM data not available from catalog.")
249 else:
250 self.log.warning("Proper motion correction not available for this reference catalog.")
251 return
252
253 applyProperMotionsImpl(self.log, catalog, epoch)
254
255
257 """This class facilitates loading reference catalogs with gen 3 middleware
258
259 The middleware preflight solver will create a list of datarefs that may
260 possibly overlap a given region. These datarefs are then used to construct
261 and instance of this class. The class instance should then be passed into
262 a task which needs reference catalogs. These tasks should then determine
263 the exact region of the sky reference catalogs will be loaded for, and
264 call a corresponding method to load the reference objects.
265 """
266 def __init__(self, dataIds, refCats, config, log=None):
267 """ Constructs an instance of ReferenceObjectLoader
268
269 Parameters
270 ----------
271 dataIds : iterable of `lsst.daf.butler.DataIds`
272 An iterable object of DataSetRefs which point to reference catalogs
273 in a gen 3 repository.
274 refCats : iterable of `lsst.daf.butler.DeferedDatasetHandle`
275 Handles to load refCats on demand
277 Configuration for the loader.
278 log : `lsst.log.Log`, `logging.Logger` or `None`, optional
279 Logger object used to write out messages. If `None` a default
280 logger will be used.
281 """
282 self.dataIdsdataIds = dataIds
283 self.refCatsrefCats = refCats
284 self.loglog = log or logging.getLogger(__name__).getChild("ReferenceObjectLoader")
285 self.configconfig = config
286
287 @staticmethod
288 def _makeBoxRegion(BBox, wcs, BBoxPadding):
289 outerLocalBBox = geom.Box2D(BBox)
290 innerLocalBBox = geom.Box2D(BBox)
291
292 # Grow the bounding box to allow for effects not fully captured by the
293 # wcs provided (which represents the current best-guess wcs solution
294 # associated with the dataset for which the calibration is to be
295 # computed using the loaded and trimmed reference catalog being defined
296 # here). These effects could include pointing errors and/or an
297 # insufficient optical distorition model for the instrument. The idea
298 # is to ensure the spherical geometric region created contains the
299 # entire region covered by the bbox.
300 # Also create an inner region that is sure to be inside the bbox.
301 outerLocalBBox.grow(BBoxPadding)
302 innerLocalBBox.grow(-1*BBoxPadding)
303
304 # Handle the case where the inner bounding box shrank to a zero sized
305 # region (which will be the case if the shrunken size of either
306 # dimension is less than or equal to zero). In this case, the inner
307 # bounding box is set to the original input bounding box. This is
308 # probably not the best way to handle an empty inner bounding box, but
309 # it is what the calling code currently expects.
310 if innerLocalBBox.getDimensions() == geom.Extent2D(0, 0):
311 innerLocalBBox = geom.Box2D(BBox)
312
313 # Convert the corners of the bounding boxes to sky coordinates.
314 innerBoxCorners = innerLocalBBox.getCorners()
315 innerSphCorners = [wcs.pixelToSky(corner).getVector() for corner in innerBoxCorners]
316 innerSkyRegion = sphgeom.ConvexPolygon(innerSphCorners)
317
318 outerBoxCorners = outerLocalBBox.getCorners()
319 outerSphCorners = [wcs.pixelToSky(corner).getVector() for corner in outerBoxCorners]
320 outerSkyRegion = sphgeom.ConvexPolygon(outerSphCorners)
321
322 return innerSkyRegion, outerSkyRegion, innerSphCorners, outerSphCorners
323
324 def loadPixelBox(self, bbox, wcs, filterName=None, epoch=None, photoCalib=None,
325 bboxToSpherePadding=100):
326 """Load reference objects that are within a pixel-based rectangular
327 region.
328
329 This algorithm works by creating a spherical box whose corners
330 correspond to the WCS converted corners of the input bounding box
331 (possibly padded). It then defines a filtering function which looks at
332 the pixel position of the reference objects and accepts only those that
333 lie within the specified bounding box.
334
335 The spherical box region and filtering function are passed to the
336 generic loadRegion method which loads and filters the reference objects
337 from the datastore and returns a single catalog containing the filtered
338 set of reference objects.
339
340 Parameters
341 ----------
342 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
343 Box which bounds a region in pixel space.
345 Wcs object defining the pixel to sky (and inverse) transform for
346 the supplied ``bbox``.
347 filterName : `str` or `None`, optional
348 Name of camera filter, or `None` or blank for the default filter.
349 epoch : `astropy.time.Time` or `None`, optional
350 Epoch to which to correct proper motion and parallax, or `None`
351 to not apply such corrections.
352 photoCalib : `None`
353 Deprecated and ignored, only included for api compatibility.
354 bboxToSpherePadding : `int`, optional
355 Padding to account for translating a set of corners into a
356 spherical (convex) boundary that is certain to encompase the
357 enitre area covered by the box.
358
359 Returns
360 -------
361 referenceCatalog : `lsst.afw.table.SimpleCatalog`
362 Catalog containing reference objects inside the specified bounding
363 box (padded by self.configconfig.pixelMargin).
364
365 Raises
366 ------
367 RuntimeError
368 Raised if no reference catalogs could be found for the specified
369 region.
370 TypeError
371 Raised if the loaded reference catalogs do not have matching
372 schemas.
373 """
374 paddedBbox = geom.Box2D(bbox)
375 paddedBbox.grow(self.configconfig.pixelMargin)
376 innerSkyRegion, outerSkyRegion, _, _ = self._makeBoxRegion_makeBoxRegion(paddedBbox, wcs, bboxToSpherePadding)
377
378 def _filterFunction(refCat, region):
379 # Perform an initial "pre filter" step based on the refCat coords
380 # and the outerSkyRegion created from the self.config.pixelMargin-
381 # paddedBbox plus an "extra" padding of bboxToSpherePadding and the
382 # raw wcs. This should ensure a large enough projected area on the
383 # sky that accounts for any projection/distortion issues, but small
384 # enough to filter out loaded reference objects that lie well
385 # beyond the projected detector of interest. This step is required
386 # due to the very local nature of the wcs available for the
387 # sky <--> pixel conversions.
388 preFiltFunc = _FilterCatalog(outerSkyRegion)
389 refCat = preFiltFunc(refCat, region)
390
391 # Add columns to the pre-filtered reference catalog relating their
392 # coordinates to equivalent pixel positions for the wcs provided
393 # and use to populate those columns.
394 refCat = self.remapReferenceCatalogSchemaremapReferenceCatalogSchema(refCat, position=True)
395 afwTable.updateRefCentroids(wcs, refCat)
396 # No need to filter the catalog if it is entirely contained in the
397 # region defined by the inner sky region.
398 if innerSkyRegion.contains(region):
399 return refCat
400 # Create a new reference catalog, and populate it only with records
401 # that fall inside the padded bbox.
402 filteredRefCat = type(refCat)(refCat.table)
403 centroidKey = afwTable.Point2DKey(refCat.schema['centroid'])
404 for record in refCat:
405 pixCoords = record[centroidKey]
406 if paddedBbox.contains(geom.Point2D(pixCoords)):
407 filteredRefCat.append(record)
408 return filteredRefCat
409 return self.loadRegionloadRegion(outerSkyRegion, filtFunc=_filterFunction, epoch=epoch, filterName=filterName)
410
411 def loadRegion(self, region, filtFunc=None, filterName=None, epoch=None):
412 """Load reference objects within a specified region.
413
414 This function loads the DataIds used to construct an instance of this
415 class which intersect or are contained within the specified region. The
416 reference catalogs which intersect but are not fully contained within
417 the input region are further filtered by the specified filter function.
418 This function returns a single source catalog containing all reference
419 objects inside the specified region.
420
421 Parameters
422 ----------
423 region : `lsst.sphgeom.Region`
424 This can be any type that is derived from `lsst.sphgeom.Region` and
425 should define the spatial region for which reference objects are to
426 be loaded.
427 filtFunc : callable or `None`, optional
428 This optional parameter should be a callable object that takes a
429 reference catalog and its corresponding region as parameters,
430 filters the catalog by some criteria and returns the filtered
431 reference catalog. If `None`, an internal filter function is used
432 which filters according to if a reference object falls within the
433 input region.
434 filterName : `str` or `None`, optional
435 Name of camera filter, or `None` or blank for the default filter.
436 epoch : `astropy.time.Time` or `None`, optional
437 Epoch to which to correct proper motion and parallax, or `None` to
438 not apply such corrections.
439
440 Returns
441 -------
442 referenceCatalog : `lsst.afw.table.SourceCatalog`
443 Catalog containing reference objects which intersect the input region,
444 filtered by the specified filter function.
445
446 Raises
447 ------
448 RuntimeError
449 Raised if no reference catalogs could be found for the specified
450 region.
451 TypeError
452 Raised if the loaded reference catalogs do not have matching
453 schemas.
454 """
455 regionLat = region.getBoundingBox().getLat()
456 regionLon = region.getBoundingBox().getLon()
457 self.loglog.info("Loading reference objects from region bounded by "
458 "[%.8f, %.8f], [%.8f, %.8f] RA Dec",
459 regionLon.getA().asDegrees(), regionLon.getB().asDegrees(),
460 regionLat.getA().asDegrees(), regionLat.getB().asDegrees())
461 if filtFunc is None:
462 filtFunc = _FilterCatalog(region)
463 # filter out all the regions supplied by the constructor that do not overlap
464 overlapList = []
465 for dataId, refCat in zip(self.dataIdsdataIds, self.refCatsrefCats):
466 # SphGeom supports some objects intersecting others, but is not symmetric,
467 # try the intersect operation in both directions
468 try:
469 intersects = dataId.region.intersects(region)
470 except TypeError:
471 intersects = region.intersects(dataId.region)
472
473 if intersects:
474 overlapList.append((dataId, refCat))
475
476 if len(overlapList) == 0:
477 raise RuntimeError("No reference tables could be found for input region")
478
479 firstCat = overlapList[0][1].get()
480 refCat = filtFunc(firstCat, overlapList[0][0].region)
481 trimmedAmount = len(firstCat) - len(refCat)
482
483 # Load in the remaining catalogs
484 for dataId, inputRefCat in overlapList[1:]:
485 tmpCat = inputRefCat.get()
486
487 if tmpCat.schema != firstCat.schema:
488 raise TypeError("Reference catalogs have mismatching schemas")
489
490 filteredCat = filtFunc(tmpCat, dataId.region)
491 refCat.extend(filteredCat)
492 trimmedAmount += len(tmpCat) - len(filteredCat)
493
494 self.loglog.debug("Trimmed %d refCat objects lying outside padded region, leaving %d",
495 trimmedAmount, len(refCat))
496 self.loglog.info("Loaded %d reference objects", len(refCat))
497
498 # Ensure that the loaded reference catalog is continuous in memory
499 if not refCat.isContiguous():
500 refCat = refCat.copy(deep=True)
501
502 self.applyProperMotionsapplyProperMotions(refCat, epoch)
503
504 # Verify the schema is in the correct units and has the correct version; automatically convert
505 # it with a warning if this is not the case.
506 if not hasNanojanskyFluxUnits(refCat.schema) or not getFormatVersionFromRefCat(refCat) >= 1:
507 self.loglog.warning("Found version 0 reference catalog with old style units in schema.")
508 self.loglog.warning("run `meas_algorithms/bin/convert_refcat_to_nJy.py` to convert fluxes to nJy.")
509 self.loglog.warning("See RFC-575 for more details.")
510 refCat = convertToNanojansky(refCat, self.loglog)
511
512 expandedCat = self.remapReferenceCatalogSchemaremapReferenceCatalogSchema(refCat, position=True)
513
514 # Add flux aliases
515 expandedCat = self.addFluxAliasesaddFluxAliases(expandedCat, self.configconfig.defaultFilter, self.configconfig.filterMap)
516
517 # Ensure that the returned reference catalog is continuous in memory
518 if not expandedCat.isContiguous():
519 expandedCat = expandedCat.copy(deep=True)
520
521 fluxField = getRefFluxField(schema=expandedCat.schema, filterName=filterName)
522 return pipeBase.Struct(refCat=expandedCat, fluxField=fluxField)
523
524 def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None):
525 """Load reference objects that lie within a circular region on the sky.
526
527 This method constructs a circular region from an input center and
528 angular radius, loads reference catalogs which are contained in or
529 intersect the circle, and filters reference catalogs which intersect
530 down to objects which lie within the defined circle.
531
532 Parameters
533 ----------
534 ctrCoord : `lsst.geom.SpherePoint`
535 Point defining the center of the circular region.
536 radius : `lsst.geom.Angle`
537 Defines the angular radius of the circular region.
538 filterName : `str` or `None`, optional
539 Name of camera filter, or `None` or blank for the default filter.
540 epoch : `astropy.time.Time` or `None`, optional
541 Epoch to which to correct proper motion and parallax, or `None` to
542 not apply such corrections.
543
544 Returns
545 -------
546 referenceCatalog : `lsst.afw.table.SourceCatalog`
547 Catalog containing reference objects inside the specified search
548 circle.
549 """
550 centerVector = ctrCoord.getVector()
551 sphRadius = sphgeom.Angle(radius.asRadians())
552 circularRegion = sphgeom.Circle(centerVector, sphRadius)
553 return self.loadRegionloadRegion(circularRegion, filterName=filterName, epoch=epoch)
554
555 def joinMatchListWithCatalog(self, matchCat, sourceCat):
556 """Relink an unpersisted match list to sources and reference objects.
557
558 A match list is persisted and unpersisted as a catalog of IDs
559 produced by afw.table.packMatches(), with match metadata
560 (as returned by the astrometry tasks) in the catalog's metadata
561 attribute. This method converts such a match catalog into a match
562 list, with links to source records and reference object records.
563
564 Parameters
565 ----------
566 matchCat : `lsst.afw.table.BaseCatalog`
567 Unpersisted packed match list.
568 ``matchCat.table.getMetadata()`` must contain match metadata,
569 as returned by the astrometry tasks.
570 sourceCat : `lsst.afw.table.SourceCatalog`
571 Source catalog. As a side effect, the catalog will be sorted
572 by ID.
573
574 Returns
575 -------
577 Match list.
578 """
579 return joinMatchListWithCatalogImpl(self, matchCat, sourceCat)
580
581 def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None,
582 bboxToSpherePadding=100):
583 """Return metadata about the load
584
585 This metadata is used for reloading the catalog (e.g., for
586 reconstituting a normalised match list.)
587
588 Parameters
589 ----------
590 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
591 Bounding box for the pixels.
593 The WCS object associated with ``bbox``.
594 filterName : `str` or `None`, optional
595 Name of the camera filter, or `None` or blank for the default
596 filter.
597 photoCalib : `None`
598 Deprecated, only included for api compatibility.
599 epoch : `astropy.time.Time` or `None`, optional
600 Epoch to which to correct proper motion and parallax, or `None` to
601 not apply such corrections.
602 bboxToSpherePadding : `int`, optional
603 Padding to account for translating a set of corners into a
604 spherical (convex) boundary that is certain to encompase the
605 enitre area covered by the box.
606
607 Returns
608 -------
610 The metadata detailing the search parameters used for this
611 dataset.
612 """
613 paddedBbox = geom.Box2D(bbox)
614 paddedBbox.grow(self.configconfig.pixelMargin)
615 _, _, innerCorners, outerCorners = self._makeBoxRegion_makeBoxRegion(paddedBbox, wcs, bboxToSpherePadding)
616 md = PropertyList()
617 for box, corners in zip(("INNER", "OUTER"), (innerCorners, outerCorners)):
618 for (name, corner) in zip(("UPPER_LEFT", "UPPER_RIGHT", "LOWER_LEFT", "LOWER_RIGHT"),
619 corners):
620 md.add(f"{box}_{name}_RA", geom.SpherePoint(corner).getRa().asDegrees(), f"{box}_corner")
621 md.add(f"{box}_{name}_DEC", geom.SpherePoint(corner).getDec().asDegrees(), f"{box}_corner")
622 md.add("SMATCHV", 1, 'SourceMatchVector version number')
623 filterName = "UNKNOWN" if filterName is None else str(filterName)
624 md.add('FILTER', filterName, 'filter name for photometric data')
625 md.add('EPOCH', "NONE" if epoch is None else epoch.mjd, 'Epoch (TAI MJD) for catalog')
626 return md
627
628 @staticmethod
629 def getMetadataCircle(coord, radius, filterName, photoCalib=None, epoch=None):
630 """Return metadata about the load.
631
632 This metadata is used for reloading the catalog (e.g. for
633 reconstituting a normalized match list.)
634
635 Parameters
636 ----------
637 coord : `lsst.geom.SpherePoint`
638 ICRS center of the search region.
639 radius : `lsst.geom.Angle`
640 Radius of the search region.
641 filterName : `str` or `None`
642 Name of the camera filter, or `None` or blank for the default
643 filter.
644 photoCalib : `None`
645 Deprecated, only included for api compatibility.
646 epoch : `astropy.time.Time` or `None`, optional
647 Epoch to which to correct proper motion and parallax, or `None` to
648 not apply such corrections.
649
650 Returns
651 -------
653 """
654 md = PropertyList()
655 md.add('RA', coord.getRa().asDegrees(), 'field center in degrees')
656 md.add('DEC', coord.getDec().asDegrees(), 'field center in degrees')
657 md.add('RADIUS', radius.asDegrees(), 'field radius in degrees, minimum')
658 md.add('SMATCHV', 1, 'SourceMatchVector version number')
659 filterName = "UNKNOWN" if filterName is None else str(filterName)
660 md.add('FILTER', filterName, 'filter name for photometric data')
661 md.add('EPOCH', "NONE" if epoch is None else epoch.mjd, 'Epoch (TAI MJD) for catalog')
662 return md
663
664 @staticmethod
665 def addFluxAliases(refCat, defaultFilter, filterReferenceMap):
666 """Add flux columns and aliases for camera to reference mapping.
667
668 Creates a new catalog containing the information of the input refCat
669 as well as added flux columns and aliases between camera and reference
670 fluxes.
671
672 Parameters
673 ----------
675 Catalog of reference objects
676 defaultFilter : `str`
677 Name of the default reference filter
678 filterReferenceMap : `dict` of `str`
679 Dictionary with keys corresponding to a filter name and values
680 which correspond to the name of the reference filter.
681
682 Returns
683 -------
685 Reference catalog with columns added to track reference filters.
686
687 Raises
688 ------
689 `RuntimeError`
690 If the specified reference filter name is not specifed as a
691 key in the reference filter map.
692 """
693 refCat = ReferenceObjectLoader.remapReferenceCatalogSchema(refCat,
694 filterNameList=filterReferenceMap.keys())
695 aliasMap = refCat.schema.getAliasMap()
696 if filterReferenceMap is None:
697 filterReferenceMap = {}
698 for filterName, refFilterName in itertools.chain([(None, defaultFilter)],
699 filterReferenceMap.items()):
700 if refFilterName:
701 camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux"
702 refFluxName = refFilterName + "_flux"
703 if refFluxName not in refCat.schema:
704 raise RuntimeError("Unknown reference filter %s" % (refFluxName,))
705 aliasMap.set(camFluxName, refFluxName)
706
707 refFluxErrName = refFluxName + "Err"
708 camFluxErrName = camFluxName + "Err"
709 aliasMap.set(camFluxErrName, refFluxErrName)
710
711 return refCat
712
713 @staticmethod
714 def remapReferenceCatalogSchema(refCat, *, filterNameList=None, position=False, photometric=False):
715 """This function takes in a reference catalog and creates a new catalog with additional
716 columns defined the remaining function arguments.
717
718 Parameters
719 ----------
721 Reference catalog to map to new catalog
722
723 Returns
724 -------
725 expandedCat : `lsst.afw.table.SimpleCatalog`
726 Deep copy of input reference catalog with additional columns added
727 """
728 mapper = afwTable.SchemaMapper(refCat.schema, True)
729 mapper.addMinimalSchema(refCat.schema, True)
730 mapper.editOutputSchema().disconnectAliases()
731 if filterNameList:
732 for filterName in filterNameList:
733 mapper.editOutputSchema().addField(f"{filterName}_flux",
734 type=numpy.float64,
735 doc=f"flux in filter {filterName}",
736 units="Jy"
737 )
738 mapper.editOutputSchema().addField(f"{filterName}_fluxErr",
739 type=numpy.float64,
740 doc=f"flux uncertanty in filter {filterName}",
741 units="Jy"
742 )
743
744 if position:
745 mapper.editOutputSchema().addField("centroid_x", type=float, doReplace=True)
746 mapper.editOutputSchema().addField("centroid_y", type=float, doReplace=True)
747 mapper.editOutputSchema().addField("hasCentroid", type="Flag", doReplace=True)
748 mapper.editOutputSchema().getAliasMap().set("slot_Centroid", "centroid")
749
750 if photometric:
751 mapper.editOutputSchema().addField("photometric",
752 type="Flag",
753 doc="set if the object can be used for photometric"
754 "calibration",
755 )
756 mapper.editOutputSchema().addField("resolved",
757 type="Flag",
758 doc="set if the object is spatially resolved"
759 )
760 mapper.editOutputSchema().addField("variable",
761 type="Flag",
762 doc="set if the object has variable brightness"
763 )
764
765 expandedCat = afwTable.SimpleCatalog(mapper.getOutputSchema())
766 expandedCat.setMetadata(refCat.getMetadata())
767 expandedCat.extend(refCat, mapper=mapper)
768
769 return expandedCat
770
771
772def getRefFluxField(schema, filterName=None):
773 """Get the name of a flux field from a schema.
774
775 return the alias of "anyFilterMapsToThis", if present
776 else if filterName is specified:
777 return "*filterName*_camFlux" if present
778 else return "*filterName*_flux" if present (camera filter name
779 matches reference filter name)
780 else throw RuntimeError
781 else:
782 return "camFlux", if present,
783 else throw RuntimeError
784
785 Parameters
786 ----------
787 schema : `lsst.afw.table.Schema`
788 Reference catalog schema.
789 filterName : `str`, optional
790 Name of camera filter. If not specified, ``defaultFilter`` needs to be
791 set in the refcat loader config.
792
793 Returns
794 -------
795 fluxFieldName : `str`
796 Name of flux field.
797
798 Raises
799 ------
800 RuntimeError
801 If an appropriate field is not found.
802 """
803 if not isinstance(schema, afwTable.Schema):
804 raise RuntimeError("schema=%s is not a schema" % (schema,))
805 try:
806 return schema.getAliasMap().get("anyFilterMapsToThis")
807 except LookupError:
808 pass # try the filterMap next
809
810 if filterName:
811 fluxFieldList = [filterName + "_camFlux", filterName + "_flux"]
812 else:
813 fluxFieldList = ["camFlux"]
814 for fluxField in fluxFieldList:
815 if fluxField in schema:
816 return fluxField
817
818 raise RuntimeError("Could not find flux field(s) %s" % (", ".join(fluxFieldList)))
819
820
821def getRefFluxKeys(schema, filterName=None):
822 """Return keys for flux and flux error.
823
824 Parameters
825 ----------
826 schema : `lsst.afw.table.Schema`
827 Reference catalog schema.
828 filterName : `str`
829 Name of camera filter.
830
831 Returns
832 -------
833 keys : `tuple` of (`lsst.afw.table.Key`, `lsst.afw.table.Key`)
834 Two keys:
835
836 - flux key
837 - flux error key, if present, else None
838
839 Raises
840 ------
841 RuntimeError
842 If flux field not found.
843 """
844 fluxField = getRefFluxField(schema, filterName)
845 fluxErrField = fluxField + "Err"
846 fluxKey = schema[fluxField].asKey()
847 try:
848 fluxErrKey = schema[fluxErrField].asKey()
849 except Exception:
850 fluxErrKey = None
851 return (fluxKey, fluxErrKey)
852
853
854class LoadReferenceObjectsConfig(pexConfig.Config):
855 pixelMargin = pexConfig.RangeField(
856 doc="Padding to add to 4 all edges of the bounding box (pixels)",
857 dtype=int,
858 default=250,
859 min=0,
860 )
861 defaultFilter = pexConfig.Field(
862 doc=("Default reference catalog filter to use if filter not specified in exposure;"
863 " if blank then filter must be specified in exposure."),
864 dtype=str,
865 default="",
866 deprecated="defaultFilter is deprecated by RFC-716. Will be removed after v22."
867 )
868 anyFilterMapsToThis = pexConfig.Field(
869 doc=("Always use this reference catalog filter, no matter whether or what filter name is "
870 "supplied to the loader. Effectively a trivial filterMap: map all filter names to this filter."
871 " This can be set for purely-astrometric catalogs (e.g. Gaia DR2) where there is only one "
872 "reasonable choice for every camera filter->refcat mapping, but not for refcats used for "
873 "photometry, which need a filterMap and/or colorterms/transmission corrections."),
874 dtype=str,
875 default=None,
876 optional=True
877 )
878 filterMap = pexConfig.DictField(
879 doc=("Mapping of camera filter name: reference catalog filter name; "
880 "each reference filter must exist in the refcat."
881 " Note that this does not perform any bandpass corrections: it is just a lookup."),
882 keytype=str,
883 itemtype=str,
884 default={},
885 )
886 requireProperMotion = pexConfig.Field(
887 doc="Require that the fields needed to correct proper motion "
888 "(epoch, pm_ra and pm_dec) are present?",
889 dtype=bool,
890 default=False,
891 )
892
893 def validate(self):
894 super().validate()
895 if self.filterMapfilterMap != {} and self.anyFilterMapsToThisanyFilterMapsToThis is not None:
896 msg = "`filterMap` and `anyFilterMapsToThis` are mutually exclusive"
897 raise pexConfig.FieldValidationError(LoadReferenceObjectsConfig.anyFilterMapsToThis,
898 self, msg)
899
900
901class LoadReferenceObjectsTask(pipeBase.Task, ReferenceObjectLoaderBase, metaclass=abc.ABCMeta):
902 """Abstract base class to load objects from reference catalogs.
903 """
904 ConfigClass = LoadReferenceObjectsConfig
905 _DefaultName = "LoadReferenceObjects"
906
907 def __init__(self, butler=None, *args, **kwargs):
908 """Construct a LoadReferenceObjectsTask
909
910 Parameters
911 ----------
912 butler : `lsst.daf.persistence.Butler`
913 Data butler, for access reference catalogs.
914 """
915 pipeBase.Task.__init__(self, *args, **kwargs)
916 self.butlerbutler = butler
917
918 @timeMethod
919 def loadPixelBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
920 """Load reference objects that overlap a rectangular pixel region.
921
922 Parameters
923 ----------
924 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
925 Bounding box for pixels.
927 WCS; used to convert pixel positions to sky coordinates
928 and vice-versa.
929 filterName : `str` or `None`, optional
930 Name of filter, or `None` or `""` for the default filter.
931 This is used for flux values in case we have flux limits
932 (which are not yet implemented).
933 photoCalib : `None`
934 Deprecated, only included for api compatibility.
935 epoch : `astropy.time.Time` or `None`, optional
936 Epoch to which to correct proper motion and parallax, or `None` to
937 not apply such corrections.
938
939 Returns
940 -------
941 results : `lsst.pipe.base.Struct`
942 A Struct containing the following fields:
943 refCat : `lsst.afw.catalog.SimpleCatalog`
944 A catalog of reference objects with the standard
945 schema, as documented in the main doc string for
946 `LoadReferenceObjects`.
947 The catalog is guaranteed to be contiguous.
948 fluxField : `str`
949 Name of flux field for specified `filterName`.
950
951 Notes
952 -----
953 The search algorithm works by searching in a region in sky
954 coordinates whose center is the center of the bbox and radius
955 is large enough to just include all 4 corners of the bbox.
956 Stars that lie outside the bbox are then trimmed from the list.
957 """
958 circle = self._calculateCircle_calculateCircle(bbox, wcs)
959
960 # find objects in circle
961 self.log.info("Loading reference objects using center %s and radius %s deg",
962 circle.coord, circle.radius.asDegrees())
963 loadRes = self.loadSkyCircleloadSkyCircle(circle.coord, circle.radius, filterName=filterName, epoch=epoch,
964 centroids=True)
965 refCat = loadRes.refCat
966 numFound = len(refCat)
967
968 # trim objects outside bbox
969 refCat = self._trimToBBox_trimToBBox(refCat=refCat, bbox=circle.bbox, wcs=wcs)
970 numTrimmed = numFound - len(refCat)
971 self.log.debug("trimmed %d out-of-bbox objects, leaving %d", numTrimmed, len(refCat))
972 self.log.info("Loaded %d reference objects", len(refCat))
973
974 # make sure catalog is contiguous
975 if not refCat.isContiguous():
976 loadRes.refCat = refCat.copy(deep=True)
977
978 return loadRes
979
980 @abc.abstractmethod
981 def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None, centroids=False):
982 """Load reference objects that overlap a circular sky region.
983
984 Parameters
985 ----------
986 ctrCoord : `lsst.geom.SpherePoint`
987 ICRS center of search region.
988 radius : `lsst.geom.Angle`
989 Radius of search region.
990 filterName : `str` or `None`, optional
991 Name of filter, or `None` or `""` for the default filter.
992 This is used for flux values in case we have flux limits
993 (which are not yet implemented).
994 epoch : `astropy.time.Time` or `None`, optional
995 Epoch to which to correct proper motion and parallax, or `None` to
996 not apply such corrections.
997 centroids : `bool`, optional
998 Add centroid fields to the loaded Schema. ``loadPixelBox`` expects
999 these fields to exist.
1000
1001 Returns
1002 -------
1003 results : `lsst.pipe.base.Struct`
1004 A Struct containing the following fields:
1005 refCat : `lsst.afw.catalog.SimpleCatalog`
1006 A catalog of reference objects with the standard
1007 schema, as documented in the main doc string for
1008 `LoadReferenceObjects`.
1009 The catalog is guaranteed to be contiguous.
1010 fluxField : `str`
1011 Name of flux field for specified `filterName`.
1012
1013 Notes
1014 -----
1015 Note that subclasses are responsible for performing the proper motion
1016 correction, since this is the lowest-level interface for retrieving
1017 the catalog.
1018 """
1019 return
1020
1021 @staticmethod
1022 def _trimToBBox(refCat, bbox, wcs):
1023 """Remove objects outside a given pixel bounding box and set
1024 centroid and hasCentroid fields.
1025
1026 Parameters
1027 ----------
1029 A catalog of objects. The schema must include fields
1030 "coord", "centroid" and "hasCentroid".
1031 The "coord" field is read.
1032 The "centroid" and "hasCentroid" fields are set.
1033 bbox : `lsst.geom.Box2D`
1034 Pixel region
1035 wcs : `lsst.afw.geom.SkyWcs`
1036 WCS; used to convert sky coordinates to pixel positions.
1037
1038 Returns
1039 -------
1041 Reference objects in the bbox, with centroid and
1042 hasCentroid fields set.
1043 """
1044 afwTable.updateRefCentroids(wcs, refCat)
1045 centroidKey = afwTable.Point2DKey(refCat.schema["centroid"])
1046 retStarCat = type(refCat)(refCat.table)
1047 for star in refCat:
1048 point = star.get(centroidKey)
1049 if bbox.contains(point):
1050 retStarCat.append(star)
1051 return retStarCat
1052
1053 def _addFluxAliases(self, schema):
1054 """Add aliases for camera filter fluxes to the schema.
1055
1056 If self.config.defaultFilter then adds these aliases:
1057 camFlux: <defaultFilter>_flux
1058 camFluxErr: <defaultFilter>_fluxErr, if the latter exists
1059
1060 For each camFilter: refFilter in self.config.filterMap adds these aliases:
1061 <camFilter>_camFlux: <refFilter>_flux
1062 <camFilter>_camFluxErr: <refFilter>_fluxErr, if the latter exists
1063
1064 Parameters
1065 ----------
1066 schema : `lsst.afw.table.Schema`
1067 Schema for reference catalog.
1068
1069 Raises
1070 ------
1071 RuntimeError
1072 If any reference flux field is missing from the schema.
1073 """
1074 aliasMap = schema.getAliasMap()
1075
1076 if self.config.anyFilterMapsToThis is not None:
1077 refFluxName = self.config.anyFilterMapsToThis + "_flux"
1078 if refFluxName not in schema:
1079 msg = f"Unknown reference filter for anyFilterMapsToThis='{refFluxName}'"
1080 raise RuntimeError(msg)
1081 aliasMap.set("anyFilterMapsToThis", refFluxName)
1082 return # this is mutually exclusive with filterMap
1083
1084 def addAliasesForOneFilter(filterName, refFilterName):
1085 """Add aliases for a single filter
1086
1087 Parameters
1088 ----------
1089 filterName : `str` (optional)
1090 Camera filter name. The resulting alias name is
1091 <filterName>_camFlux, or simply "camFlux" if `filterName`
1092 is `None` or `""`.
1093 refFilterName : `str`
1094 Reference catalog filter name; the field
1095 <refFilterName>_flux must exist.
1096 """
1097 camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux"
1098 refFluxName = refFilterName + "_flux"
1099 if refFluxName not in schema:
1100 raise RuntimeError("Unknown reference filter %s" % (refFluxName,))
1101 aliasMap.set(camFluxName, refFluxName)
1102 refFluxErrName = refFluxName + "Err"
1103 if refFluxErrName in schema:
1104 camFluxErrName = camFluxName + "Err"
1105 aliasMap.set(camFluxErrName, refFluxErrName)
1106
1107 if self.config.defaultFilter:
1108 addAliasesForOneFilter(None, self.config.defaultFilter)
1109
1110 for filterName, refFilterName in self.config.filterMap.items():
1111 addAliasesForOneFilter(filterName, refFilterName)
1112
1113 @staticmethod
1114 def makeMinimalSchema(filterNameList, *, addCentroid=False,
1115 addIsPhotometric=False, addIsResolved=False,
1116 addIsVariable=False, coordErrDim=2,
1117 addProperMotion=False, properMotionErrDim=2,
1118 addParallax=False):
1119 """Make a standard schema for reference object catalogs.
1120
1121 Parameters
1122 ----------
1123 filterNameList : `list` of `str`
1124 List of filter names. Used to create <filterName>_flux fields.
1125 addIsPhotometric : `bool`
1126 If True then add field "photometric".
1127 addIsResolved : `bool`
1128 If True then add field "resolved".
1129 addIsVariable : `bool`
1130 If True then add field "variable".
1131 coordErrDim : `int`
1132 Number of coord error fields; must be one of 0, 2, 3:
1133
1134 - If 2 or 3: add fields "coord_raErr" and "coord_decErr".
1135 - If 3: also add field "coord_radecErr".
1136 addProperMotion : `bool`
1137 If True add fields "epoch", "pm_ra", "pm_dec" and "pm_flag".
1138 properMotionErrDim : `int`
1139 Number of proper motion error fields; must be one of 0, 2, 3;
1140 ignored if addProperMotion false:
1141 - If 2 or 3: add fields "pm_raErr" and "pm_decErr".
1142 - If 3: also add field "pm_radecErr".
1143 addParallax : `bool`
1144 If True add fields "epoch", "parallax", "parallaxErr"
1145 and "parallax_flag".
1146
1147 Returns
1148 -------
1149 schema : `lsst.afw.table.Schema`
1150 Schema for reference catalog, an
1152
1153 Notes
1154 -----
1155 Reference catalogs support additional covariances, such as
1156 covariance between RA and proper motion in declination,
1157 that are not supported by this method, but can be added after
1158 calling this method.
1159 """
1160 schema = afwTable.SimpleTable.makeMinimalSchema()
1161 if addCentroid:
1162 afwTable.Point2DKey.addFields(
1163 schema,
1164 "centroid",
1165 "centroid on an exposure, if relevant",
1166 "pixel",
1167 )
1168 schema.addField(
1169 field="hasCentroid",
1170 type="Flag",
1171 doc="is position known?",
1172 )
1173 for filterName in filterNameList:
1174 schema.addField(
1175 field="%s_flux" % (filterName,),
1176 type=numpy.float64,
1177 doc="flux in filter %s" % (filterName,),
1178 units="nJy",
1179 )
1180 for filterName in filterNameList:
1181 schema.addField(
1182 field="%s_fluxErr" % (filterName,),
1183 type=numpy.float64,
1184 doc="flux uncertainty in filter %s" % (filterName,),
1185 units="nJy",
1186 )
1187 if addIsPhotometric:
1188 schema.addField(
1189 field="photometric",
1190 type="Flag",
1191 doc="set if the object can be used for photometric calibration",
1192 )
1193 if addIsResolved:
1194 schema.addField(
1195 field="resolved",
1196 type="Flag",
1197 doc="set if the object is spatially resolved",
1198 )
1199 if addIsVariable:
1200 schema.addField(
1201 field="variable",
1202 type="Flag",
1203 doc="set if the object has variable brightness",
1204 )
1205 if coordErrDim not in (0, 2, 3):
1206 raise ValueError("coordErrDim={}; must be (0, 2, 3)".format(coordErrDim))
1207 if coordErrDim > 0:
1208 afwTable.CovarianceMatrix2fKey.addFields(
1209 schema=schema,
1210 prefix="coord",
1211 names=["ra", "dec"],
1212 units=["rad", "rad"],
1213 diagonalOnly=(coordErrDim == 2),
1214 )
1215
1216 if addProperMotion or addParallax:
1217 schema.addField(
1218 field="epoch",
1219 type=numpy.float64,
1220 doc="date of observation (TAI, MJD)",
1221 units="day",
1222 )
1223
1224 if addProperMotion:
1225 schema.addField(
1226 field="pm_ra",
1227 type="Angle",
1228 doc="proper motion in the right ascension direction = dra/dt * cos(dec)",
1229 units="rad/year",
1230 )
1231 schema.addField(
1232 field="pm_dec",
1233 type="Angle",
1234 doc="proper motion in the declination direction",
1235 units="rad/year",
1236 )
1237 if properMotionErrDim not in (0, 2, 3):
1238 raise ValueError("properMotionErrDim={}; must be (0, 2, 3)".format(properMotionErrDim))
1239 if properMotionErrDim > 0:
1240 afwTable.CovarianceMatrix2fKey.addFields(
1241 schema=schema,
1242 prefix="pm",
1243 names=["ra", "dec"],
1244 units=["rad/year", "rad/year"],
1245 diagonalOnly=(properMotionErrDim == 2),
1246 )
1247 schema.addField(
1248 field="pm_flag",
1249 type="Flag",
1250 doc="Set if proper motion or proper motion error is bad",
1251 )
1252
1253 if addParallax:
1254 schema.addField(
1255 field="parallax",
1256 type="Angle",
1257 doc="parallax",
1258 units="rad",
1259 )
1260 schema.addField(
1261 field="parallaxErr",
1262 type="Angle",
1263 doc="uncertainty in parallax",
1264 units="rad",
1265 )
1266 schema.addField(
1267 field="parallax_flag",
1268 type="Flag",
1269 doc="Set if parallax or parallax error is bad",
1270 )
1271 return schema
1272
1273 def _calculateCircle(self, bbox, wcs):
1274 """Compute on-sky center and radius of search region.
1275
1276 Parameters
1277 ----------
1278 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1279 Pixel bounding box.
1280 wcs : `lsst.afw.geom.SkyWcs`
1281 WCS; used to convert pixel positions to sky coordinates.
1282
1283 Returns
1284 -------
1285 results : `lsst.pipe.base.Struct`
1286 A Struct containing:
1287
1288 - coord : `lsst.geom.SpherePoint`
1289 ICRS center of the search region.
1290 - radius : `lsst.geom.Angle`
1291 Radius of the search region.
1292 - bbox : `lsst.geom.Box2D`
1293 Bounding box used to compute the circle.
1294 """
1295 bbox = geom.Box2D(bbox) # make sure bbox is double and that we have a copy
1296 bbox.grow(self.config.pixelMargin)
1297 coord = wcs.pixelToSky(bbox.getCenter())
1298 radius = max(coord.separation(wcs.pixelToSky(pp)) for pp in bbox.getCorners())
1299 return pipeBase.Struct(coord=coord, radius=radius, bbox=bbox)
1300
1301 def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
1302 """Return metadata about the load.
1303
1304 This metadata is used for reloading the catalog (e.g., for
1305 reconstituting a normalised match list.
1306
1307 Parameters
1308 ----------
1309 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1310 Pixel bounding box.
1311 wcs : `lsst.afw.geom.SkyWcs`
1312 WCS; used to convert pixel positions to sky coordinates.
1313 filterName : `str` or `None`, optional
1314 Name of camera filter, or `None` or `""` for the default
1315 filter.
1316 photoCalib : `None`
1317 Deprecated, only included for api compatibility.
1318 epoch : `astropy.time.Time` or `None`, optional
1319 Epoch to which to correct proper motion and parallax,
1320 or None to not apply such corrections.
1321
1322 Returns
1323 -------
1324 metadata : `lsst.daf.base.PropertyList`
1325 Metadata about the load.
1326 """
1327 circle = self._calculateCircle_calculateCircle(bbox, wcs)
1328 return self.getMetadataCirclegetMetadataCircle(circle.coord, circle.radius, filterName, epoch=epoch)
1329
1330 def getMetadataCircle(self, coord, radius, filterName, photoCalib=None, epoch=None):
1331 """Return metadata about the load.
1332
1333 This metadata is used for reloading the catalog (e.g., for
1334 reconstituting a normalised match list.
1335
1336 Parameters
1337 ----------
1338 coord : `lsst.geom.SpherePoint`
1339 ICRS center of the search region.
1340 radius : `lsst.geom.Angle`
1341 Radius of the search region.
1342 filterName : `str`
1343 Name of camera filter, or `None` or `""` for the default
1344 filter.
1345 photoCalib : `None`
1346 Deprecated, only included for api compatibility.
1347 epoch : `astropy.time.Time` (optional)
1348 Epoch to which to correct proper motion and parallax, or `None` to
1349 not apply such corrections.
1350
1351 Returns
1352 -------
1354 Metadata about the load
1355 """
1356 md = PropertyList()
1357 md.add('RA', coord.getRa().asDegrees(), 'field center in degrees')
1358 md.add('DEC', coord.getDec().asDegrees(), 'field center in degrees')
1359 md.add('RADIUS', radius.asDegrees(), 'field radius in degrees, minimum')
1360 md.add('SMATCHV', 1, 'SourceMatchVector version number')
1361 filterName = "UNKNOWN" if filterName is None else str(filterName)
1362 md.add('FILTER', filterName, 'filter name for photometric data')
1363 md.add('EPOCH', "NONE" if epoch is None else epoch.mjd, 'Epoch (TAI MJD) for catalog')
1364 return md
1365
1366 def joinMatchListWithCatalog(self, matchCat, sourceCat):
1367 """Relink an unpersisted match list to sources and reference
1368 objects.
1369
1370 A match list is persisted and unpersisted as a catalog of IDs
1371 produced by afw.table.packMatches(), with match metadata
1372 (as returned by the astrometry tasks) in the catalog's metadata
1373 attribute. This method converts such a match catalog into a match
1374 list, with links to source records and reference object records.
1375
1376 Parameters
1377 ----------
1378 matchCat : `lsst.afw.table.BaseCatalog`
1379 Unperisted packed match list.
1380 ``matchCat.table.getMetadata()`` must contain match metadata,
1381 as returned by the astrometry tasks.
1382 sourceCat : `lsst.afw.table.SourceCatalog`
1383 Source catalog. As a side effect, the catalog will be sorted
1384 by ID.
1385
1386 Returns
1387 -------
1389 Match list.
1390 """
1391 return joinMatchListWithCatalogImpl(self, matchCat, sourceCat)
1392
1393
1394def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat):
1395 """Relink an unpersisted match list to sources and reference
1396 objects.
1397
1398 A match list is persisted and unpersisted as a catalog of IDs
1399 produced by afw.table.packMatches(), with match metadata
1400 (as returned by the astrometry tasks) in the catalog's metadata
1401 attribute. This method converts such a match catalog into a match
1402 list, with links to source records and reference object records.
1403
1404 Parameters
1405 ----------
1406 refObjLoader
1407 Reference object loader to use in getting reference objects
1408 matchCat : `lsst.afw.table.BaseCatalog`
1409 Unperisted packed match list.
1410 ``matchCat.table.getMetadata()`` must contain match metadata,
1411 as returned by the astrometry tasks.
1412 sourceCat : `lsst.afw.table.SourceCatalog`
1413 Source catalog. As a side effect, the catalog will be sorted
1414 by ID.
1415
1416 Returns
1417 -------
1419 Match list.
1420 """
1421 matchmeta = matchCat.table.getMetadata()
1422 version = matchmeta.getInt('SMATCHV')
1423 if version != 1:
1424 raise ValueError('SourceMatchVector version number is %i, not 1.' % version)
1425 filterName = matchmeta.getString('FILTER').strip()
1426 try:
1427 epoch = matchmeta.getDouble('EPOCH')
1428 except (LookupError, TypeError):
1429 epoch = None # Not present, or not correct type means it's not set
1430 if 'RADIUS' in matchmeta:
1431 # This is a circle style metadata, call loadSkyCircle
1432 ctrCoord = geom.SpherePoint(matchmeta.getDouble('RA'),
1433 matchmeta.getDouble('DEC'), geom.degrees)
1434 rad = matchmeta.getDouble('RADIUS')*geom.degrees
1435 refCat = refObjLoader.loadSkyCircle(ctrCoord, rad, filterName, epoch=epoch).refCat
1436 elif "INNER_UPPER_LEFT_RA" in matchmeta:
1437 # This is the sky box type (only triggers in the LoadReferenceObject class, not task)
1438 # Only the outer box is required to be loaded to get the maximum region, all filtering
1439 # will be done by the unpackMatches function, and no spatial filtering needs to be done
1440 # by the refObjLoader
1441 box = []
1442 for place in ("UPPER_LEFT", "UPPER_RIGHT", "LOWER_LEFT", "LOWER_RIGHT"):
1443 coord = geom.SpherePoint(matchmeta.getDouble(f"OUTER_{place}_RA"),
1444 matchmeta.getDouble(f"OUTER_{place}_DEC"),
1445 geom.degrees).getVector()
1446 box.append(coord)
1447 outerBox = sphgeom.ConvexPolygon(box)
1448 refCat = refObjLoader.loadRegion(outerBox, filterName=filterName, epoch=epoch).refCat
1449
1450 refCat.sort()
1451 sourceCat.sort()
1452 return afwTable.unpackMatches(matchCat, refCat, sourceCat)
1453
1454
1455def applyProperMotionsImpl(log, catalog, epoch):
1456 """Apply proper motion correction to a reference catalog.
1457
1458 Adjust position and position error in the ``catalog``
1459 for proper motion to the specified ``epoch``,
1460 modifying the catalog in place.
1461
1462 Parameters
1463 ----------
1464 log : `lsst.log.Log` or `logging.getLogger`
1465 Log object to write to.
1467 Catalog of positions, containing:
1468
1469 - Coordinates, retrieved by the table's coordinate key.
1470 - ``coord_raErr`` : Error in Right Ascension (rad).
1471 - ``coord_decErr`` : Error in Declination (rad).
1472 - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
1473 East positive)
1474 - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
1475 - ``pm_dec`` : Proper motion in Declination (rad/yr,
1476 North positive)
1477 - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
1478 - ``epoch`` : Mean epoch of object (an astropy.time.Time)
1479 epoch : `astropy.time.Time`
1480 Epoch to which to correct proper motion.
1481 """
1482 if "epoch" not in catalog.schema or "pm_ra" not in catalog.schema or "pm_dec" not in catalog.schema:
1483 log.warning("Proper motion correction not available from catalog")
1484 return
1485 if not catalog.isContiguous():
1486 raise RuntimeError("Catalog must be contiguous")
1487 catEpoch = astropy.time.Time(catalog["epoch"], scale="tai", format="mjd")
1488 log.info("Correcting reference catalog for proper motion to %r", epoch)
1489 # Use `epoch.tai` to make sure the time difference is in TAI
1490 timeDiffsYears = (epoch.tai - catEpoch).to(astropy.units.yr).value
1491 coordKey = catalog.table.getCoordKey()
1492 # Compute the offset of each object due to proper motion
1493 # as components of the arc of a great circle along RA and Dec
1494 pmRaRad = catalog["pm_ra"]
1495 pmDecRad = catalog["pm_dec"]
1496 offsetsRaRad = pmRaRad*timeDiffsYears
1497 offsetsDecRad = pmDecRad*timeDiffsYears
1498 # Compute the corresponding bearing and arc length of each offset
1499 # due to proper motion, and apply the offset
1500 # The factor of 1e6 for computing bearing is intended as
1501 # a reasonable scale for typical values of proper motion
1502 # in order to avoid large errors for small values of proper motion;
1503 # using the offsets is another option, but it can give
1504 # needlessly large errors for short duration
1505 offsetBearingsRad = numpy.arctan2(pmDecRad*1e6, pmRaRad*1e6)
1506 offsetAmountsRad = numpy.hypot(offsetsRaRad, offsetsDecRad)
1507 for record, bearingRad, amountRad in zip(catalog, offsetBearingsRad, offsetAmountsRad):
1508 record.set(coordKey,
1509 record.get(coordKey).offset(bearing=bearingRad*geom.radians,
1510 amount=amountRad*geom.radians))
1511 # Increase error in RA and Dec based on error in proper motion
1512 if "coord_raErr" in catalog.schema:
1513 catalog["coord_raErr"] = numpy.hypot(catalog["coord_raErr"],
1514 catalog["pm_raErr"]*timeDiffsYears)
1515 if "coord_decErr" in catalog.schema:
1516 catalog["coord_decErr"] = numpy.hypot(catalog["coord_decErr"],
1517 catalog["pm_decErr"]*timeDiffsYears)
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 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 remapReferenceCatalogSchema(refCat, *filterNameList=None, position=False, photometric=False)
def addFluxAliases(refCat, defaultFilter, filterReferenceMap)
def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None, bboxToSpherePadding=100)
def loadPixelBox(self, bbox, wcs, filterName=None, epoch=None, photoCalib=None, bboxToSpherePadding=100)
def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None)
def convertToNanojansky(catalog, log, doConvert=True)
def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat)