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1#
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#
24__all__ = ["getRefFluxField", "getRefFluxKeys", "LoadReferenceObjectsTask", "LoadReferenceObjectsConfig",
25 "ReferenceObjectLoader"]
27import abc
28import itertools
30import astropy.time
31import astropy.units
32import numpy
34import lsst.geom
35import lsst.afw.table as afwTable
36import lsst.pex.config as pexConfig
37import lsst.pex.exceptions as pexExceptions
38import lsst.pipe.base as pipeBase
39import lsst.pex.exceptions as pexExcept
40import lsst.log
41from lsst import geom
42from lsst import sphgeom
43from lsst.daf.base import PropertyList
46def isOldFluxField(name, units):
47 """Return True if this name/units combination corresponds to an
48 "old-style" reference catalog flux field.
49 """
50 unitsCheck = units != 'nJy' # (units == 'Jy' or units == '' or units == '?')
51 isFlux = name.endswith('_flux')
52 isFluxSigma = name.endswith('_fluxSigma')
53 isFluxErr = name.endswith('_fluxErr')
54 return (isFlux or isFluxSigma or isFluxErr) and unitsCheck
57def hasNanojanskyFluxUnits(schema):
58 """Return True if the units of all flux and fluxErr are correct (nJy).
59 """
60 for field in schema:
61 if isOldFluxField(field.field.getName(), field.field.getUnits()):
62 return False
63 return True
66def getFormatVersionFromRefCat(refCat):
67 """"Return the format version stored in a reference catalog header.
69 Parameters
70 ----------
71 refCat : `lsst.afw.table.SimpleCatalog`
72 Reference catalog to inspect.
74 Returns
75 -------
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.
79 """
80 md = refCat.getMetadata()
81 if md is None: 81 ↛ 82line 81 didn't jump to line 82, because the condition on line 81 was never true
82 return None
83 try:
84 return md.getScalar("REFCAT_FORMAT_VERSION")
85 except KeyError:
86 return None
89def convertToNanojansky(catalog, log, doConvert=True):
90 """Convert fluxes in a catalog from jansky to nanojansky.
92 Parameters
93 ----------
94 catalog : `lsst.afw.table.SimpleCatalog`
95 The catalog to convert.
96 log : `lsst.log.Log`
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`.
102 Returns
103 -------
104 catalog : `lsst.afw.table.SimpleCatalog` or None
105 The converted catalog, or None if ``doConvert`` is False.
107 Notes
108 -----
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.
112 """
113 # Do not share the AliasMap: for refcats, that gets created when the
114 # catalog is read from disk and should not be propagated.
115 mapper = lsst.afw.table.SchemaMapper(catalog.schema, shareAliasMap=False)
116 mapper.addMinimalSchema(lsst.afw.table.SimpleTable.makeMinimalSchema())
117 input_fields = []
118 output_fields = []
119 for field in catalog.schema:
120 oldName = field.field.getName()
121 oldUnits = field.field.getUnits()
122 if isOldFluxField(oldName, oldUnits):
123 units = 'nJy'
124 # remap Sigma flux fields to Err, so we can drop the alias
125 if oldName.endswith('_fluxSigma'):
126 name = oldName.replace('_fluxSigma', '_fluxErr')
127 else:
128 name = oldName
129 newField = lsst.afw.table.Field[field.dtype](name, field.field.getDoc(), units)
130 mapper.addMapping(field.getKey(), newField)
131 input_fields.append(field.field)
132 output_fields.append(newField)
133 else:
134 mapper.addMapping(field.getKey())
136 fluxFieldsStr = '; '.join("(%s, '%s')" % (field.getName(), field.getUnits()) for field in input_fields)
138 if doConvert:
139 newSchema = mapper.getOutputSchema()
140 output = lsst.afw.table.SimpleCatalog(newSchema)
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}")
145 return output
146 else:
147 log.info(f"Found old-style refcat flux fields (name, units): {fluxFieldsStr}")
148 return None
151class _FilterCatalog:
152 """This is a private helper class which filters catalogs by
153 row based on the row being inside the region used to initialize
154 the class.
156 Parameters
157 ----------
158 region : `lsst.sphgeom.Region`
159 The spatial region which all objects should lie within
160 """
161 def __init__(self, region):
162 self.region = region
164 def __call__(self, refCat, catRegion):
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.
177 Parameters
178 ---------
179 refCat : `lsst.afw.table.SourceCatalog`
180 SourceCatalog to be filtered.
181 catRegion : `lsst.sphgeom.Region`
182 Region in which the catalog was created
183 """
184 if catRegion.isWithin(self.region):
185 # no filtering needed, region completely contains refcat
186 return refCat
188 filteredRefCat = type(refCat)(refCat.table)
189 for record in refCat:
190 if self.region.contains(record.getCoord().getVector()):
191 filteredRefCat.append(record)
192 return filteredRefCat
195class ReferenceObjectLoader:
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.
204 """
205 def __init__(self, dataIds, refCats, config, log=None):
206 """ Constructs an instance of ReferenceObjectLoader
208 Parameters
209 ----------
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
215 log : `lsst.log.Log`
216 Logger object used to write out messages. If `None` (default) the default
217 lsst logger will be used
219 """
220 self.dataIds = dataIds
221 self.refCats = refCats
222 self.log = log or lsst.log.Log.getDefaultLogger()
223 self.config = config
225 @staticmethod
226 def _makeBoxRegion(BBox, wcs, BBoxPadding):
227 outerLocalBBox = geom.Box2D(BBox)
228 innerLocalBBox = geom.Box2D(BBox)
230 # Grow the bounding box to make sure the spherical geometry bbox will contain
231 # the same region, as non-padded boxes may contain different regions because of optical distortion.
232 # Also create an inner region that is sure to be inside the bbox
233 outerLocalBBox.grow(BBoxPadding)
234 innerLocalBBox.grow(-1*BBoxPadding)
236 # Handle the fact that the inner bounding box shrunk to a zero sized region in at least one
237 # dimension, in which case all reference catalogs must be checked fully against the input
238 # bounding box
239 if innerLocalBBox.getDimensions() == geom.Extent2D(0, 0):
240 innerSkyRegion = sphgeom.Box()
241 else:
242 innerBoxCorners = innerLocalBBox.getCorners()
243 innerSphCorners = [wcs.pixelToSky(corner).getVector() for corner in innerBoxCorners]
245 innerSkyRegion = sphgeom.ConvexPolygon(innerSphCorners)
247 # Convert the corners of the box to sky coordinates
248 outerBoxCorners = outerLocalBBox.getCorners()
249 outerSphCorners = [wcs.pixelToSky(corner).getVector() for corner in outerBoxCorners]
251 outerSkyRegion = sphgeom.ConvexPolygon(outerSphCorners)
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
262 bounding box.
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
268 Parameters
269 ----------
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
275 filterName : `str`
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.
280 photoCalib : None
281 Deprecated and ignored, only included for api compatibility
282 bboxPadding : `int`
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.
292 Returns
293 -------
294 referenceCatalog : `lsst.afw.table.SimpleCatalog`
295 Catalog containing reference objects inside the specified bounding box
297 Raises
298 ------
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
304 """
305 innerSkyRegion, outerSkyRegion, _, _ = self._makeBoxRegion(bbox, wcs, bboxPadding)
307 def _filterFunction(refCat, region):
308 # Add columns to the reference catalog relating to center positions and use afwTable
309 # to populate those columns
310 refCat = self.remapReferenceCatalogSchema(refCat, position=True)
311 afwTable.updateRefCentroids(wcs, refCat)
312 # no need to filter the catalog if it is sure that it is entirely contained in the region
313 # defined by given bbox
314 if innerSkyRegion.contains(region):
315 return refCat
316 # Create a new reference catalog, and populate it with records which fall inside the bbox
317 filteredRefCat = type(refCat)(refCat.table)
318 centroidKey = afwTable.Point2DKey(refCat.schema['centroid'])
319 for record in refCat:
320 pixCoords = record[centroidKey]
321 if bbox.contains(geom.Point2I(pixCoords)):
322 filteredRefCat.append(record)
323 return filteredRefCat
324 return self.loadRegion(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.
335 Parameters
336 ----------
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.
340 filtFunc : callable
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.
346 filterName : `str`
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.
352 Returns
353 -------
354 referenceCatalog : `lsst.afw.table.SourceCatalog`
355 Catalog containing reference objects which intersect the input region,
356 filtered by the specified filter function
358 Raises
359 ------
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
366 """
367 regionBounding = region.getBoundingBox()
368 self.log.info("Loading reference objects from region bounded by {}, {} lat lon".format(
369 regionBounding.getLat(), regionBounding.getLon()))
370 if filtFunc is None:
371 filtFunc = _FilterCatalog(region)
372 # filter out all the regions supplied by the constructor that do not overlap
373 overlapList = []
374 for dataId, refCat in zip(self.dataIds, self.refCats):
375 # SphGeom supports some objects intersecting others, but is not symmetric,
376 # try the intersect operation in both directions
377 try:
378 intersects = dataId.region.intersects(region)
379 except TypeError:
380 intersects = region.intersects(dataId.region)
382 if intersects:
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)
392 # Load in the remaining catalogs
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.log.debug(f"Trimmed {trimmedAmount} out of region objects, leaving {len(refCat)}")
404 self.log.info(f"Loaded {len(refCat)} reference objects")
406 # Ensure that the loaded reference catalog is continuous in memory
407 if not refCat.isContiguous():
408 refCat = refCat.copy(deep=True)
410 if epoch is not None and "pm_ra" in refCat.schema:
411 # check for a catalog in a non-standard format
412 if isinstance(refCat.schema["pm_ra"].asKey(), lsst.afw.table.KeyAngle):
413 applyProperMotionsImpl(self.log, refCat, epoch)
414 else:
415 self.log.warn("Catalog pm_ra field is not an Angle; not applying proper motion")
417 # Verify the schema is in the correct units and has the correct version; automatically convert
418 # it with a warning if this is not the case.
419 if not hasNanojanskyFluxUnits(refCat.schema) or not getFormatVersionFromRefCat(refCat) >= 1:
420 self.log.warn("Found version 0 reference catalog with old style units in schema.")
421 self.log.warn("run `meas_algorithms/bin/convert_refcat_to_nJy.py` to convert fluxes to nJy.")
422 self.log.warn("See RFC-575 for more details.")
423 refCat = convertToNanojansky(refCat, self.log)
425 expandedCat = self.remapReferenceCatalogSchema(refCat, position=True)
427 # Add flux aliases
428 expandedCat = self.addFluxAliases(expandedCat, self.config.defaultFilter, self.config.filterMap)
430 # Ensure that the returned reference catalog is continuous in memory
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)
437 def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None):
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
443 the defined circle.
445 Parameters
446 ----------
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
451 filterName : `str`
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.
457 Returns
458 -------
459 referenceCatalog : `lsst.afw.table.SourceCatalog`
460 Catalog containing reference objects inside the specified bounding box
462 Raises
463 ------
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
470 """
471 centerVector = ctrCoord.getVector()
472 sphRadius = sphgeom.Angle(radius.asRadians())
473 circularRegion = sphgeom.Circle(centerVector, sphRadius)
474 return self.loadRegion(circularRegion, filterName=filterName, epoch=None)
476 def joinMatchListWithCatalog(self, matchCat, sourceCat):
477 """Relink an unpersisted match list to sources and reference
478 objects.
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.
486 Parameters
487 ----------
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
494 by ID.
496 Returns
497 -------
498 matchList : `lsst.afw.table.ReferenceMatchVector`
499 Match list.
500 """
501 return joinMatchListWithCatalogImpl(self, matchCat, sourceCat)
503 @classmethod
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.)
510 Parameters
511 ----------
512 bbox : `lsst.geom.Box2I`
513 Bounding bos for the pixels
514 wcs : `lsst.afw.geom.SkyWcs
515 WCS object
516 filterName : `str` or None
517 filterName of the camera filter, or None or blank for the default filter
518 photoCalib : None
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.
523 bboxPadding : `int`
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.
532 Returns
533 -------
534 md : `lsst.daf.base.PropertyList`
535 """
536 _, _, innerCorners, outerCorners = cls._makeBoxRegion(bbox, wcs, bboxPadding)
537 md = PropertyList()
538 for box, corners in zip(("INNER", "OUTER"), (innerCorners, outerCorners)):
539 for (name, corner) in zip(("UPPER_LEFT", "UPPER_RIGHT", "LOWER_LEFT", "LOWER_RIGHT"),
540 corners):
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 # Calling str on the epoch is a workaround for code that never worked anyway and was not used
547 # see DM-17438
548 md.add('EPOCH', "NONE" if epoch is None else str(epoch), 'Epoch (TAI MJD) for catalog')
549 return md
551 @staticmethod
552 def getMetadataCircle(coord, radius, filterName, photoCalib=None, epoch=None):
553 """Return metadata about the load
555 This metadata is used for reloading the catalog (e.g. for reconstituting
556 a normalized match list.)
558 Parameters
559 ----------
560 coord : `lsst.geom.SpherePoint`
561 ICRS center of a circle
562 radius : `lsst.geom.angle`
563 radius of a circle
564 filterName : `str` or None
565 filterName of the camera filter, or None or blank for the default filter
566 photoCalib : None
567 Deprecated, only included for api compatibility
568 epoch : `astropy.time.Time` (optional)
569 Epoch to which to correct proper motion and parallax,
570 or None to not apply such corrections.
572 Returns
573 -------
574 md : `lsst.daf.base.PropertyList`
575 """
576 md = PropertyList()
577 md.add('RA', coord.getRa().asDegrees(), 'field center in degrees')
578 md.add('DEC', coord.getDec().asDegrees(), 'field center in degrees')
579 md.add('RADIUS', radius.asDegrees(), 'field radius in degrees, minimum')
580 md.add('SMATCHV', 1, 'SourceMatchVector version number')
581 filterName = "UNKNOWN" if filterName is None else str(filterName)
582 md.add('FILTER', filterName, 'filter name for photometric data')
583 md.add('EPOCH', "NONE" if epoch is None else epoch, 'Epoch (TAI MJD) for catalog')
584 return md
586 @staticmethod
587 def addFluxAliases(refCat, defaultFilter, filterReferenceMap):
588 """This function creates a new catalog containing the information of the input refCat
589 as well as added flux columns and aliases between camera and reference flux.
591 Parameters
592 ----------
593 refCat : `lsst.afw.table.SimpleCatalog`
594 Catalog of reference objects
595 defaultFilter : `str`
596 Name of the default reference filter
597 filterReferenceMap : `dict` of `str`
598 Dictionary with keys corresponding to a filter name, and values which
599 correspond to the name of the reference filter.
601 Returns
602 -------
603 refCat : `lsst.afw.table.SimpleCatalog`
604 Reference catalog with columns added to track reference filters
606 Raises
607 ------
608 `RuntimeError`
609 If specified reference filter name is not a filter specifed as a key in the
610 reference filter map.
611 """
612 refCat = ReferenceObjectLoader.remapReferenceCatalogSchema(refCat,
613 filterNameList=filterReferenceMap.keys())
614 aliasMap = refCat.schema.getAliasMap()
615 if filterReferenceMap is None:
616 filterReferenceMap = {}
617 for filterName, refFilterName in itertools.chain([(None, defaultFilter)],
618 filterReferenceMap.items()):
619 if refFilterName:
620 camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux"
621 refFluxName = refFilterName + "_flux"
622 if refFluxName not in refCat.schema:
623 raise RuntimeError("Unknown reference filter %s" % (refFluxName,))
624 aliasMap.set(camFluxName, refFluxName)
626 refFluxErrName = refFluxName + "Err"
627 camFluxErrName = camFluxName + "Err"
628 aliasMap.set(camFluxErrName, refFluxErrName)
630 return refCat
632 @staticmethod
633 def remapReferenceCatalogSchema(refCat, *, filterNameList=None, position=False, photometric=False):
634 """This function takes in a reference catalog and creates a new catalog with additional
635 columns defined the remaining function arguments.
637 Parameters
638 ----------
639 refCat : `lsst.afw.table.SimpleCatalog`
640 Reference catalog to map to new catalog
642 Returns
643 -------
644 expandedCat : `lsst.afw.table.SimpleCatalog`
645 Deep copy of input reference catalog with additional columns added
646 """
647 mapper = afwTable.SchemaMapper(refCat.schema, True)
648 mapper.addMinimalSchema(refCat.schema, True)
649 mapper.editOutputSchema().disconnectAliases()
650 if filterNameList:
651 for filterName in filterNameList:
652 mapper.editOutputSchema().addField(f"{filterName}_flux",
653 type=numpy.float64,
654 doc=f"flux in filter {filterName}",
655 units="Jy"
656 )
657 mapper.editOutputSchema().addField(f"{filterName}_fluxErr",
658 type=numpy.float64,
659 doc=f"flux uncertanty in filter {filterName}",
660 units="Jy"
661 )
663 if position:
664 mapper.editOutputSchema().addField("centroid_x", type=float, doReplace=True)
665 mapper.editOutputSchema().addField("centroid_y", type=float, doReplace=True)
666 mapper.editOutputSchema().addField("hasCentroid", type="Flag", doReplace=True)
667 mapper.editOutputSchema().getAliasMap().set("slot_Centroid", "centroid")
669 if photometric:
670 mapper.editOutputSchema().addField("photometric",
671 type="Flag",
672 doc="set if the object can be used for photometric"
673 "calibration",
674 )
675 mapper.editOutputSchema().addField("resolved",
676 type="Flag",
677 doc="set if the object is spatially resolved"
678 )
679 mapper.editOutputSchema().addField("variable",
680 type="Flag",
681 doc="set if the object has variable brightness"
682 )
684 expandedCat = afwTable.SimpleCatalog(mapper.getOutputSchema())
685 expandedCat.setMetadata(refCat.getMetadata())
686 expandedCat.extend(refCat, mapper=mapper)
688 return expandedCat
691def getRefFluxField(schema, filterName=None):
692 """Get the name of a flux field from a schema.
694 return the alias of "anyFilterMapsToThis", if present
695 else if filterName is specified:
696 return "*filterName*_camFlux" if present
697 else return "*filterName*_flux" if present (camera filter name
698 matches reference filter name)
699 else throw RuntimeError
700 else:
701 return "camFlux", if present,
702 else throw RuntimeError
704 Parameters
705 ----------
706 schema : `lsst.afw.table.Schema`
707 Reference catalog schema.
708 filterName : `str`, optional
709 Name of camera filter. If not specified, ``defaultFilter`` needs to be
710 set in the refcat loader config.
712 Returns
713 -------
714 fluxFieldName : `str`
715 Name of flux field.
717 Raises
718 ------
719 RuntimeError
720 If an appropriate field is not found.
721 """
722 if not isinstance(schema, afwTable.Schema): 722 ↛ 723line 722 didn't jump to line 723, because the condition on line 722 was never true
723 raise RuntimeError("schema=%s is not a schema" % (schema,))
724 try:
725 return schema.getAliasMap().get("anyFilterMapsToThis")
726 except LookupError:
727 pass # try the filterMap next
729 if filterName:
730 fluxFieldList = [filterName + "_camFlux", filterName + "_flux"]
731 else:
732 fluxFieldList = ["camFlux"]
733 for fluxField in fluxFieldList:
734 if fluxField in schema:
735 return fluxField
737 raise RuntimeError("Could not find flux field(s) %s" % (", ".join(fluxFieldList)))
740def getRefFluxKeys(schema, filterName=None):
741 """Return keys for flux and flux error.
743 Parameters
744 ----------
745 schema : `lsst.afw.table.Schema`
746 Reference catalog schema.
747 filterName : `str`
748 Name of camera filter.
750 Returns
751 -------
752 keys : `tuple` of (`lsst.afw.table.Key`, `lsst.afw.table.Key`)
753 Two keys:
755 - flux key
756 - flux error key, if present, else None
758 Raises
759 ------
760 RuntimeError
761 If flux field not found.
762 """
763 fluxField = getRefFluxField(schema, filterName)
764 fluxErrField = fluxField + "Err"
765 fluxKey = schema[fluxField].asKey()
766 try:
767 fluxErrKey = schema[fluxErrField].asKey()
768 except Exception:
769 fluxErrKey = None
770 return (fluxKey, fluxErrKey)
773class LoadReferenceObjectsConfig(pexConfig.Config):
774 pixelMargin = pexConfig.RangeField(
775 doc="Padding to add to 4 all edges of the bounding box (pixels)",
776 dtype=int,
777 default=300,
778 min=0,
779 )
780 defaultFilter = pexConfig.Field(
781 doc=("Default reference catalog filter to use if filter not specified in exposure;"
782 " if blank then filter must be specified in exposure."),
783 dtype=str,
784 default="",
785 )
786 anyFilterMapsToThis = pexConfig.Field(
787 doc=("Always use this reference catalog filter, no matter whether or what filter name is "
788 "supplied to the loader. Effectively a trivial filterMap: map all filter names to this filter."
789 " This can be set for purely-astrometric catalogs (e.g. Gaia DR2) where there is only one "
790 "reasonable choice for every camera filter->refcat mapping, but not for refcats used for "
791 "photometry, which need a filterMap and/or colorterms/transmission corrections."),
792 dtype=str,
793 default=None,
794 optional=True
795 )
796 filterMap = pexConfig.DictField(
797 doc=("Mapping of camera filter name: reference catalog filter name; "
798 "each reference filter must exist in the refcat."
799 " Note that this does not perform any bandpass corrections: it is just a lookup."),
800 keytype=str,
801 itemtype=str,
802 default={},
803 )
804 requireProperMotion = pexConfig.Field(
805 doc="Require that the fields needed to correct proper motion "
806 "(epoch, pm_ra and pm_dec) are present?",
807 dtype=bool,
808 default=False,
809 )
811 def validate(self):
812 super().validate()
813 if self.filterMap != {} and self.anyFilterMapsToThis is not None:
814 msg = "`filterMap` and `anyFilterMapsToThis` are mutually exclusive"
815 raise pexConfig.FieldValidationError(LoadReferenceObjectsConfig.anyFilterMapsToThis,
816 self, msg)
819# The following comment block adds a link to this task from the Task Documentation page.
820## @addtogroup LSST_task_documentation
821## @{
822## @page LoadReferenceObjectsTask
823## @ref LoadReferenceObjectsTask_ "LoadReferenceObjectsTask"
824## @copybrief LoadReferenceObjectsTask
825## @}
828class LoadReferenceObjectsTask(pipeBase.Task, metaclass=abc.ABCMeta):
829 r"""!Abstract base class to load objects from reference catalogs
831 @anchor LoadReferenceObjectsTask_
833 @section meas_algorithms_loadReferenceObjects_Contents Contents
835 - @ref meas_algorithms_loadReferenceObjects_Purpose
836 - @ref meas_algorithms_loadReferenceObjects_Initialize
837 - @ref meas_algorithms_loadReferenceObjects_IO
838 - @ref meas_algorithms_loadReferenceObjects_Schema
839 - @ref meas_algorithms_loadReferenceObjects_Config
841 @section meas_algorithms_loadReferenceObjects_Purpose Description
843 Abstract base class for tasks that load objects from a reference catalog
844 in a particular region of the sky.
846 Implementations must subclass this class, override the loadSkyCircle method,
847 and will typically override the value of ConfigClass with a task-specific config class.
849 @section meas_algorithms_loadReferenceObjects_Initialize Task initialisation
851 @copydoc \_\_init\_\_
853 @section meas_algorithms_loadReferenceObjects_IO Invoking the Task
855 @copydoc loadPixelBox
857 @section meas_algorithms_loadReferenceObjects_Schema Schema of the reference object catalog
859 Reference object catalogs are instances of lsst.afw.table.SimpleCatalog with the following schema
860 (other fields may also be present).
861 The units use astropy quantity conventions, so a 2 suffix means squared.
862 See also makeMinimalSchema.
863 - coord: ICRS position of star on sky (an lsst.geom.SpherePoint)
864 - centroid: position of star on an exposure, if relevant (an lsst.afw.Point2D)
865 - hasCentroid: is centroid usable? (a Flag)
866 - *referenceFilterName*_flux: brightness in the specified reference catalog filter (nJy)
867 Note: you can use astropy.units to convert from AB Magnitude to nJy:
868 `u.Magnitude(value, u.ABmag).to_value(u.nJy)`
869 - *referenceFilterName*_fluxErr (optional): brightness standard deviation (nJy);
870 omitted if no data is available; possibly nan if data is available for some objects but not others
871 - camFlux: brightness in default camera filter (nJy); omitted if defaultFilter not specified
872 - camFluxErr: brightness standard deviation for default camera filter;
873 omitted if defaultFilter not specified or standard deviation not available that filter
874 - *cameraFilterName*_camFlux: brightness in specified camera filter (nJy)
875 - *cameraFilterName*_camFluxErr (optional): brightness standard deviation
876 in specified camera filter (nJy); omitted if no data is available;
877 possibly nan if data is available for some objects but not others
878 - photometric (optional): is the object usable for photometric calibration? (a Flag)
879 - resolved (optional): is the object spatially resolved? (a Flag)
880 - variable (optional): does the object have variable brightness? (a Flag)
881 - coord_raErr: uncertainty in `coord` along the direction of right ascension (radian, an Angle)
882 = uncertainty in ra * cos(dec); nan if unknown
883 - coord_decErr: uncertainty in `coord` along the direction of declination (radian, an Angle);
884 nan if unknown
886 The following are optional; fields should only be present if the
887 information is available for at least some objects.
888 Numeric values are `nan` if unknown:
889 - epoch: date of observation as TAI MJD (day)
891 - pm_ra: proper motion along the direction of right ascension (rad/year, an Angle) = dra/dt * cos(dec)
892 - pm_dec: proper motion along the direction of declination (rad/year, and Angle)
893 - pm_raErr: uncertainty in `pm_ra` (rad/year)
894 - pm_decErr: uncertainty in `pm_dec` (rad/year)
895 - pm_ra_dec_Cov: covariance between pm_ra and pm_dec (rad2/year2)
896 - pm_flag: set if proper motion, error or covariance is bad
898 - parallax: parallax (rad, an Angle)
899 - parallaxErr: uncertainty in `parallax` (rad)
900 - parallax_flag: set if parallax value or parallaxErr is bad
902 - coord_ra_pm_ra_Cov: covariance between coord_ra and pm_ra (rad2/year)
903 - coord_ra_pm_dec_Cov: covariance between coord_ra and pm_dec (rad2/year)
904 - coord_ra_parallax_Cov: covariance between coord_ra and parallax (rad2/year)
905 - coord_dec_pm_ra_Cov: covariance between coord_dec and pm_ra (rad2/year)
906 - coord_dec_pm_dec_Cov: covariance between coord_dec and pm_dec (rad2/year)
907 - coord_dec_parallax_Cov: covariance between coord_dec and parallax (rad2/year)
908 - pm_ra_parallax_Cov: covariance between pm_ra and parallax (rad2/year)
909 - pm_dec_parallax_Cov: covariance between pm_dec and parallax (rad2/year)
911 @section meas_algorithms_loadReferenceObjects_Config Configuration parameters
913 See @ref LoadReferenceObjectsConfig for a base set of configuration parameters.
914 Most subclasses will add configuration variables.
915 """
916 ConfigClass = LoadReferenceObjectsConfig
917 _DefaultName = "LoadReferenceObjects"
919 def __init__(self, butler=None, *args, **kwargs):
920 """Construct a LoadReferenceObjectsTask
922 Parameters
923 ----------
924 butler : `lsst.daf.persistence.Butler`
925 Data butler, for access reference catalogs.
926 """
927 pipeBase.Task.__init__(self, *args, **kwargs)
928 self.butler = butler
930 @pipeBase.timeMethod
931 def loadPixelBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
932 """Load reference objects that overlap a rectangular pixel region.
934 Parameters
935 ----------
936 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
937 Bounding box for pixels.
938 wcs : `lsst.afw.geom.SkyWcs`
939 WCS; used to convert pixel positions to sky coordinates
940 and vice-versa.
941 filterName : `str`
942 Name of filter, or `None` or `""` for the default filter.
943 This is used for flux values in case we have flux limits
944 (which are not yet implemented).
945 photoCalib : `lsst.afw.image.PhotoCalib` (optional)
946 Calibration, or `None` if unknown.
947 epoch : `astropy.time.Time` (optional)
948 Epoch to which to correct proper motion and parallax,
949 or None to not apply such corrections.
951 Returns
952 -------
953 results : `lsst.pipe.base.Struct`
954 A Struct containing the following fields:
955 refCat : `lsst.afw.catalog.SimpleCatalog`
956 A catalog of reference objects with the standard
957 schema, as documented in the main doc string for
958 `LoadReferenceObjects`.
959 The catalog is guaranteed to be contiguous.
960 fluxField : `str`
961 Name of flux field for specified `filterName`.
963 Notes
964 -----
965 The search algorithm works by searching in a region in sky
966 coordinates whose center is the center of the bbox and radius
967 is large enough to just include all 4 corners of the bbox.
968 Stars that lie outside the bbox are then trimmed from the list.
969 """
970 circle = self._calculateCircle(bbox, wcs)
972 # find objects in circle
973 self.log.info("Loading reference objects using center %s and radius %s deg" %
974 (circle.coord, circle.radius.asDegrees()))
975 loadRes = self.loadSkyCircle(circle.coord, circle.radius, filterName, centroids=True)
976 refCat = loadRes.refCat
977 numFound = len(refCat)
979 # trim objects outside bbox
980 refCat = self._trimToBBox(refCat=refCat, bbox=circle.bbox, wcs=wcs)
981 numTrimmed = numFound - len(refCat)
982 self.log.debug("trimmed %d out-of-bbox objects, leaving %d", numTrimmed, len(refCat))
983 self.log.info("Loaded %d reference objects", len(refCat))
985 # make sure catalog is contiguous
986 if not refCat.isContiguous():
987 loadRes.refCat = refCat.copy(deep=True)
989 return loadRes
991 @abc.abstractmethod
992 def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None, centroids=False):
993 """Load reference objects that overlap a circular sky region.
995 Parameters
996 ----------
997 ctrCoord : `lsst.geom.SpherePoint`
998 ICRS center of search region.
999 radius : `lsst.geom.Angle`
1000 Radius of search region.
1001 filterName : `str` (optional)
1002 Name of filter, or `None` or `""` for the default filter.
1003 This is used for flux values in case we have flux limits
1004 (which are not yet implemented).
1005 epoch : `astropy.time.Time` (optional)
1006 Epoch to which to correct proper motion and parallax,
1007 or None to not apply such corrections.
1008 centroids : `bool` (optional)
1009 Add centroid fields to the loaded Schema. ``loadPixelBox`` expects
1010 these fields to exist.
1012 Returns
1013 -------
1014 results : `lsst.pipe.base.Struct`
1015 A Struct containing the following fields:
1016 refCat : `lsst.afw.catalog.SimpleCatalog`
1017 A catalog of reference objects with the standard
1018 schema, as documented in the main doc string for
1019 `LoadReferenceObjects`.
1020 The catalog is guaranteed to be contiguous.
1021 fluxField : `str`
1022 Name of flux field for specified `filterName`.
1024 Notes
1025 -----
1026 Note that subclasses are responsible for performing the proper motion
1027 correction, since this is the lowest-level interface for retrieving
1028 the catalog.
1029 """
1030 return
1032 @staticmethod
1033 def _trimToBBox(refCat, bbox, wcs):
1034 """Remove objects outside a given pixel bounding box and set
1035 centroid and hasCentroid fields.
1037 Parameters
1038 ----------
1039 refCat : `lsst.afw.table.SimpleCatalog`
1040 A catalog of objects. The schema must include fields
1041 "coord", "centroid" and "hasCentroid".
1042 The "coord" field is read.
1043 The "centroid" and "hasCentroid" fields are set.
1044 bbox : `lsst.geom.Box2D`
1045 Pixel region
1046 wcs : `lsst.afw.geom.SkyWcs`
1047 WCS; used to convert sky coordinates to pixel positions.
1049 @return a catalog of reference objects in bbox, with centroid and hasCentroid fields set
1050 """
1051 afwTable.updateRefCentroids(wcs, refCat)
1052 centroidKey = afwTable.Point2DKey(refCat.schema["centroid"])
1053 retStarCat = type(refCat)(refCat.table)
1054 for star in refCat:
1055 point = star.get(centroidKey)
1056 if bbox.contains(point):
1057 retStarCat.append(star)
1058 return retStarCat
1060 def _addFluxAliases(self, schema):
1061 """Add aliases for camera filter fluxes to the schema.
1063 If self.config.defaultFilter then adds these aliases:
1064 camFlux: <defaultFilter>_flux
1065 camFluxErr: <defaultFilter>_fluxErr, if the latter exists
1067 For each camFilter: refFilter in self.config.filterMap adds these aliases:
1068 <camFilter>_camFlux: <refFilter>_flux
1069 <camFilter>_camFluxErr: <refFilter>_fluxErr, if the latter exists
1071 Parameters
1072 ----------
1073 schema : `lsst.afw.table.Schema`
1074 Schema for reference catalog.
1076 Raises
1077 ------
1078 RuntimeError
1079 If any reference flux field is missing from the schema.
1080 """
1081 aliasMap = schema.getAliasMap()
1083 if self.config.anyFilterMapsToThis is not None:
1084 refFluxName = self.config.anyFilterMapsToThis + "_flux"
1085 if refFluxName not in schema:
1086 msg = f"Unknown reference filter for anyFilterMapsToThis='{refFluxName}'"
1087 raise RuntimeError(msg)
1088 aliasMap.set("anyFilterMapsToThis", refFluxName)
1089 return # this is mutually exclusive with filterMap
1091 def addAliasesForOneFilter(filterName, refFilterName):
1092 """Add aliases for a single filter
1094 Parameters
1095 ----------
1096 filterName : `str` (optional)
1097 Camera filter name. The resulting alias name is
1098 <filterName>_camFlux, or simply "camFlux" if `filterName`
1099 is `None` or `""`.
1100 refFilterName : `str`
1101 Reference catalog filter name; the field
1102 <refFilterName>_flux must exist.
1103 """
1104 camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux"
1105 refFluxName = refFilterName + "_flux"
1106 if refFluxName not in schema:
1107 raise RuntimeError("Unknown reference filter %s" % (refFluxName,))
1108 aliasMap.set(camFluxName, refFluxName)
1109 refFluxErrName = refFluxName + "Err"
1110 if refFluxErrName in schema: 1110 ↛ exitline 1110 didn't return from function 'addAliasesForOneFilter', because the condition on line 1110 was never false
1111 camFluxErrName = camFluxName + "Err"
1112 aliasMap.set(camFluxErrName, refFluxErrName)
1114 if self.config.defaultFilter:
1115 addAliasesForOneFilter(None, self.config.defaultFilter)
1117 for filterName, refFilterName in self.config.filterMap.items():
1118 addAliasesForOneFilter(filterName, refFilterName)
1120 @staticmethod
1121 def makeMinimalSchema(filterNameList, *, addCentroid=False,
1122 addIsPhotometric=False, addIsResolved=False,
1123 addIsVariable=False, coordErrDim=2,
1124 addProperMotion=False, properMotionErrDim=2,
1125 addParallax=False):
1126 """Make a standard schema for reference object catalogs.
1128 Parameters
1129 ----------
1130 filterNameList : `list` of `str`
1131 List of filter names. Used to create <filterName>_flux fields.
1132 addIsPhotometric : `bool`
1133 If True then add field "photometric".
1134 addIsResolved : `bool`
1135 If True then add field "resolved".
1136 addIsVariable : `bool`
1137 If True then add field "variable".
1138 coordErrDim : `int`
1139 Number of coord error fields; must be one of 0, 2, 3:
1141 - If 2 or 3: add fields "coord_raErr" and "coord_decErr".
1142 - If 3: also add field "coord_radecErr".
1143 addProperMotion : `bool`
1144 If True add fields "epoch", "pm_ra", "pm_dec" and "pm_flag".
1145 properMotionErrDim : `int`
1146 Number of proper motion error fields; must be one of 0, 2, 3;
1147 ignored if addProperMotion false:
1148 - If 2 or 3: add fields "pm_raErr" and "pm_decErr".
1149 - If 3: also add field "pm_radecErr".
1150 addParallax : `bool`
1151 If True add fields "epoch", "parallax", "parallaxErr"
1152 and "parallax_flag".
1154 Returns
1155 -------
1156 schema : `lsst.afw.table.Schema`
1157 Schema for reference catalog, an
1158 `lsst.afw.table.SimpleCatalog`.
1160 Notes
1161 -----
1162 Reference catalogs support additional covariances, such as
1163 covariance between RA and proper motion in declination,
1164 that are not supported by this method, but can be added after
1165 calling this method.
1166 """
1167 schema = afwTable.SimpleTable.makeMinimalSchema()
1168 if addCentroid: 1168 ↛ 1169line 1168 didn't jump to line 1169, because the condition on line 1168 was never true
1169 afwTable.Point2DKey.addFields(
1170 schema,
1171 "centroid",
1172 "centroid on an exposure, if relevant",
1173 "pixel",
1174 )
1175 schema.addField(
1176 field="hasCentroid",
1177 type="Flag",
1178 doc="is position known?",
1179 )
1180 for filterName in filterNameList:
1181 schema.addField(
1182 field="%s_flux" % (filterName,),
1183 type=numpy.float64,
1184 doc="flux in filter %s" % (filterName,),
1185 units="nJy",
1186 )
1187 for filterName in filterNameList:
1188 schema.addField(
1189 field="%s_fluxErr" % (filterName,),
1190 type=numpy.float64,
1191 doc="flux uncertainty in filter %s" % (filterName,),
1192 units="nJy",
1193 )
1194 if addIsPhotometric:
1195 schema.addField(
1196 field="photometric",
1197 type="Flag",
1198 doc="set if the object can be used for photometric calibration",
1199 )
1200 if addIsResolved:
1201 schema.addField(
1202 field="resolved",
1203 type="Flag",
1204 doc="set if the object is spatially resolved",
1205 )
1206 if addIsVariable:
1207 schema.addField(
1208 field="variable",
1209 type="Flag",
1210 doc="set if the object has variable brightness",
1211 )
1212 if coordErrDim not in (0, 2, 3):
1213 raise ValueError("coordErrDim={}; must be (0, 2, 3)".format(coordErrDim))
1214 if coordErrDim > 0:
1215 afwTable.CovarianceMatrix2fKey.addFields(
1216 schema=schema,
1217 prefix="coord",
1218 names=["ra", "dec"],
1219 units=["rad", "rad"],
1220 diagonalOnly=(coordErrDim == 2),
1221 )
1223 if addProperMotion or addParallax:
1224 schema.addField(
1225 field="epoch",
1226 type=numpy.float64,
1227 doc="date of observation (TAI, MJD)",
1228 units="day",
1229 )
1231 if addProperMotion:
1232 schema.addField(
1233 field="pm_ra",
1234 type="Angle",
1235 doc="proper motion in the right ascension direction = dra/dt * cos(dec)",
1236 units="rad/year",
1237 )
1238 schema.addField(
1239 field="pm_dec",
1240 type="Angle",
1241 doc="proper motion in the declination direction",
1242 units="rad/year",
1243 )
1244 if properMotionErrDim not in (0, 2, 3):
1245 raise ValueError("properMotionErrDim={}; must be (0, 2, 3)".format(properMotionErrDim))
1246 if properMotionErrDim > 0:
1247 afwTable.CovarianceMatrix2fKey.addFields(
1248 schema=schema,
1249 prefix="pm",
1250 names=["ra", "dec"],
1251 units=["rad/year", "rad/year"],
1252 diagonalOnly=(properMotionErrDim == 2),
1253 )
1254 schema.addField(
1255 field="pm_flag",
1256 type="Flag",
1257 doc="Set if proper motion or proper motion error is bad",
1258 )
1260 if addParallax:
1261 schema.addField(
1262 field="parallax",
1263 type="Angle",
1264 doc="parallax",
1265 units="rad",
1266 )
1267 schema.addField(
1268 field="parallaxErr",
1269 type="Angle",
1270 doc="uncertainty in parallax",
1271 units="rad",
1272 )
1273 schema.addField(
1274 field="parallax_flag",
1275 type="Flag",
1276 doc="Set if parallax or parallax error is bad",
1277 )
1278 return schema
1280 def _calculateCircle(self, bbox, wcs):
1281 """Compute on-sky center and radius of search region.
1283 Parameters
1284 ----------
1285 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1286 Pixel bounding box.
1287 wcs : `lsst.afw.geom.SkyWcs`
1288 WCS; used to convert pixel positions to sky coordinates.
1290 Returns
1291 -------
1292 results : `lsst.pipe.base.Struct`
1293 A Struct containing:
1295 - coord : `lsst.geom.SpherePoint`
1296 ICRS center of the search region.
1297 - radius : `lsst.geom.Angle`
1298 Radius of the search region.
1299 - bbox : `lsst.geom.Box2D`
1300 Bounding box used to compute the circle.
1301 """
1302 bbox = lsst.geom.Box2D(bbox) # make sure bbox is double and that we have a copy
1303 bbox.grow(self.config.pixelMargin)
1304 coord = wcs.pixelToSky(bbox.getCenter())
1305 radius = max(coord.separation(wcs.pixelToSky(pp)) for pp in bbox.getCorners())
1306 return pipeBase.Struct(coord=coord, radius=radius, bbox=bbox)
1308 def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
1309 """Return metadata about the load.
1311 This metadata is used for reloading the catalog (e.g., for
1312 reconstituting a normalised match list.
1314 Parameters
1315 ----------
1316 bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1317 Pixel bounding box.
1318 wcs : `lsst.afw.geom.SkyWcs`
1319 WCS; used to convert pixel positions to sky coordinates.
1320 filterName : `str`
1321 Name of camera filter, or `None` or `""` for the default
1322 filter.
1323 photoCalib : `lsst.afw.image.PhotoCalib` (optional)
1324 Calibration, or `None` if unknown.
1325 epoch : `astropy.time.Time` (optional)
1326 Epoch to which to correct proper motion and parallax,
1327 or None to not apply such corrections.
1329 Returns
1330 -------
1331 metadata : lsst.daf.base.PropertyList
1332 Metadata about the load.
1333 """
1334 circle = self._calculateCircle(bbox, wcs)
1335 return self.getMetadataCircle(circle.coord, circle.radius, filterName, photoCalib)
1337 def getMetadataCircle(self, coord, radius, filterName, photoCalib=None, epoch=None):
1338 """Return metadata about the load.
1340 This metadata is used for reloading the catalog (e.g., for
1341 reconstituting a normalised match list.
1343 Parameters
1344 ----------
1345 coord : `lsst.geom.SpherePoint`
1346 ICRS center of the search region.
1347 radius : `lsst.geom.Angle`
1348 Radius of the search region.
1349 filterName : `str`
1350 Name of camera filter, or `None` or `""` for the default
1351 filter.
1352 photoCalib : `lsst.afw.image.PhotoCalib` (optional)
1353 Calibration, or `None` if unknown.
1354 epoch : `astropy.time.Time` (optional)
1355 Epoch to which to correct proper motion and parallax,
1356 or None to not apply such corrections.
1358 Returns
1359 -------
1360 metadata : lsst.daf.base.PropertyList
1361 Metadata about the load
1362 """
1363 md = PropertyList()
1364 md.add('RA', coord.getRa().asDegrees(), 'field center in degrees')
1365 md.add('DEC', coord.getDec().asDegrees(), 'field center in degrees')
1366 md.add('RADIUS', radius.asDegrees(), 'field radius in degrees, minimum')
1367 md.add('SMATCHV', 1, 'SourceMatchVector version number')
1368 filterName = "UNKNOWN" if filterName is None else str(filterName)
1369 md.add('FILTER', filterName, 'filter name for photometric data')
1370 md.add('EPOCH', "NONE" if epoch is None else epoch, 'Epoch (TAI MJD) for catalog')
1371 return md
1373 def joinMatchListWithCatalog(self, matchCat, sourceCat):
1374 """Relink an unpersisted match list to sources and reference
1375 objects.
1377 A match list is persisted and unpersisted as a catalog of IDs
1378 produced by afw.table.packMatches(), with match metadata
1379 (as returned by the astrometry tasks) in the catalog's metadata
1380 attribute. This method converts such a match catalog into a match
1381 list, with links to source records and reference object records.
1383 Parameters
1384 ----------
1385 matchCat : `lsst.afw.table.BaseCatalog`
1386 Unperisted packed match list.
1387 ``matchCat.table.getMetadata()`` must contain match metadata,
1388 as returned by the astrometry tasks.
1389 sourceCat : `lsst.afw.table.SourceCatalog`
1390 Source catalog. As a side effect, the catalog will be sorted
1391 by ID.
1393 Returns
1394 -------
1395 matchList : `lsst.afw.table.ReferenceMatchVector`
1396 Match list.
1397 """
1398 return joinMatchListWithCatalogImpl(self, matchCat, sourceCat)
1400 def applyProperMotions(self, catalog, epoch):
1401 """Apply proper motion correction to a reference catalog.
1403 Adjust position and position error in the ``catalog``
1404 for proper motion to the specified ``epoch``,
1405 modifying the catalog in place.
1407 Parameters
1408 ----------
1409 catalog : `lsst.afw.table.SimpleCatalog`
1410 Catalog of positions, containing:
1412 - Coordinates, retrieved by the table's coordinate key.
1413 - ``coord_raErr`` : Error in Right Ascension (rad).
1414 - ``coord_decErr`` : Error in Declination (rad).
1415 - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
1416 East positive)
1417 - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
1418 - ``pm_dec`` : Proper motion in Declination (rad/yr,
1419 North positive)
1420 - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
1421 - ``epoch`` : Mean epoch of object (an astropy.time.Time)
1422 epoch : `astropy.time.Time`
1423 Epoch to which to correct proper motion,
1424 """
1425 if ("epoch" not in catalog.schema or "pm_ra" not in catalog.schema or "pm_dec" not in catalog.schema): 1425 ↛ 1426line 1425 didn't jump to line 1426, because the condition on line 1425 was never true
1426 if self.config.requireProperMotion:
1427 raise RuntimeError("Proper motion correction required but not available from catalog")
1428 self.log.warn("Proper motion correction not available from catalog")
1429 return
1430 applyProperMotionsImpl(self.log, catalog, epoch)
1433def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat):
1434 """Relink an unpersisted match list to sources and reference
1435 objects.
1437 A match list is persisted and unpersisted as a catalog of IDs
1438 produced by afw.table.packMatches(), with match metadata
1439 (as returned by the astrometry tasks) in the catalog's metadata
1440 attribute. This method converts such a match catalog into a match
1441 list, with links to source records and reference object records.
1443 Parameters
1444 ----------
1445 refObjLoader
1446 Reference object loader to use in getting reference objects
1447 matchCat : `lsst.afw.table.BaseCatalog`
1448 Unperisted packed match list.
1449 ``matchCat.table.getMetadata()`` must contain match metadata,
1450 as returned by the astrometry tasks.
1451 sourceCat : `lsst.afw.table.SourceCatalog`
1452 Source catalog. As a side effect, the catalog will be sorted
1453 by ID.
1455 Returns
1456 -------
1457 matchList : `lsst.afw.table.ReferenceMatchVector`
1458 Match list.
1459 """
1460 matchmeta = matchCat.table.getMetadata()
1461 version = matchmeta.getInt('SMATCHV')
1462 if version != 1:
1463 raise ValueError('SourceMatchVector version number is %i, not 1.' % version)
1464 filterName = matchmeta.getString('FILTER').strip()
1465 try:
1466 epoch = matchmeta.getDouble('EPOCH')
1467 except (pexExcept.NotFoundError, pexExcept.TypeError):
1468 epoch = None # Not present, or not correct type means it's not set
1469 if 'RADIUS' in matchmeta:
1470 # This is a circle style metadata, call loadSkyCircle
1471 ctrCoord = lsst.geom.SpherePoint(matchmeta.getDouble('RA'),
1472 matchmeta.getDouble('DEC'), lsst.geom.degrees)
1473 rad = matchmeta.getDouble('RADIUS') * lsst.geom.degrees
1474 refCat = refObjLoader.loadSkyCircle(ctrCoord, rad, filterName, epoch=epoch).refCat
1475 elif "INNER_UPPER_LEFT_RA" in matchmeta:
1476 # This is the sky box type (only triggers in the LoadReferenceObject class, not task)
1477 # Only the outer box is required to be loaded to get the maximum region, all filtering
1478 # will be done by the unpackMatches function, and no spatial filtering needs to be done
1479 # by the refObjLoader
1480 box = []
1481 for place in ("UPPER_LEFT", "UPPER_RIGHT", "LOWER_LEFT", "LOWER_RIGHT"):
1482 coord = lsst.geom.SpherePoint(matchmeta.getDouble(f"OUTER_{place}_RA"),
1483 matchmeta.getDouble(f"OUTER_{place}_DEC"),
1484 lsst.geom.degrees).getVector()
1485 box.append(coord)
1486 outerBox = sphgeom.ConvexPolygon(box)
1487 refCat = refObjLoader.loadRegion(outerBox, filterName=filterName, epoch=epoch).refCat
1489 refCat.sort()
1490 sourceCat.sort()
1491 return afwTable.unpackMatches(matchCat, refCat, sourceCat)
1494def applyProperMotionsImpl(log, catalog, epoch):
1495 """Apply proper motion correction to a reference catalog.
1497 Adjust position and position error in the ``catalog``
1498 for proper motion to the specified ``epoch``,
1499 modifying the catalog in place.
1501 Parameters
1502 ----------
1503 log : `lsst.log.Log`
1504 Log object to write to.
1505 catalog : `lsst.afw.table.SimpleCatalog`
1506 Catalog of positions, containing:
1508 - Coordinates, retrieved by the table's coordinate key.
1509 - ``coord_raErr`` : Error in Right Ascension (rad).
1510 - ``coord_decErr`` : Error in Declination (rad).
1511 - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
1512 East positive)
1513 - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
1514 - ``pm_dec`` : Proper motion in Declination (rad/yr,
1515 North positive)
1516 - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
1517 - ``epoch`` : Mean epoch of object (an astropy.time.Time)
1518 epoch : `astropy.time.Time`
1519 Epoch to which to correct proper motion.
1520 """
1521 if "epoch" not in catalog.schema or "pm_ra" not in catalog.schema or "pm_dec" not in catalog.schema: 1521 ↛ 1522line 1521 didn't jump to line 1522, because the condition on line 1521 was never true
1522 log.warn("Proper motion correction not available from catalog")
1523 return
1524 if not catalog.isContiguous(): 1524 ↛ 1525line 1524 didn't jump to line 1525, because the condition on line 1524 was never true
1525 raise RuntimeError("Catalog must be contiguous")
1526 catEpoch = astropy.time.Time(catalog["epoch"], scale="tai", format="mjd")
1527 log.info("Correcting reference catalog for proper motion to %r", epoch)
1528 # Use `epoch.tai` to make sure the time difference is in TAI
1529 timeDiffsYears = (epoch.tai - catEpoch).to(astropy.units.yr).value
1530 coordKey = catalog.table.getCoordKey()
1531 # Compute the offset of each object due to proper motion
1532 # as components of the arc of a great circle along RA and Dec
1533 pmRaRad = catalog["pm_ra"]
1534 pmDecRad = catalog["pm_dec"]
1535 offsetsRaRad = pmRaRad*timeDiffsYears
1536 offsetsDecRad = pmDecRad*timeDiffsYears
1537 # Compute the corresponding bearing and arc length of each offset
1538 # due to proper motion, and apply the offset
1539 # The factor of 1e6 for computing bearing is intended as
1540 # a reasonable scale for typical values of proper motion
1541 # in order to avoid large errors for small values of proper motion;
1542 # using the offsets is another option, but it can give
1543 # needlessly large errors for short duration
1544 offsetBearingsRad = numpy.arctan2(pmDecRad*1e6, pmRaRad*1e6)
1545 offsetAmountsRad = numpy.hypot(offsetsRaRad, offsetsDecRad)
1546 for record, bearingRad, amountRad in zip(catalog, offsetBearingsRad, offsetAmountsRad):
1547 record.set(coordKey,
1548 record.get(coordKey).offset(bearing=bearingRad*lsst.geom.radians,
1549 amount=amountRad*lsst.geom.radians))
1550 # Increase error in RA and Dec based on error in proper motion
1551 if "coord_raErr" in catalog.schema: 1551 ↛ 1554line 1551 didn't jump to line 1554, because the condition on line 1551 was never false
1552 catalog["coord_raErr"] = numpy.hypot(catalog["coord_raErr"],
1553 catalog["pm_raErr"]*timeDiffsYears)
1554 if "coord_decErr" in catalog.schema: 1554 ↛ exitline 1554 didn't return from function 'applyProperMotionsImpl', because the condition on line 1554 was never false
1555 catalog["coord_decErr"] = numpy.hypot(catalog["coord_decErr"],
1556 catalog["pm_decErr"]*timeDiffsYears)