lsst.meas.algorithms  21.0.0-10-gbfb87ad6+afd195133e
loadReferenceObjects.py
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23 
24 __all__ = ["getRefFluxField", "getRefFluxKeys", "LoadReferenceObjectsTask", "LoadReferenceObjectsConfig",
25  "ReferenceObjectLoader"]
26 
27 import abc
28 import itertools
29 
30 import astropy.time
31 import astropy.units
32 import numpy
33 
34 import lsst.geom
35 import lsst.afw.table as afwTable
36 import lsst.pex.config as pexConfig
37 import lsst.pex.exceptions as pexExceptions
38 import lsst.pipe.base as pipeBase
39 import lsst.pex.exceptions as pexExcept
40 import lsst.log
41 from lsst import geom
42 from lsst import sphgeom
43 from lsst.daf.base import PropertyList
44 
45 
46 def 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
55 
56 
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
64 
65 
67  """"Return the format version stored in a reference catalog header.
68 
69  Parameters
70  ----------
71  refCat : `lsst.afw.table.SimpleCatalog`
72  Reference catalog to inspect.
73 
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:
82  return None
83  try:
84  return md.getScalar("REFCAT_FORMAT_VERSION")
85  except KeyError:
86  return None
87 
88 
89 def convertToNanojansky(catalog, log, doConvert=True):
90  """Convert fluxes in a catalog from jansky to nanojansky.
91 
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`.
101 
102  Returns
103  -------
104  catalog : `lsst.afw.table.SimpleCatalog` or None
105  The converted catalog, or None if ``doConvert`` is False.
106 
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())
135 
136  fluxFieldsStr = '; '.join("(%s, '%s')" % (field.getName(), field.getUnits()) for field in input_fields)
137 
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
149 
150 
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.
155 
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.regionregion = region
163 
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.
167 
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.
171 
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.
176 
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.regionregion):
185  # no filtering needed, region completely contains refcat
186  return refCat
187 
188  filteredRefCat = type(refCat)(refCat.table)
189  for record in refCat:
190  if self.regionregion.contains(record.getCoord().getVector()):
191  filteredRefCat.append(record)
192  return filteredRefCat
193 
194 
196  """ This class facilitates loading reference catalogs with gen 3 middleware
197 
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
207 
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
218 
219  """
220  self.dataIdsdataIds = dataIds
221  self.refCatsrefCats = refCats
223  self.configconfig = config
224 
225  @staticmethod
226  def _makeBoxRegion(BBox, wcs, BBoxPadding):
227  outerLocalBBox = geom.Box2D(BBox)
228  innerLocalBBox = geom.Box2D(BBox)
229 
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)
235 
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]
244 
245  innerSkyRegion = sphgeom.ConvexPolygon(innerSphCorners)
246 
247  # Convert the corners of the box to sky coordinates
248  outerBoxCorners = outerLocalBBox.getCorners()
249  outerSphCorners = [wcs.pixelToSky(corner).getVector() for corner in outerBoxCorners]
250 
251  outerSkyRegion = sphgeom.ConvexPolygon(outerSphCorners)
252 
253  return innerSkyRegion, outerSkyRegion, innerSphCorners, outerSphCorners
254 
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
257 
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.
263 
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
267 
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.
291 
292  Returns
293  -------
294  referenceCatalog : `lsst.afw.table.SimpleCatalog`
295  Catalog containing reference objects inside the specified bounding box
296 
297  Raises
298  ------
299  `lsst.pex.exception.RuntimeError`
300  Raised if no reference catalogs could be found for the specified region
301 
302  `lsst.pex.exception.TypeError`
303  Raised if the loaded reference catalogs do not have matching schemas
304  """
305  innerSkyRegion, outerSkyRegion, _, _ = self._makeBoxRegion_makeBoxRegion(bbox, wcs, bboxPadding)
306 
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.remapReferenceCatalogSchemaremapReferenceCatalogSchema(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.loadRegionloadRegion(outerSkyRegion, filtFunc=_filterFunction, epoch=epoch, filterName=filterName)
325 
326  def loadRegion(self, region, filtFunc=None, filterName=None, epoch=None):
327  """ Load reference objects within a specified region
328 
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.
334 
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.
351 
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
357 
358  Raises
359  ------
360  `lsst.pex.exception.RuntimeError`
361  Raised if no reference catalogs could be found for the specified region
362 
363  `lsst.pex.exception.TypeError`
364  Raised if the loaded reference catalogs do not have matching schemas
365 
366  """
367  regionBounding = region.getBoundingBox()
368  self.loglog.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.dataIdsdataIds, self.refCatsrefCats):
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)
381 
382  if intersects:
383  overlapList.append((dataId, refCat))
384 
385  if len(overlapList) == 0:
386  raise pexExceptions.RuntimeError("No reference tables could be found for input region")
387 
388  firstCat = overlapList[0][1].get()
389  refCat = filtFunc(firstCat, overlapList[0][0].region)
390  trimmedAmount = len(firstCat) - len(refCat)
391 
392  # Load in the remaining catalogs
393  for dataId, inputRefCat in overlapList[1:]:
394  tmpCat = inputRefCat.get()
395 
396  if tmpCat.schema != firstCat.schema:
397  raise pexExceptions.TypeError("Reference catalogs have mismatching schemas")
398 
399  filteredCat = filtFunc(tmpCat, dataId.region)
400  refCat.extend(filteredCat)
401  trimmedAmount += len(tmpCat) - len(filteredCat)
402 
403  self.loglog.debug(f"Trimmed {trimmedAmount} out of region objects, leaving {len(refCat)}")
404  self.loglog.info(f"Loaded {len(refCat)} reference objects")
405 
406  # Ensure that the loaded reference catalog is continuous in memory
407  if not refCat.isContiguous():
408  refCat = refCat.copy(deep=True)
409 
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.loglog, refCat, epoch)
414  else:
415  self.loglog.warn("Catalog pm_ra field is not an Angle; not applying proper motion")
416 
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.loglog.warn("Found version 0 reference catalog with old style units in schema.")
421  self.loglog.warn("run `meas_algorithms/bin/convert_refcat_to_nJy.py` to convert fluxes to nJy.")
422  self.loglog.warn("See RFC-575 for more details.")
423  refCat = convertToNanojansky(refCat, self.loglog)
424 
425  expandedCat = self.remapReferenceCatalogSchemaremapReferenceCatalogSchema(refCat, position=True)
426 
427  # Add flux aliases
428  expandedCat = self.addFluxAliasesaddFluxAliases(expandedCat, self.configconfig.defaultFilter, self.configconfig.filterMap)
429 
430  # Ensure that the returned reference catalog is continuous in memory
431  if not expandedCat.isContiguous():
432  expandedCat = expandedCat.copy(deep=True)
433 
434  fluxField = getRefFluxField(schema=expandedCat.schema, filterName=filterName)
435  return pipeBase.Struct(refCat=expandedCat, fluxField=fluxField)
436 
437  def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None):
438  """Load reference objects that lie within a circular region on the sky
439 
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.
444 
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.
456 
457  Returns
458  -------
459  referenceCatalog : `lsst.afw.table.SourceCatalog`
460  Catalog containing reference objects inside the specified bounding box
461 
462  Raises
463  ------
464  `lsst.pex.exception.RuntimeError`
465  Raised if no reference catalogs could be found for the specified region
466 
467  `lsst.pex.exception.TypeError`
468  Raised if the loaded reference catalogs do not have matching schemas
469 
470  """
471  centerVector = ctrCoord.getVector()
472  sphRadius = sphgeom.Angle(radius.asRadians())
473  circularRegion = sphgeom.Circle(centerVector, sphRadius)
474  return self.loadRegionloadRegion(circularRegion, filterName=filterName, epoch=epoch)
475 
476  def joinMatchListWithCatalog(self, matchCat, sourceCat):
477  """Relink an unpersisted match list to sources and reference
478  objects.
479 
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.
485 
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.
495 
496  Returns
497  -------
498  matchList : `lsst.afw.table.ReferenceMatchVector`
499  Match list.
500  """
501  return joinMatchListWithCatalogImpl(self, matchCat, sourceCat)
502 
503  @classmethod
504  def getMetadataBox(cls, bbox, wcs, filterName=None, photoCalib=None, epoch=None, bboxPadding=100):
505  """Return metadata about the load
506 
507  This metadata is used for reloading the catalog (e.g., for
508  reconstituting a normalised match list.)
509 
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_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  md.add('EPOCH', "NONE" if epoch is None else epoch.mjd, 'Epoch (TAI MJD) for catalog')
547  return md
548 
549  @staticmethod
550  def getMetadataCircle(coord, radius, filterName, photoCalib=None, epoch=None):
551  """Return metadata about the load
552 
553  This metadata is used for reloading the catalog (e.g. for reconstituting
554  a normalized match list.)
555 
556  Parameters
557  ----------
558  coord : `lsst.geom.SpherePoint`
559  ICRS center of a circle
560  radius : `lsst.geom.angle`
561  radius of a circle
562  filterName : `str` or None
563  filterName of the camera filter, or None or blank for the default filter
564  photoCalib : None
565  Deprecated, only included for api compatibility
566  epoch : `astropy.time.Time` (optional)
567  Epoch to which to correct proper motion and parallax,
568  or None to not apply such corrections.
569 
570  Returns
571  -------
572  md : `lsst.daf.base.PropertyList`
573  """
574  md = PropertyList()
575  md.add('RA', coord.getRa().asDegrees(), 'field center in degrees')
576  md.add('DEC', coord.getDec().asDegrees(), 'field center in degrees')
577  md.add('RADIUS', radius.asDegrees(), 'field radius in degrees, minimum')
578  md.add('SMATCHV', 1, 'SourceMatchVector version number')
579  filterName = "UNKNOWN" if filterName is None else str(filterName)
580  md.add('FILTER', filterName, 'filter name for photometric data')
581  md.add('EPOCH', "NONE" if epoch is None else epoch.mjd, 'Epoch (TAI MJD) for catalog')
582  return md
583 
584  @staticmethod
585  def addFluxAliases(refCat, defaultFilter, filterReferenceMap):
586  """This function creates a new catalog containing the information of the input refCat
587  as well as added flux columns and aliases between camera and reference flux.
588 
589  Parameters
590  ----------
591  refCat : `lsst.afw.table.SimpleCatalog`
592  Catalog of reference objects
593  defaultFilter : `str`
594  Name of the default reference filter
595  filterReferenceMap : `dict` of `str`
596  Dictionary with keys corresponding to a filter name, and values which
597  correspond to the name of the reference filter.
598 
599  Returns
600  -------
601  refCat : `lsst.afw.table.SimpleCatalog`
602  Reference catalog with columns added to track reference filters
603 
604  Raises
605  ------
606  `RuntimeError`
607  If specified reference filter name is not a filter specifed as a key in the
608  reference filter map.
609  """
610  refCat = ReferenceObjectLoader.remapReferenceCatalogSchema(refCat,
611  filterNameList=filterReferenceMap.keys())
612  aliasMap = refCat.schema.getAliasMap()
613  if filterReferenceMap is None:
614  filterReferenceMap = {}
615  for filterName, refFilterName in itertools.chain([(None, defaultFilter)],
616  filterReferenceMap.items()):
617  if refFilterName:
618  camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux"
619  refFluxName = refFilterName + "_flux"
620  if refFluxName not in refCat.schema:
621  raise RuntimeError("Unknown reference filter %s" % (refFluxName,))
622  aliasMap.set(camFluxName, refFluxName)
623 
624  refFluxErrName = refFluxName + "Err"
625  camFluxErrName = camFluxName + "Err"
626  aliasMap.set(camFluxErrName, refFluxErrName)
627 
628  return refCat
629 
630  @staticmethod
631  def remapReferenceCatalogSchema(refCat, *, filterNameList=None, position=False, photometric=False):
632  """This function takes in a reference catalog and creates a new catalog with additional
633  columns defined the remaining function arguments.
634 
635  Parameters
636  ----------
637  refCat : `lsst.afw.table.SimpleCatalog`
638  Reference catalog to map to new catalog
639 
640  Returns
641  -------
642  expandedCat : `lsst.afw.table.SimpleCatalog`
643  Deep copy of input reference catalog with additional columns added
644  """
645  mapper = afwTable.SchemaMapper(refCat.schema, True)
646  mapper.addMinimalSchema(refCat.schema, True)
647  mapper.editOutputSchema().disconnectAliases()
648  if filterNameList:
649  for filterName in filterNameList:
650  mapper.editOutputSchema().addField(f"{filterName}_flux",
651  type=numpy.float64,
652  doc=f"flux in filter {filterName}",
653  units="Jy"
654  )
655  mapper.editOutputSchema().addField(f"{filterName}_fluxErr",
656  type=numpy.float64,
657  doc=f"flux uncertanty in filter {filterName}",
658  units="Jy"
659  )
660 
661  if position:
662  mapper.editOutputSchema().addField("centroid_x", type=float, doReplace=True)
663  mapper.editOutputSchema().addField("centroid_y", type=float, doReplace=True)
664  mapper.editOutputSchema().addField("hasCentroid", type="Flag", doReplace=True)
665  mapper.editOutputSchema().getAliasMap().set("slot_Centroid", "centroid")
666 
667  if photometric:
668  mapper.editOutputSchema().addField("photometric",
669  type="Flag",
670  doc="set if the object can be used for photometric"
671  "calibration",
672  )
673  mapper.editOutputSchema().addField("resolved",
674  type="Flag",
675  doc="set if the object is spatially resolved"
676  )
677  mapper.editOutputSchema().addField("variable",
678  type="Flag",
679  doc="set if the object has variable brightness"
680  )
681 
682  expandedCat = afwTable.SimpleCatalog(mapper.getOutputSchema())
683  expandedCat.setMetadata(refCat.getMetadata())
684  expandedCat.extend(refCat, mapper=mapper)
685 
686  return expandedCat
687 
688 
689 def getRefFluxField(schema, filterName=None):
690  """Get the name of a flux field from a schema.
691 
692  return the alias of "anyFilterMapsToThis", if present
693  else if filterName is specified:
694  return "*filterName*_camFlux" if present
695  else return "*filterName*_flux" if present (camera filter name
696  matches reference filter name)
697  else throw RuntimeError
698  else:
699  return "camFlux", if present,
700  else throw RuntimeError
701 
702  Parameters
703  ----------
704  schema : `lsst.afw.table.Schema`
705  Reference catalog schema.
706  filterName : `str`, optional
707  Name of camera filter. If not specified, ``defaultFilter`` needs to be
708  set in the refcat loader config.
709 
710  Returns
711  -------
712  fluxFieldName : `str`
713  Name of flux field.
714 
715  Raises
716  ------
717  RuntimeError
718  If an appropriate field is not found.
719  """
720  if not isinstance(schema, afwTable.Schema):
721  raise RuntimeError("schema=%s is not a schema" % (schema,))
722  try:
723  return schema.getAliasMap().get("anyFilterMapsToThis")
724  except LookupError:
725  pass # try the filterMap next
726 
727  if filterName:
728  fluxFieldList = [filterName + "_camFlux", filterName + "_flux"]
729  else:
730  fluxFieldList = ["camFlux"]
731  for fluxField in fluxFieldList:
732  if fluxField in schema:
733  return fluxField
734 
735  raise RuntimeError("Could not find flux field(s) %s" % (", ".join(fluxFieldList)))
736 
737 
738 def getRefFluxKeys(schema, filterName=None):
739  """Return keys for flux and flux error.
740 
741  Parameters
742  ----------
743  schema : `lsst.afw.table.Schema`
744  Reference catalog schema.
745  filterName : `str`
746  Name of camera filter.
747 
748  Returns
749  -------
750  keys : `tuple` of (`lsst.afw.table.Key`, `lsst.afw.table.Key`)
751  Two keys:
752 
753  - flux key
754  - flux error key, if present, else None
755 
756  Raises
757  ------
758  RuntimeError
759  If flux field not found.
760  """
761  fluxField = getRefFluxField(schema, filterName)
762  fluxErrField = fluxField + "Err"
763  fluxKey = schema[fluxField].asKey()
764  try:
765  fluxErrKey = schema[fluxErrField].asKey()
766  except Exception:
767  fluxErrKey = None
768  return (fluxKey, fluxErrKey)
769 
770 
771 class LoadReferenceObjectsConfig(pexConfig.Config):
772  pixelMargin = pexConfig.RangeField(
773  doc="Padding to add to 4 all edges of the bounding box (pixels)",
774  dtype=int,
775  default=300,
776  min=0,
777  )
778  defaultFilter = pexConfig.Field(
779  doc=("Default reference catalog filter to use if filter not specified in exposure;"
780  " if blank then filter must be specified in exposure."),
781  dtype=str,
782  default="",
783  )
784  anyFilterMapsToThis = pexConfig.Field(
785  doc=("Always use this reference catalog filter, no matter whether or what filter name is "
786  "supplied to the loader. Effectively a trivial filterMap: map all filter names to this filter."
787  " This can be set for purely-astrometric catalogs (e.g. Gaia DR2) where there is only one "
788  "reasonable choice for every camera filter->refcat mapping, but not for refcats used for "
789  "photometry, which need a filterMap and/or colorterms/transmission corrections."),
790  dtype=str,
791  default=None,
792  optional=True
793  )
794  filterMap = pexConfig.DictField(
795  doc=("Mapping of camera filter name: reference catalog filter name; "
796  "each reference filter must exist in the refcat."
797  " Note that this does not perform any bandpass corrections: it is just a lookup."),
798  keytype=str,
799  itemtype=str,
800  default={},
801  )
802  requireProperMotion = pexConfig.Field(
803  doc="Require that the fields needed to correct proper motion "
804  "(epoch, pm_ra and pm_dec) are present?",
805  dtype=bool,
806  default=False,
807  )
808 
809  def validate(self):
810  super().validate()
811  if self.filterMapfilterMap != {} and self.anyFilterMapsToThisanyFilterMapsToThis is not None:
812  msg = "`filterMap` and `anyFilterMapsToThis` are mutually exclusive"
813  raise pexConfig.FieldValidationError(LoadReferenceObjectsConfig.anyFilterMapsToThis,
814  self, msg)
815 
816 
817 # The following comment block adds a link to this task from the Task Documentation page.
818 
824 
825 
826 class LoadReferenceObjectsTask(pipeBase.Task, metaclass=abc.ABCMeta):
827  r"""!Abstract base class to load objects from reference catalogs
828 
829  @anchor LoadReferenceObjectsTask_
830 
831  @section meas_algorithms_loadReferenceObjects_Contents Contents
832 
833  - @ref meas_algorithms_loadReferenceObjects_Purpose
834  - @ref meas_algorithms_loadReferenceObjects_Initialize
835  - @ref meas_algorithms_loadReferenceObjects_IO
836  - @ref meas_algorithms_loadReferenceObjects_Schema
837  - @ref meas_algorithms_loadReferenceObjects_Config
838 
839  @section meas_algorithms_loadReferenceObjects_Purpose Description
840 
841  Abstract base class for tasks that load objects from a reference catalog
842  in a particular region of the sky.
843 
844  Implementations must subclass this class, override the loadSkyCircle method,
845  and will typically override the value of ConfigClass with a task-specific config class.
846 
847  @section meas_algorithms_loadReferenceObjects_Initialize Task initialisation
848 
849  @copydoc \_\_init\_\_
850 
851  @section meas_algorithms_loadReferenceObjects_IO Invoking the Task
852 
853  @copydoc loadPixelBox
854 
855  @section meas_algorithms_loadReferenceObjects_Schema Schema of the reference object catalog
856 
857  Reference object catalogs are instances of lsst.afw.table.SimpleCatalog with the following schema
858  (other fields may also be present).
859  The units use astropy quantity conventions, so a 2 suffix means squared.
860  See also makeMinimalSchema.
861  - coord: ICRS position of star on sky (an lsst.geom.SpherePoint)
862  - centroid: position of star on an exposure, if relevant (an lsst.afw.Point2D)
863  - hasCentroid: is centroid usable? (a Flag)
864  - *referenceFilterName*_flux: brightness in the specified reference catalog filter (nJy)
865  Note: you can use astropy.units to convert from AB Magnitude to nJy:
866  `u.Magnitude(value, u.ABmag).to_value(u.nJy)`
867  - *referenceFilterName*_fluxErr (optional): brightness standard deviation (nJy);
868  omitted if no data is available; possibly nan if data is available for some objects but not others
869  - camFlux: brightness in default camera filter (nJy); omitted if defaultFilter not specified
870  - camFluxErr: brightness standard deviation for default camera filter;
871  omitted if defaultFilter not specified or standard deviation not available that filter
872  - *cameraFilterName*_camFlux: brightness in specified camera filter (nJy)
873  - *cameraFilterName*_camFluxErr (optional): brightness standard deviation
874  in specified camera filter (nJy); omitted if no data is available;
875  possibly nan if data is available for some objects but not others
876  - photometric (optional): is the object usable for photometric calibration? (a Flag)
877  - resolved (optional): is the object spatially resolved? (a Flag)
878  - variable (optional): does the object have variable brightness? (a Flag)
879  - coord_raErr: uncertainty in `coord` along the direction of right ascension (radian, an Angle)
880  = uncertainty in ra * cos(dec); nan if unknown
881  - coord_decErr: uncertainty in `coord` along the direction of declination (radian, an Angle);
882  nan if unknown
883 
884  The following are optional; fields should only be present if the
885  information is available for at least some objects.
886  Numeric values are `nan` if unknown:
887  - epoch: date of observation as TAI MJD (day)
888 
889  - pm_ra: proper motion along the direction of right ascension (rad/year, an Angle) = dra/dt * cos(dec)
890  - pm_dec: proper motion along the direction of declination (rad/year, and Angle)
891  - pm_raErr: uncertainty in `pm_ra` (rad/year)
892  - pm_decErr: uncertainty in `pm_dec` (rad/year)
893  - pm_ra_dec_Cov: covariance between pm_ra and pm_dec (rad2/year2)
894  - pm_flag: set if proper motion, error or covariance is bad
895 
896  - parallax: parallax (rad, an Angle)
897  - parallaxErr: uncertainty in `parallax` (rad)
898  - parallax_flag: set if parallax value or parallaxErr is bad
899 
900  - coord_ra_pm_ra_Cov: covariance between coord_ra and pm_ra (rad2/year)
901  - coord_ra_pm_dec_Cov: covariance between coord_ra and pm_dec (rad2/year)
902  - coord_ra_parallax_Cov: covariance between coord_ra and parallax (rad2/year)
903  - coord_dec_pm_ra_Cov: covariance between coord_dec and pm_ra (rad2/year)
904  - coord_dec_pm_dec_Cov: covariance between coord_dec and pm_dec (rad2/year)
905  - coord_dec_parallax_Cov: covariance between coord_dec and parallax (rad2/year)
906  - pm_ra_parallax_Cov: covariance between pm_ra and parallax (rad2/year)
907  - pm_dec_parallax_Cov: covariance between pm_dec and parallax (rad2/year)
908 
909  @section meas_algorithms_loadReferenceObjects_Config Configuration parameters
910 
911  See @ref LoadReferenceObjectsConfig for a base set of configuration parameters.
912  Most subclasses will add configuration variables.
913  """
914  ConfigClass = LoadReferenceObjectsConfig
915  _DefaultName = "LoadReferenceObjects"
916 
917  def __init__(self, butler=None, *args, **kwargs):
918  """Construct a LoadReferenceObjectsTask
919 
920  Parameters
921  ----------
922  butler : `lsst.daf.persistence.Butler`
923  Data butler, for access reference catalogs.
924  """
925  pipeBase.Task.__init__(self, *args, **kwargs)
926  self.butlerbutler = butler
927 
928  @pipeBase.timeMethod
929  def loadPixelBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
930  """Load reference objects that overlap a rectangular pixel region.
931 
932  Parameters
933  ----------
934  bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
935  Bounding box for pixels.
936  wcs : `lsst.afw.geom.SkyWcs`
937  WCS; used to convert pixel positions to sky coordinates
938  and vice-versa.
939  filterName : `str`
940  Name of filter, or `None` or `""` for the default filter.
941  This is used for flux values in case we have flux limits
942  (which are not yet implemented).
943  photoCalib : `lsst.afw.image.PhotoCalib` (optional)
944  Calibration, or `None` if unknown.
945  epoch : `astropy.time.Time` (optional)
946  Epoch to which to correct proper motion and parallax,
947  or None to not apply such corrections.
948 
949  Returns
950  -------
951  results : `lsst.pipe.base.Struct`
952  A Struct containing the following fields:
953  refCat : `lsst.afw.catalog.SimpleCatalog`
954  A catalog of reference objects with the standard
955  schema, as documented in the main doc string for
956  `LoadReferenceObjects`.
957  The catalog is guaranteed to be contiguous.
958  fluxField : `str`
959  Name of flux field for specified `filterName`.
960 
961  Notes
962  -----
963  The search algorithm works by searching in a region in sky
964  coordinates whose center is the center of the bbox and radius
965  is large enough to just include all 4 corners of the bbox.
966  Stars that lie outside the bbox are then trimmed from the list.
967  """
968  circle = self._calculateCircle_calculateCircle(bbox, wcs)
969 
970  # find objects in circle
971  self.log.info("Loading reference objects using center %s and radius %s deg" %
972  (circle.coord, circle.radius.asDegrees()))
973  loadRes = self.loadSkyCircleloadSkyCircle(circle.coord, circle.radius, filterName=filterName, epoch=epoch,
974  centroids=True)
975  refCat = loadRes.refCat
976  numFound = len(refCat)
977 
978  # trim objects outside bbox
979  refCat = self._trimToBBox_trimToBBox(refCat=refCat, bbox=circle.bbox, wcs=wcs)
980  numTrimmed = numFound - len(refCat)
981  self.log.debug("trimmed %d out-of-bbox objects, leaving %d", numTrimmed, len(refCat))
982  self.log.info("Loaded %d reference objects", len(refCat))
983 
984  # make sure catalog is contiguous
985  if not refCat.isContiguous():
986  loadRes.refCat = refCat.copy(deep=True)
987 
988  return loadRes
989 
990  @abc.abstractmethod
991  def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None, centroids=False):
992  """Load reference objects that overlap a circular sky region.
993 
994  Parameters
995  ----------
996  ctrCoord : `lsst.geom.SpherePoint`
997  ICRS center of search region.
998  radius : `lsst.geom.Angle`
999  Radius of search region.
1000  filterName : `str` (optional)
1001  Name of filter, or `None` or `""` for the default filter.
1002  This is used for flux values in case we have flux limits
1003  (which are not yet implemented).
1004  epoch : `astropy.time.Time` (optional)
1005  Epoch to which to correct proper motion and parallax,
1006  or None to not apply such corrections.
1007  centroids : `bool` (optional)
1008  Add centroid fields to the loaded Schema. ``loadPixelBox`` expects
1009  these fields to exist.
1010 
1011  Returns
1012  -------
1013  results : `lsst.pipe.base.Struct`
1014  A Struct containing the following fields:
1015  refCat : `lsst.afw.catalog.SimpleCatalog`
1016  A catalog of reference objects with the standard
1017  schema, as documented in the main doc string for
1018  `LoadReferenceObjects`.
1019  The catalog is guaranteed to be contiguous.
1020  fluxField : `str`
1021  Name of flux field for specified `filterName`.
1022 
1023  Notes
1024  -----
1025  Note that subclasses are responsible for performing the proper motion
1026  correction, since this is the lowest-level interface for retrieving
1027  the catalog.
1028  """
1029  return
1030 
1031  @staticmethod
1032  def _trimToBBox(refCat, bbox, wcs):
1033  """Remove objects outside a given pixel bounding box and set
1034  centroid and hasCentroid fields.
1035 
1036  Parameters
1037  ----------
1038  refCat : `lsst.afw.table.SimpleCatalog`
1039  A catalog of objects. The schema must include fields
1040  "coord", "centroid" and "hasCentroid".
1041  The "coord" field is read.
1042  The "centroid" and "hasCentroid" fields are set.
1043  bbox : `lsst.geom.Box2D`
1044  Pixel region
1045  wcs : `lsst.afw.geom.SkyWcs`
1046  WCS; used to convert sky coordinates to pixel positions.
1047 
1048  @return a catalog of reference objects in bbox, with centroid and hasCentroid fields set
1049  """
1050  afwTable.updateRefCentroids(wcs, refCat)
1051  centroidKey = afwTable.Point2DKey(refCat.schema["centroid"])
1052  retStarCat = type(refCat)(refCat.table)
1053  for star in refCat:
1054  point = star.get(centroidKey)
1055  if bbox.contains(point):
1056  retStarCat.append(star)
1057  return retStarCat
1058 
1059  def _addFluxAliases(self, schema):
1060  """Add aliases for camera filter fluxes to the schema.
1061 
1062  If self.config.defaultFilter then adds these aliases:
1063  camFlux: <defaultFilter>_flux
1064  camFluxErr: <defaultFilter>_fluxErr, if the latter exists
1065 
1066  For each camFilter: refFilter in self.config.filterMap adds these aliases:
1067  <camFilter>_camFlux: <refFilter>_flux
1068  <camFilter>_camFluxErr: <refFilter>_fluxErr, if the latter exists
1069 
1070  Parameters
1071  ----------
1072  schema : `lsst.afw.table.Schema`
1073  Schema for reference catalog.
1074 
1075  Raises
1076  ------
1077  RuntimeError
1078  If any reference flux field is missing from the schema.
1079  """
1080  aliasMap = schema.getAliasMap()
1081 
1082  if self.config.anyFilterMapsToThis is not None:
1083  refFluxName = self.config.anyFilterMapsToThis + "_flux"
1084  if refFluxName not in schema:
1085  msg = f"Unknown reference filter for anyFilterMapsToThis='{refFluxName}'"
1086  raise RuntimeError(msg)
1087  aliasMap.set("anyFilterMapsToThis", refFluxName)
1088  return # this is mutually exclusive with filterMap
1089 
1090  def addAliasesForOneFilter(filterName, refFilterName):
1091  """Add aliases for a single filter
1092 
1093  Parameters
1094  ----------
1095  filterName : `str` (optional)
1096  Camera filter name. The resulting alias name is
1097  <filterName>_camFlux, or simply "camFlux" if `filterName`
1098  is `None` or `""`.
1099  refFilterName : `str`
1100  Reference catalog filter name; the field
1101  <refFilterName>_flux must exist.
1102  """
1103  camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux"
1104  refFluxName = refFilterName + "_flux"
1105  if refFluxName not in schema:
1106  raise RuntimeError("Unknown reference filter %s" % (refFluxName,))
1107  aliasMap.set(camFluxName, refFluxName)
1108  refFluxErrName = refFluxName + "Err"
1109  if refFluxErrName in schema:
1110  camFluxErrName = camFluxName + "Err"
1111  aliasMap.set(camFluxErrName, refFluxErrName)
1112 
1113  if self.config.defaultFilter:
1114  addAliasesForOneFilter(None, self.config.defaultFilter)
1115 
1116  for filterName, refFilterName in self.config.filterMap.items():
1117  addAliasesForOneFilter(filterName, refFilterName)
1118 
1119  @staticmethod
1120  def makeMinimalSchema(filterNameList, *, addCentroid=False,
1121  addIsPhotometric=False, addIsResolved=False,
1122  addIsVariable=False, coordErrDim=2,
1123  addProperMotion=False, properMotionErrDim=2,
1124  addParallax=False):
1125  """Make a standard schema for reference object catalogs.
1126 
1127  Parameters
1128  ----------
1129  filterNameList : `list` of `str`
1130  List of filter names. Used to create <filterName>_flux fields.
1131  addIsPhotometric : `bool`
1132  If True then add field "photometric".
1133  addIsResolved : `bool`
1134  If True then add field "resolved".
1135  addIsVariable : `bool`
1136  If True then add field "variable".
1137  coordErrDim : `int`
1138  Number of coord error fields; must be one of 0, 2, 3:
1139 
1140  - If 2 or 3: add fields "coord_raErr" and "coord_decErr".
1141  - If 3: also add field "coord_radecErr".
1142  addProperMotion : `bool`
1143  If True add fields "epoch", "pm_ra", "pm_dec" and "pm_flag".
1144  properMotionErrDim : `int`
1145  Number of proper motion error fields; must be one of 0, 2, 3;
1146  ignored if addProperMotion false:
1147  - If 2 or 3: add fields "pm_raErr" and "pm_decErr".
1148  - If 3: also add field "pm_radecErr".
1149  addParallax : `bool`
1150  If True add fields "epoch", "parallax", "parallaxErr"
1151  and "parallax_flag".
1152 
1153  Returns
1154  -------
1155  schema : `lsst.afw.table.Schema`
1156  Schema for reference catalog, an
1157  `lsst.afw.table.SimpleCatalog`.
1158 
1159  Notes
1160  -----
1161  Reference catalogs support additional covariances, such as
1162  covariance between RA and proper motion in declination,
1163  that are not supported by this method, but can be added after
1164  calling this method.
1165  """
1166  schema = afwTable.SimpleTable.makeMinimalSchema()
1167  if addCentroid:
1168  afwTable.Point2DKey.addFields(
1169  schema,
1170  "centroid",
1171  "centroid on an exposure, if relevant",
1172  "pixel",
1173  )
1174  schema.addField(
1175  field="hasCentroid",
1176  type="Flag",
1177  doc="is position known?",
1178  )
1179  for filterName in filterNameList:
1180  schema.addField(
1181  field="%s_flux" % (filterName,),
1182  type=numpy.float64,
1183  doc="flux in filter %s" % (filterName,),
1184  units="nJy",
1185  )
1186  for filterName in filterNameList:
1187  schema.addField(
1188  field="%s_fluxErr" % (filterName,),
1189  type=numpy.float64,
1190  doc="flux uncertainty in filter %s" % (filterName,),
1191  units="nJy",
1192  )
1193  if addIsPhotometric:
1194  schema.addField(
1195  field="photometric",
1196  type="Flag",
1197  doc="set if the object can be used for photometric calibration",
1198  )
1199  if addIsResolved:
1200  schema.addField(
1201  field="resolved",
1202  type="Flag",
1203  doc="set if the object is spatially resolved",
1204  )
1205  if addIsVariable:
1206  schema.addField(
1207  field="variable",
1208  type="Flag",
1209  doc="set if the object has variable brightness",
1210  )
1211  if coordErrDim not in (0, 2, 3):
1212  raise ValueError("coordErrDim={}; must be (0, 2, 3)".format(coordErrDim))
1213  if coordErrDim > 0:
1214  afwTable.CovarianceMatrix2fKey.addFields(
1215  schema=schema,
1216  prefix="coord",
1217  names=["ra", "dec"],
1218  units=["rad", "rad"],
1219  diagonalOnly=(coordErrDim == 2),
1220  )
1221 
1222  if addProperMotion or addParallax:
1223  schema.addField(
1224  field="epoch",
1225  type=numpy.float64,
1226  doc="date of observation (TAI, MJD)",
1227  units="day",
1228  )
1229 
1230  if addProperMotion:
1231  schema.addField(
1232  field="pm_ra",
1233  type="Angle",
1234  doc="proper motion in the right ascension direction = dra/dt * cos(dec)",
1235  units="rad/year",
1236  )
1237  schema.addField(
1238  field="pm_dec",
1239  type="Angle",
1240  doc="proper motion in the declination direction",
1241  units="rad/year",
1242  )
1243  if properMotionErrDim not in (0, 2, 3):
1244  raise ValueError("properMotionErrDim={}; must be (0, 2, 3)".format(properMotionErrDim))
1245  if properMotionErrDim > 0:
1246  afwTable.CovarianceMatrix2fKey.addFields(
1247  schema=schema,
1248  prefix="pm",
1249  names=["ra", "dec"],
1250  units=["rad/year", "rad/year"],
1251  diagonalOnly=(properMotionErrDim == 2),
1252  )
1253  schema.addField(
1254  field="pm_flag",
1255  type="Flag",
1256  doc="Set if proper motion or proper motion error is bad",
1257  )
1258 
1259  if addParallax:
1260  schema.addField(
1261  field="parallax",
1262  type="Angle",
1263  doc="parallax",
1264  units="rad",
1265  )
1266  schema.addField(
1267  field="parallaxErr",
1268  type="Angle",
1269  doc="uncertainty in parallax",
1270  units="rad",
1271  )
1272  schema.addField(
1273  field="parallax_flag",
1274  type="Flag",
1275  doc="Set if parallax or parallax error is bad",
1276  )
1277  return schema
1278 
1279  def _calculateCircle(self, bbox, wcs):
1280  """Compute on-sky center and radius of search region.
1281 
1282  Parameters
1283  ----------
1284  bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1285  Pixel bounding box.
1286  wcs : `lsst.afw.geom.SkyWcs`
1287  WCS; used to convert pixel positions to sky coordinates.
1288 
1289  Returns
1290  -------
1291  results : `lsst.pipe.base.Struct`
1292  A Struct containing:
1293 
1294  - coord : `lsst.geom.SpherePoint`
1295  ICRS center of the search region.
1296  - radius : `lsst.geom.Angle`
1297  Radius of the search region.
1298  - bbox : `lsst.geom.Box2D`
1299  Bounding box used to compute the circle.
1300  """
1301  bbox = lsst.geom.Box2D(bbox) # make sure bbox is double and that we have a copy
1302  bbox.grow(self.config.pixelMargin)
1303  coord = wcs.pixelToSky(bbox.getCenter())
1304  radius = max(coord.separation(wcs.pixelToSky(pp)) for pp in bbox.getCorners())
1305  return pipeBase.Struct(coord=coord, radius=radius, bbox=bbox)
1306 
1307  def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
1308  """Return metadata about the load.
1309 
1310  This metadata is used for reloading the catalog (e.g., for
1311  reconstituting a normalised match list.
1312 
1313  Parameters
1314  ----------
1315  bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1316  Pixel bounding box.
1317  wcs : `lsst.afw.geom.SkyWcs`
1318  WCS; used to convert pixel positions to sky coordinates.
1319  filterName : `str`
1320  Name of camera filter, or `None` or `""` for the default
1321  filter.
1322  photoCalib : `lsst.afw.image.PhotoCalib` (optional)
1323  Calibration, or `None` if unknown.
1324  epoch : `astropy.time.Time` (optional)
1325  Epoch to which to correct proper motion and parallax,
1326  or None to not apply such corrections.
1327 
1328  Returns
1329  -------
1330  metadata : lsst.daf.base.PropertyList
1331  Metadata about the load.
1332  """
1333  circle = self._calculateCircle_calculateCircle(bbox, wcs)
1334  return self.getMetadataCirclegetMetadataCircle(circle.coord, circle.radius, filterName, photoCalib=photoCalib,
1335  epoch=epoch)
1336 
1337  def getMetadataCircle(self, coord, radius, filterName, photoCalib=None, epoch=None):
1338  """Return metadata about the load.
1339 
1340  This metadata is used for reloading the catalog (e.g., for
1341  reconstituting a normalised match list.
1342 
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.
1357 
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.mjd, 'Epoch (TAI MJD) for catalog')
1371  return md
1372 
1373  def joinMatchListWithCatalog(self, matchCat, sourceCat):
1374  """Relink an unpersisted match list to sources and reference
1375  objects.
1376 
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.
1382 
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.
1392 
1393  Returns
1394  -------
1395  matchList : `lsst.afw.table.ReferenceMatchVector`
1396  Match list.
1397  """
1398  return joinMatchListWithCatalogImpl(self, matchCat, sourceCat)
1399 
1400  def applyProperMotions(self, catalog, epoch):
1401  """Apply proper motion correction to a reference catalog.
1402 
1403  Adjust position and position error in the ``catalog``
1404  for proper motion to the specified ``epoch``,
1405  modifying the catalog in place.
1406 
1407  Parameters
1408  ----------
1409  catalog : `lsst.afw.table.SimpleCatalog`
1410  Catalog of positions, containing:
1411 
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):
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)
1431 
1432 
1433 def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat):
1434  """Relink an unpersisted match list to sources and reference
1435  objects.
1436 
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.
1442 
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.
1454 
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
1488 
1489  refCat.sort()
1490  sourceCat.sort()
1491  return afwTable.unpackMatches(matchCat, refCat, sourceCat)
1492 
1493 
1494 def applyProperMotionsImpl(log, catalog, epoch):
1495  """Apply proper motion correction to a reference catalog.
1496 
1497  Adjust position and position error in the ``catalog``
1498  for proper motion to the specified ``epoch``,
1499  modifying the catalog in place.
1500 
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:
1507 
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:
1522  log.warn("Proper motion correction not available from catalog")
1523  return
1524  if not catalog.isContiguous():
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:
1552  catalog["coord_raErr"] = numpy.hypot(catalog["coord_raErr"],
1553  catalog["pm_raErr"]*timeDiffsYears)
1554  if "coord_decErr" in catalog.schema:
1555  catalog["coord_decErr"] = numpy.hypot(catalog["coord_decErr"],
1556  catalog["pm_decErr"]*timeDiffsYears)
static Schema makeMinimalSchema()
static Log getDefaultLogger()
Abstract base class to load objects from reference catalogs.
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 getMetadataBox(cls, bbox, wcs, filterName=None, photoCalib=None, epoch=None, bboxPadding=100)
def addFluxAliases(refCat, defaultFilter, filterReferenceMap)
def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None)
def loadPixelBox(self, bbox, wcs, filterName=None, epoch=None, photoCalib=None, bboxPadding=100)
def convertToNanojansky(catalog, log, doConvert=True)
def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat)