lsst.meas.algorithms  19.0.0-21-gf63060fa+1
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.region = 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.region):
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.region.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.dataIds = dataIds
221  self.refCats = refCats
223  self.config = 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(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.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)
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.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)
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.log.debug(f"Trimmed {trimmedAmount} out of region objects, leaving {len(refCat)}")
404  self.log.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.log, refCat, epoch)
414  else:
415  self.log.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.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)
424 
425  expandedCat = self.remapReferenceCatalogSchema(refCat, position=True)
426 
427  # Add flux aliases
428  expandedCat = self.addFluxAliases(expandedCat, self.config.defaultFilter, self.config.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.loadRegion(circularRegion, filterName=filterName, epoch=None)
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(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
550 
551  @staticmethod
552  def getMetadataCircle(coord, radius, filterName, photoCalib=None, epoch=None):
553  """Return metadata about the load
554 
555  This metadata is used for reloading the catalog (e.g. for reconstituting
556  a normalized match list.)
557 
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.
571 
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
585 
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.
590 
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.
600 
601  Returns
602  -------
603  refCat : `lsst.afw.table.SimpleCatalog`
604  Reference catalog with columns added to track reference filters
605 
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)
625 
626  refFluxErrName = refFluxName + "Err"
627  camFluxErrName = camFluxName + "Err"
628  aliasMap.set(camFluxErrName, refFluxErrName)
629 
630  return refCat
631 
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.
636 
637  Parameters
638  ----------
639  refCat : `lsst.afw.table.SimpleCatalog`
640  Reference catalog to map to new catalog
641 
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  )
662 
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")
668 
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  )
683 
684  expandedCat = afwTable.SimpleCatalog(mapper.getOutputSchema())
685  expandedCat.setMetadata(refCat.getMetadata())
686  expandedCat.extend(refCat, mapper=mapper)
687 
688  return expandedCat
689 
690 
691 def getRefFluxField(schema, filterName=None):
692  """Get the name of a flux field from a schema.
693 
694  if filterName is specified:
695  return *filterName*_camFlux if present
696  else return *filterName*_flux if present (camera filter name 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`
707  Name of camera filter.
708 
709  Returns
710  -------
711  fluxFieldName : `str`
712  Name of flux field.
713 
714  Raises
715  ------
716  RuntimeError
717  If an appropriate field is not found.
718  """
719  if not isinstance(schema, afwTable.Schema):
720  raise RuntimeError("schema=%s is not a schema" % (schema,))
721  if filterName:
722  fluxFieldList = [filterName + "_camFlux", filterName + "_flux"]
723  else:
724  fluxFieldList = ["camFlux"]
725  for fluxField in fluxFieldList:
726  if fluxField in schema:
727  return fluxField
728 
729  raise RuntimeError("Could not find flux field(s) %s" % (", ".join(fluxFieldList)))
730 
731 
732 def getRefFluxKeys(schema, filterName=None):
733  """Return keys for flux and flux error.
734 
735  Parameters
736  ----------
737  schema : `lsst.afw.table.Schema`
738  Reference catalog schema.
739  filterName : `str`
740  Name of camera filter.
741 
742  Returns
743  -------
744  keys : `tuple` of (`lsst.afw.table.Key`, `lsst.afw.table.Key`)
745  Two keys:
746 
747  - flux key
748  - flux error key, if present, else None
749 
750  Raises
751  ------
752  RuntimeError
753  If flux field not found.
754  """
755  fluxField = getRefFluxField(schema, filterName)
756  fluxErrField = fluxField + "Err"
757  fluxKey = schema[fluxField].asKey()
758  try:
759  fluxErrKey = schema[fluxErrField].asKey()
760  except Exception:
761  fluxErrKey = None
762  return (fluxKey, fluxErrKey)
763 
764 
765 class LoadReferenceObjectsConfig(pexConfig.Config):
766  pixelMargin = pexConfig.RangeField(
767  doc="Padding to add to 4 all edges of the bounding box (pixels)",
768  dtype=int,
769  default=300,
770  min=0,
771  )
772  defaultFilter = pexConfig.Field(
773  doc="Default reference catalog filter to use if filter not specified in exposure; "
774  "if blank then filter must be specified in exposure",
775  dtype=str,
776  default="",
777  )
778  filterMap = pexConfig.DictField(
779  doc="Mapping of camera filter name: reference catalog filter name; "
780  "each reference filter must exist",
781  keytype=str,
782  itemtype=str,
783  default={},
784  )
785  requireProperMotion = pexConfig.Field(
786  doc="Require that the fields needed to correct proper motion "
787  "(epoch, pm_ra and pm_dec) are present?",
788  dtype=bool,
789  default=False,
790  )
791 
792 # The following comment block adds a link to this task from the Task Documentation page.
793 
799 
800 
801 class LoadReferenceObjectsTask(pipeBase.Task, metaclass=abc.ABCMeta):
802  r"""!Abstract base class to load objects from reference catalogs
803 
804  @anchor LoadReferenceObjectsTask_
805 
806  @section meas_algorithms_loadReferenceObjects_Contents Contents
807 
808  - @ref meas_algorithms_loadReferenceObjects_Purpose
809  - @ref meas_algorithms_loadReferenceObjects_Initialize
810  - @ref meas_algorithms_loadReferenceObjects_IO
811  - @ref meas_algorithms_loadReferenceObjects_Schema
812  - @ref meas_algorithms_loadReferenceObjects_Config
813 
814  @section meas_algorithms_loadReferenceObjects_Purpose Description
815 
816  Abstract base class for tasks that load objects from a reference catalog
817  in a particular region of the sky.
818 
819  Implementations must subclass this class, override the loadSkyCircle method,
820  and will typically override the value of ConfigClass with a task-specific config class.
821 
822  @section meas_algorithms_loadReferenceObjects_Initialize Task initialisation
823 
824  @copydoc \_\_init\_\_
825 
826  @section meas_algorithms_loadReferenceObjects_IO Invoking the Task
827 
828  @copydoc loadPixelBox
829 
830  @section meas_algorithms_loadReferenceObjects_Schema Schema of the reference object catalog
831 
832  Reference object catalogs are instances of lsst.afw.table.SimpleCatalog with the following schema
833  (other fields may also be present).
834  The units use astropy quantity conventions, so a 2 suffix means squared.
835  See also makeMinimalSchema.
836  - coord: ICRS position of star on sky (an lsst.geom.SpherePoint)
837  - centroid: position of star on an exposure, if relevant (an lsst.afw.Point2D)
838  - hasCentroid: is centroid usable? (a Flag)
839  - *referenceFilterName*_flux: brightness in the specified reference catalog filter (nJy)
840  Note: you can use astropy.units to convert from AB Magnitude to nJy:
841  `u.Magnitude(value, u.ABmag).to_value(u.nJy)`
842  - *referenceFilterName*_fluxErr (optional): brightness standard deviation (nJy);
843  omitted if no data is available; possibly nan if data is available for some objects but not others
844  - camFlux: brightness in default camera filter (nJy); omitted if defaultFilter not specified
845  - camFluxErr: brightness standard deviation for default camera filter;
846  omitted if defaultFilter not specified or standard deviation not available that filter
847  - *cameraFilterName*_camFlux: brightness in specified camera filter (nJy)
848  - *cameraFilterName*_camFluxErr (optional): brightness standard deviation
849  in specified camera filter (nJy); omitted if no data is available;
850  possibly nan if data is available for some objects but not others
851  - photometric (optional): is the object usable for photometric calibration? (a Flag)
852  - resolved (optional): is the object spatially resolved? (a Flag)
853  - variable (optional): does the object have variable brightness? (a Flag)
854  - coord_raErr: uncertainty in `coord` along the direction of right ascension (radian, an Angle)
855  = uncertainty in ra * cos(dec); nan if unknown
856  - coord_decErr: uncertainty in `coord` along the direction of declination (radian, an Angle);
857  nan if unknown
858 
859  The following are optional; fields should only be present if the
860  information is available for at least some objects.
861  Numeric values are `nan` if unknown:
862  - epoch: date of observation as TAI MJD (day)
863 
864  - pm_ra: proper motion along the direction of right ascension (rad/year, an Angle) = dra/dt * cos(dec)
865  - pm_dec: proper motion along the direction of declination (rad/year, and Angle)
866  - pm_raErr: uncertainty in `pm_ra` (rad/year)
867  - pm_decErr: uncertainty in `pm_dec` (rad/year)
868  - pm_ra_dec_Cov: covariance between pm_ra and pm_dec (rad2/year2)
869  - pm_flag: set if proper motion, error or covariance is bad
870 
871  - parallax: parallax (rad, an Angle)
872  - parallaxErr: uncertainty in `parallax` (rad)
873  - parallax_flag: set if parallax value or parallaxErr is bad
874 
875  - coord_ra_pm_ra_Cov: covariance between coord_ra and pm_ra (rad2/year)
876  - coord_ra_pm_dec_Cov: covariance between coord_ra and pm_dec (rad2/year)
877  - coord_ra_parallax_Cov: covariance between coord_ra and parallax (rad2/year)
878  - coord_dec_pm_ra_Cov: covariance between coord_dec and pm_ra (rad2/year)
879  - coord_dec_pm_dec_Cov: covariance between coord_dec and pm_dec (rad2/year)
880  - coord_dec_parallax_Cov: covariance between coord_dec and parallax (rad2/year)
881  - pm_ra_parallax_Cov: covariance between pm_ra and parallax (rad2/year)
882  - pm_dec_parallax_Cov: covariance between pm_dec and parallax (rad2/year)
883 
884  @section meas_algorithms_loadReferenceObjects_Config Configuration parameters
885 
886  See @ref LoadReferenceObjectsConfig for a base set of configuration parameters.
887  Most subclasses will add configuration variables.
888  """
889  ConfigClass = LoadReferenceObjectsConfig
890  _DefaultName = "LoadReferenceObjects"
891 
892  def __init__(self, butler=None, *args, **kwargs):
893  """Construct a LoadReferenceObjectsTask
894 
895  Parameters
896  ----------
897  butler : `lsst.daf.persistence.Butler`
898  Data butler, for access reference catalogs.
899  """
900  pipeBase.Task.__init__(self, *args, **kwargs)
901  self.butler = butler
902 
903  @pipeBase.timeMethod
904  def loadPixelBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
905  """Load reference objects that overlap a rectangular pixel region.
906 
907  Parameters
908  ----------
909  bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
910  Bounding box for pixels.
911  wcs : `lsst.afw.geom.SkyWcs`
912  WCS; used to convert pixel positions to sky coordinates
913  and vice-versa.
914  filterName : `str`
915  Name of filter, or `None` or `""` for the default filter.
916  This is used for flux values in case we have flux limits
917  (which are not yet implemented).
918  photoCalib : `lsst.afw.image.PhotoCalib` (optional)
919  Calibration, or `None` if unknown.
920  epoch : `astropy.time.Time` (optional)
921  Epoch to which to correct proper motion and parallax,
922  or None to not apply such corrections.
923 
924  Returns
925  -------
926  results : `lsst.pipe.base.Struct`
927  A Struct containing the following fields:
928  refCat : `lsst.afw.catalog.SimpleCatalog`
929  A catalog of reference objects with the standard
930  schema, as documented in the main doc string for
931  `LoadReferenceObjects`.
932  The catalog is guaranteed to be contiguous.
933  fluxField : `str`
934  Name of flux field for specified `filterName`.
935 
936  Notes
937  -----
938  The search algorithm works by searching in a region in sky
939  coordinates whose center is the center of the bbox and radius
940  is large enough to just include all 4 corners of the bbox.
941  Stars that lie outside the bbox are then trimmed from the list.
942  """
943  circle = self._calculateCircle(bbox, wcs)
944 
945  # find objects in circle
946  self.log.info("Loading reference objects using center %s and radius %s deg" %
947  (circle.coord, circle.radius.asDegrees()))
948  loadRes = self.loadSkyCircle(circle.coord, circle.radius, filterName, centroids=True)
949  refCat = loadRes.refCat
950  numFound = len(refCat)
951 
952  # trim objects outside bbox
953  refCat = self._trimToBBox(refCat=refCat, bbox=circle.bbox, wcs=wcs)
954  numTrimmed = numFound - len(refCat)
955  self.log.debug("trimmed %d out-of-bbox objects, leaving %d", numTrimmed, len(refCat))
956  self.log.info("Loaded %d reference objects", len(refCat))
957 
958  # make sure catalog is contiguous
959  if not refCat.isContiguous():
960  loadRes.refCat = refCat.copy(deep=True)
961 
962  return loadRes
963 
964  @abc.abstractmethod
965  def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None, centroids=False):
966  """Load reference objects that overlap a circular sky region.
967 
968  Parameters
969  ----------
970  ctrCoord : `lsst.geom.SpherePoint`
971  ICRS center of search region.
972  radius : `lsst.geom.Angle`
973  Radius of search region.
974  filterName : `str` (optional)
975  Name of filter, or `None` or `""` for the default filter.
976  This is used for flux values in case we have flux limits
977  (which are not yet implemented).
978  epoch : `astropy.time.Time` (optional)
979  Epoch to which to correct proper motion and parallax,
980  or None to not apply such corrections.
981  centroids : `bool` (optional)
982  Add centroid fields to the loaded Schema. ``loadPixelBox`` expects
983  these fields to exist.
984 
985  Returns
986  -------
987  results : `lsst.pipe.base.Struct`
988  A Struct containing the following fields:
989  refCat : `lsst.afw.catalog.SimpleCatalog`
990  A catalog of reference objects with the standard
991  schema, as documented in the main doc string for
992  `LoadReferenceObjects`.
993  The catalog is guaranteed to be contiguous.
994  fluxField : `str`
995  Name of flux field for specified `filterName`.
996 
997  Notes
998  -----
999  Note that subclasses are responsible for performing the proper motion
1000  correction, since this is the lowest-level interface for retrieving
1001  the catalog.
1002  """
1003  return
1004 
1005  @staticmethod
1006  def _trimToBBox(refCat, bbox, wcs):
1007  """Remove objects outside a given pixel bounding box and set
1008  centroid and hasCentroid fields.
1009 
1010  Parameters
1011  ----------
1012  refCat : `lsst.afw.table.SimpleCatalog`
1013  A catalog of objects. The schema must include fields
1014  "coord", "centroid" and "hasCentroid".
1015  The "coord" field is read.
1016  The "centroid" and "hasCentroid" fields are set.
1017  bbox : `lsst.geom.Box2D`
1018  Pixel region
1019  wcs : `lsst.afw.geom.SkyWcs`
1020  WCS; used to convert sky coordinates to pixel positions.
1021 
1022  @return a catalog of reference objects in bbox, with centroid and hasCentroid fields set
1023  """
1024  afwTable.updateRefCentroids(wcs, refCat)
1025  centroidKey = afwTable.Point2DKey(refCat.schema["centroid"])
1026  retStarCat = type(refCat)(refCat.table)
1027  for star in refCat:
1028  point = star.get(centroidKey)
1029  if bbox.contains(point):
1030  retStarCat.append(star)
1031  return retStarCat
1032 
1033  def _addFluxAliases(self, schema):
1034  """Add aliases for camera filter fluxes to the schema.
1035 
1036  If self.config.defaultFilter then adds these aliases:
1037  camFlux: <defaultFilter>_flux
1038  camFluxErr: <defaultFilter>_fluxErr, if the latter exists
1039 
1040  For each camFilter: refFilter in self.config.filterMap adds these aliases:
1041  <camFilter>_camFlux: <refFilter>_flux
1042  <camFilter>_camFluxErr: <refFilter>_fluxErr, if the latter exists
1043 
1044  Parameters
1045  ----------
1046  schema : `lsst.afw.table.Schema`
1047  Schema for reference catalog.
1048 
1049  Throws
1050  ------
1051  RuntimeError
1052  If any reference flux field is missing from the schema.
1053  """
1054  aliasMap = schema.getAliasMap()
1055 
1056  def addAliasesForOneFilter(filterName, refFilterName):
1057  """Add aliases for a single filter
1058 
1059  Parameters
1060  ----------
1061  filterName : `str` (optional)
1062  Camera filter name. The resulting alias name is
1063  <filterName>_camFlux, or simply "camFlux" if `filterName`
1064  is `None` or `""`.
1065  refFilterName : `str`
1066  Reference catalog filter name; the field
1067  <refFilterName>_flux must exist.
1068  """
1069  camFluxName = filterName + "_camFlux" if filterName is not None else "camFlux"
1070  refFluxName = refFilterName + "_flux"
1071  if refFluxName not in schema:
1072  raise RuntimeError("Unknown reference filter %s" % (refFluxName,))
1073  aliasMap.set(camFluxName, refFluxName)
1074  refFluxErrName = refFluxName + "Err"
1075  if refFluxErrName in schema:
1076  camFluxErrName = camFluxName + "Err"
1077  aliasMap.set(camFluxErrName, refFluxErrName)
1078 
1079  if self.config.defaultFilter:
1080  addAliasesForOneFilter(None, self.config.defaultFilter)
1081 
1082  for filterName, refFilterName in self.config.filterMap.items():
1083  addAliasesForOneFilter(filterName, refFilterName)
1084 
1085  @staticmethod
1086  def makeMinimalSchema(filterNameList, *, addCentroid=False,
1087  addIsPhotometric=False, addIsResolved=False,
1088  addIsVariable=False, coordErrDim=2,
1089  addProperMotion=False, properMotionErrDim=2,
1090  addParallax=False):
1091  """Make a standard schema for reference object catalogs.
1092 
1093  Parameters
1094  ----------
1095  filterNameList : `list` of `str`
1096  List of filter names. Used to create <filterName>_flux fields.
1097  addIsPhotometric : `bool`
1098  If True then add field "photometric".
1099  addIsResolved : `bool`
1100  If True then add field "resolved".
1101  addIsVariable : `bool`
1102  If True then add field "variable".
1103  coordErrDim : `int`
1104  Number of coord error fields; must be one of 0, 2, 3:
1105 
1106  - If 2 or 3: add fields "coord_raErr" and "coord_decErr".
1107  - If 3: also add field "coord_radecErr".
1108  addProperMotion : `bool`
1109  If True add fields "epoch", "pm_ra", "pm_dec" and "pm_flag".
1110  properMotionErrDim : `int`
1111  Number of proper motion error fields; must be one of 0, 2, 3;
1112  ignored if addProperMotion false:
1113  - If 2 or 3: add fields "pm_raErr" and "pm_decErr".
1114  - If 3: also add field "pm_radecErr".
1115  addParallax : `bool`
1116  If True add fields "epoch", "parallax", "parallaxErr"
1117  and "parallax_flag".
1118 
1119  Returns
1120  -------
1121  schema : `lsst.afw.table.Schema`
1122  Schema for reference catalog, an
1123  `lsst.afw.table.SimpleCatalog`.
1124 
1125  Notes
1126  -----
1127  Reference catalogs support additional covariances, such as
1128  covariance between RA and proper motion in declination,
1129  that are not supported by this method, but can be added after
1130  calling this method.
1131  """
1132  schema = afwTable.SimpleTable.makeMinimalSchema()
1133  if addCentroid:
1134  afwTable.Point2DKey.addFields(
1135  schema,
1136  "centroid",
1137  "centroid on an exposure, if relevant",
1138  "pixel",
1139  )
1140  schema.addField(
1141  field="hasCentroid",
1142  type="Flag",
1143  doc="is position known?",
1144  )
1145  for filterName in filterNameList:
1146  schema.addField(
1147  field="%s_flux" % (filterName,),
1148  type=numpy.float64,
1149  doc="flux in filter %s" % (filterName,),
1150  units="nJy",
1151  )
1152  for filterName in filterNameList:
1153  schema.addField(
1154  field="%s_fluxErr" % (filterName,),
1155  type=numpy.float64,
1156  doc="flux uncertainty in filter %s" % (filterName,),
1157  units="nJy",
1158  )
1159  if addIsPhotometric:
1160  schema.addField(
1161  field="photometric",
1162  type="Flag",
1163  doc="set if the object can be used for photometric calibration",
1164  )
1165  if addIsResolved:
1166  schema.addField(
1167  field="resolved",
1168  type="Flag",
1169  doc="set if the object is spatially resolved",
1170  )
1171  if addIsVariable:
1172  schema.addField(
1173  field="variable",
1174  type="Flag",
1175  doc="set if the object has variable brightness",
1176  )
1177  if coordErrDim not in (0, 2, 3):
1178  raise ValueError("coordErrDim={}; must be (0, 2, 3)".format(coordErrDim))
1179  if coordErrDim > 0:
1180  afwTable.CovarianceMatrix2fKey.addFields(
1181  schema=schema,
1182  prefix="coord",
1183  names=["ra", "dec"],
1184  units=["rad", "rad"],
1185  diagonalOnly=(coordErrDim == 2),
1186  )
1187 
1188  if addProperMotion or addParallax:
1189  schema.addField(
1190  field="epoch",
1191  type=numpy.float64,
1192  doc="date of observation (TAI, MJD)",
1193  units="day",
1194  )
1195 
1196  if addProperMotion:
1197  schema.addField(
1198  field="pm_ra",
1199  type="Angle",
1200  doc="proper motion in the right ascension direction = dra/dt * cos(dec)",
1201  units="rad/year",
1202  )
1203  schema.addField(
1204  field="pm_dec",
1205  type="Angle",
1206  doc="proper motion in the declination direction",
1207  units="rad/year",
1208  )
1209  if properMotionErrDim not in (0, 2, 3):
1210  raise ValueError("properMotionErrDim={}; must be (0, 2, 3)".format(properMotionErrDim))
1211  if properMotionErrDim > 0:
1212  afwTable.CovarianceMatrix2fKey.addFields(
1213  schema=schema,
1214  prefix="pm",
1215  names=["ra", "dec"],
1216  units=["rad/year", "rad/year"],
1217  diagonalOnly=(properMotionErrDim == 2),
1218  )
1219  schema.addField(
1220  field="pm_flag",
1221  type="Flag",
1222  doc="Set if proper motion or proper motion error is bad",
1223  )
1224 
1225  if addParallax:
1226  schema.addField(
1227  field="parallax",
1228  type="Angle",
1229  doc="parallax",
1230  units="rad",
1231  )
1232  schema.addField(
1233  field="parallaxErr",
1234  type="Angle",
1235  doc="uncertainty in parallax",
1236  units="rad",
1237  )
1238  schema.addField(
1239  field="parallax_flag",
1240  type="Flag",
1241  doc="Set if parallax or parallax error is bad",
1242  )
1243  return schema
1244 
1245  def _calculateCircle(self, bbox, wcs):
1246  """Compute on-sky center and radius of search region.
1247 
1248  Parameters
1249  ----------
1250  bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1251  Pixel bounding box.
1252  wcs : `lsst.afw.geom.SkyWcs`
1253  WCS; used to convert pixel positions to sky coordinates.
1254 
1255  Returns
1256  -------
1257  results : `lsst.pipe.base.Struct`
1258  A Struct containing:
1259 
1260  - coord : `lsst.geom.SpherePoint`
1261  ICRS center of the search region.
1262  - radius : `lsst.geom.Angle`
1263  Radius of the search region.
1264  - bbox : `lsst.geom.Box2D`
1265  Bounding box used to compute the circle.
1266  """
1267  bbox = lsst.geom.Box2D(bbox) # make sure bbox is double and that we have a copy
1268  bbox.grow(self.config.pixelMargin)
1269  coord = wcs.pixelToSky(bbox.getCenter())
1270  radius = max(coord.separation(wcs.pixelToSky(pp)) for pp in bbox.getCorners())
1271  return pipeBase.Struct(coord=coord, radius=radius, bbox=bbox)
1272 
1273  def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None):
1274  """Return metadata about the load.
1275 
1276  This metadata is used for reloading the catalog (e.g., for
1277  reconstituting a normalised match list.
1278 
1279  Parameters
1280  ----------
1281  bbox : `lsst.geom.Box2I` or `lsst.geom.Box2D`
1282  Pixel bounding box.
1283  wcs : `lsst.afw.geom.SkyWcs`
1284  WCS; used to convert pixel positions to sky coordinates.
1285  filterName : `str`
1286  Name of camera filter, or `None` or `""` for the default
1287  filter.
1288  photoCalib : `lsst.afw.image.PhotoCalib` (optional)
1289  Calibration, or `None` if unknown.
1290  epoch : `astropy.time.Time` (optional)
1291  Epoch to which to correct proper motion and parallax,
1292  or None to not apply such corrections.
1293 
1294  Returns
1295  -------
1296  metadata : lsst.daf.base.PropertyList
1297  Metadata about the load.
1298  """
1299  circle = self._calculateCircle(bbox, wcs)
1300  return self.getMetadataCircle(circle.coord, circle.radius, filterName, photoCalib)
1301 
1302  def getMetadataCircle(self, coord, radius, filterName, photoCalib=None, epoch=None):
1303  """Return metadata about the load.
1304 
1305  This metadata is used for reloading the catalog (e.g., for
1306  reconstituting a normalised match list.
1307 
1308  Parameters
1309  ----------
1310  coord : `lsst.geom.SpherePoint`
1311  ICRS center of the search region.
1312  radius : `lsst.geom.Angle`
1313  Radius of the search region.
1314  filterName : `str`
1315  Name of camera filter, or `None` or `""` for the default
1316  filter.
1317  photoCalib : `lsst.afw.image.PhotoCalib` (optional)
1318  Calibration, or `None` if unknown.
1319  epoch : `astropy.time.Time` (optional)
1320  Epoch to which to correct proper motion and parallax,
1321  or None to not apply such corrections.
1322 
1323  Returns
1324  -------
1325  metadata : lsst.daf.base.PropertyList
1326  Metadata about the load
1327  """
1328  md = PropertyList()
1329  md.add('RA', coord.getRa().asDegrees(), 'field center in degrees')
1330  md.add('DEC', coord.getDec().asDegrees(), 'field center in degrees')
1331  md.add('RADIUS', radius.asDegrees(), 'field radius in degrees, minimum')
1332  md.add('SMATCHV', 1, 'SourceMatchVector version number')
1333  filterName = "UNKNOWN" if filterName is None else str(filterName)
1334  md.add('FILTER', filterName, 'filter name for photometric data')
1335  md.add('EPOCH', "NONE" if epoch is None else epoch, 'Epoch (TAI MJD) for catalog')
1336  return md
1337 
1338  def joinMatchListWithCatalog(self, matchCat, sourceCat):
1339  """Relink an unpersisted match list to sources and reference
1340  objects.
1341 
1342  A match list is persisted and unpersisted as a catalog of IDs
1343  produced by afw.table.packMatches(), with match metadata
1344  (as returned by the astrometry tasks) in the catalog's metadata
1345  attribute. This method converts such a match catalog into a match
1346  list, with links to source records and reference object records.
1347 
1348  Parameters
1349  ----------
1350  matchCat : `lsst.afw.table.BaseCatalog`
1351  Unperisted packed match list.
1352  ``matchCat.table.getMetadata()`` must contain match metadata,
1353  as returned by the astrometry tasks.
1354  sourceCat : `lsst.afw.table.SourceCatalog`
1355  Source catalog. As a side effect, the catalog will be sorted
1356  by ID.
1357 
1358  Returns
1359  -------
1360  matchList : `lsst.afw.table.ReferenceMatchVector`
1361  Match list.
1362  """
1363  return joinMatchListWithCatalogImpl(self, matchCat, sourceCat)
1364 
1365  def applyProperMotions(self, catalog, epoch):
1366  """Apply proper motion correction to a reference catalog.
1367 
1368  Adjust position and position error in the ``catalog``
1369  for proper motion to the specified ``epoch``,
1370  modifying the catalong in place.
1371 
1372  Parameters
1373  ----------
1374  catalog : `lsst.afw.table.SimpleCatalog`
1375  Catalog of positions, containing:
1376 
1377  - Coordinates, retrieved by the table's coordinate key.
1378  - ``coord_raErr`` : Error in Right Ascension (rad).
1379  - ``coord_decErr`` : Error in Declination (rad).
1380  - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
1381  East positive)
1382  - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
1383  - ``pm_dec`` : Proper motion in Declination (rad/yr,
1384  North positive)
1385  - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
1386  - ``epoch`` : Mean epoch of object (an astropy.time.Time)
1387  epoch : `astropy.time.Time` (optional)
1388  Epoch to which to correct proper motion and parallax,
1389  or None to not apply such corrections.
1390  """
1391  if ("epoch" not in catalog.schema or "pm_ra" not in catalog.schema or "pm_dec" not in catalog.schema):
1392  if self.config.requireProperMotion:
1393  raise RuntimeError("Proper motion correction required but not available from catalog")
1394  self.log.warn("Proper motion correction not available from catalog")
1395  return
1396  applyProperMotionsImpl(self.log, catalog, epoch)
1397 
1398 
1399 def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat):
1400  """Relink an unpersisted match list to sources and reference
1401  objects.
1402 
1403  A match list is persisted and unpersisted as a catalog of IDs
1404  produced by afw.table.packMatches(), with match metadata
1405  (as returned by the astrometry tasks) in the catalog's metadata
1406  attribute. This method converts such a match catalog into a match
1407  list, with links to source records and reference object records.
1408 
1409  Parameters
1410  ----------
1411  refObjLoader
1412  Reference object loader to use in getting reference objects
1413  matchCat : `lsst.afw.table.BaseCatalog`
1414  Unperisted packed match list.
1415  ``matchCat.table.getMetadata()`` must contain match metadata,
1416  as returned by the astrometry tasks.
1417  sourceCat : `lsst.afw.table.SourceCatalog`
1418  Source catalog. As a side effect, the catalog will be sorted
1419  by ID.
1420 
1421  Returns
1422  -------
1423  matchList : `lsst.afw.table.ReferenceMatchVector`
1424  Match list.
1425  """
1426  matchmeta = matchCat.table.getMetadata()
1427  version = matchmeta.getInt('SMATCHV')
1428  if version != 1:
1429  raise ValueError('SourceMatchVector version number is %i, not 1.' % version)
1430  filterName = matchmeta.getString('FILTER').strip()
1431  try:
1432  epoch = matchmeta.getDouble('EPOCH')
1433  except (pexExcept.NotFoundError, pexExcept.TypeError):
1434  epoch = None # Not present, or not correct type means it's not set
1435  if 'RADIUS' in matchmeta:
1436  # This is a circle style metadata, call loadSkyCircle
1437  ctrCoord = lsst.geom.SpherePoint(matchmeta.getDouble('RA'),
1438  matchmeta.getDouble('DEC'), lsst.geom.degrees)
1439  rad = matchmeta.getDouble('RADIUS') * lsst.geom.degrees
1440  refCat = refObjLoader.loadSkyCircle(ctrCoord, rad, filterName, epoch=epoch).refCat
1441  elif "INNER_UPPER_LEFT_RA" in matchmeta:
1442  # This is the sky box type (only triggers in the LoadReferenceObject class, not task)
1443  # Only the outer box is required to be loaded to get the maximum region, all filtering
1444  # will be done by the unpackMatches function, and no spatial filtering needs to be done
1445  # by the refObjLoader
1446  box = []
1447  for place in ("UPPER_LEFT", "UPPER_RIGHT", "LOWER_LEFT", "LOWER_RIGHT"):
1448  coord = lsst.geom.SpherePoint(matchmeta.getDouble(f"OUTER_{place}_RA"),
1449  matchmeta.getDouble(f"OUTER_{place}_DEC"),
1450  lsst.geom.degrees).getVector()
1451  box.append(coord)
1452  outerBox = sphgeom.ConvexPolygon(box)
1453  refCat = refObjLoader.loadRegion(outerBox, filterName=filterName, epoch=epoch).refCat
1454 
1455  refCat.sort()
1456  sourceCat.sort()
1457  return afwTable.unpackMatches(matchCat, refCat, sourceCat)
1458 
1459 
1460 def applyProperMotionsImpl(log, catalog, epoch):
1461  """Apply proper motion correction to a reference catalog.
1462 
1463  Adjust position and position error in the ``catalog``
1464  for proper motion to the specified ``epoch``,
1465  modifying the catalong in place.
1466 
1467  Parameters
1468  ----------
1469  log : `lsst.log.log`
1470  log object to write to
1471  catalog : `lsst.afw.table.SimpleCatalog`
1472  Catalog of positions, containing:
1473 
1474  - Coordinates, retrieved by the table's coordinate key.
1475  - ``coord_raErr`` : Error in Right Ascension (rad).
1476  - ``coord_decErr`` : Error in Declination (rad).
1477  - ``pm_ra`` : Proper motion in Right Ascension (rad/yr,
1478  East positive)
1479  - ``pm_raErr`` : Error in ``pm_ra`` (rad/yr), optional.
1480  - ``pm_dec`` : Proper motion in Declination (rad/yr,
1481  North positive)
1482  - ``pm_decErr`` : Error in ``pm_dec`` (rad/yr), optional.
1483  - ``epoch`` : Mean epoch of object (an astropy.time.Time)
1484  epoch : `astropy.time.Time` (optional)
1485  Epoch to which to correct proper motion and parallax,
1486  or None to not apply such corrections.
1487  """
1488  if "epoch" not in catalog.schema or "pm_ra" not in catalog.schema or "pm_dec" not in catalog.schema:
1489  log.warn("Proper motion correction not available from catalog")
1490  return
1491  if not catalog.isContiguous():
1492  raise RuntimeError("Catalog must be contiguous")
1493  catEpoch = astropy.time.Time(catalog["epoch"], scale="tai", format="mjd")
1494  log.debug("Correcting reference catalog for proper motion to %r", epoch)
1495  # Use `epoch.tai` to make sure the time difference is in TAI
1496  timeDiffsYears = (epoch.tai - catEpoch).to(astropy.units.yr).value
1497  coordKey = catalog.table.getCoordKey()
1498  # Compute the offset of each object due to proper motion
1499  # as components of the arc of a great circle along RA and Dec
1500  pmRaRad = catalog["pm_ra"]
1501  pmDecRad = catalog["pm_dec"]
1502  offsetsRaRad = pmRaRad*timeDiffsYears
1503  offsetsDecRad = pmDecRad*timeDiffsYears
1504  # Compute the corresponding bearing and arc length of each offset
1505  # due to proper motion, and apply the offset
1506  # The factor of 1e6 for computing bearing is intended as
1507  # a reasonable scale for typical values of proper motion
1508  # in order to avoid large errors for small values of proper motion;
1509  # using the offsets is another option, but it can give
1510  # needlessly large errors for short duration
1511  offsetBearingsRad = numpy.arctan2(pmDecRad*1e6, pmRaRad*1e6)
1512  offsetAmountsRad = numpy.hypot(offsetsRaRad, offsetsDecRad)
1513  for record, bearingRad, amountRad in zip(catalog, offsetBearingsRad, offsetAmountsRad):
1514  record.set(coordKey,
1515  record.get(coordKey).offset(bearing=bearingRad*lsst.geom.radians,
1516  amount=amountRad*lsst.geom.radians))
1517  # Increase error in RA and Dec based on error in proper motion
1518  if "coord_raErr" in catalog.schema:
1519  catalog["coord_raErr"] = numpy.hypot(catalog["coord_raErr"],
1520  catalog["pm_raErr"]*timeDiffsYears)
1521  if "coord_decErr" in catalog.schema:
1522  catalog["coord_decErr"] = numpy.hypot(catalog["coord_decErr"],
1523  catalog["pm_decErr"]*timeDiffsYears)
lsst::sphgeom::Box
lsst::sphgeom::ConvexPolygon
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.getMetadataBox
def getMetadataBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None)
Definition: loadReferenceObjects.py:1273
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.addFluxAliases
def addFluxAliases(refCat, defaultFilter, filterReferenceMap)
Definition: loadReferenceObjects.py:587
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.getMetadataCircle
def getMetadataCircle(self, coord, radius, filterName, photoCalib=None, epoch=None)
Definition: loadReferenceObjects.py:1302
lsst::sphgeom::Circle
lsst::log::Log::getDefaultLogger
static Log getDefaultLogger()
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader._makeBoxRegion
def _makeBoxRegion(BBox, wcs, BBoxPadding)
Definition: loadReferenceObjects.py:226
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsConfig
Definition: loadReferenceObjects.py:765
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.loadRegion
def loadRegion(self, region, filtFunc=None, filterName=None, epoch=None)
Definition: loadReferenceObjects.py:326
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask._trimToBBox
def _trimToBBox(refCat, bbox, wcs)
Definition: loadReferenceObjects.py:1006
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask
Abstract base class to load objects from reference catalogs.
Definition: loadReferenceObjects.py:801
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader
Definition: loadReferenceObjects.py:195
lsst::daf::base::PropertyList
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.__init__
def __init__(self, dataIds, refCats, config, log=None)
Definition: loadReferenceObjects.py:205
lsst::meas::algorithms.loadReferenceObjects.isOldFluxField
def isOldFluxField(name, units)
Definition: loadReferenceObjects.py:46
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.refCats
refCats
Definition: loadReferenceObjects.py:221
lsst::meas::algorithms.loadReferenceObjects.getRefFluxField
def getRefFluxField(schema, filterName=None)
Definition: loadReferenceObjects.py:691
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.loadSkyCircle
def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None)
Definition: loadReferenceObjects.py:437
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.dataIds
dataIds
Definition: loadReferenceObjects.py:220
lsst::meas::algorithms.loadReferenceObjects.getFormatVersionFromRefCat
def getFormatVersionFromRefCat(refCat)
Definition: loadReferenceObjects.py:66
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.butler
butler
Definition: loadReferenceObjects.py:901
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.config
config
Definition: loadReferenceObjects.py:223
lsst::meas::algorithms.loadReferenceObjects.applyProperMotionsImpl
def applyProperMotionsImpl(log, catalog, epoch)
Definition: loadReferenceObjects.py:1460
lsst::meas::algorithms.loadReferenceObjects.joinMatchListWithCatalogImpl
def joinMatchListWithCatalogImpl(refObjLoader, matchCat, sourceCat)
Definition: loadReferenceObjects.py:1399
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.joinMatchListWithCatalog
def joinMatchListWithCatalog(self, matchCat, sourceCat)
Definition: loadReferenceObjects.py:476
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask._calculateCircle
def _calculateCircle(self, bbox, wcs)
Definition: loadReferenceObjects.py:1245
lsst::meas::algorithms.loadReferenceObjects.convertToNanojansky
def convertToNanojansky(catalog, log, doConvert=True)
Definition: loadReferenceObjects.py:89
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.__init__
def __init__(self, butler=None, *args, **kwargs)
Definition: loadReferenceObjects.py:892
lsst::sphgeom::Angle
lsst::afw::table::SchemaMapper
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.getMetadataCircle
def getMetadataCircle(coord, radius, filterName, photoCalib=None, epoch=None)
Definition: loadReferenceObjects.py:552
lsst::meas::algorithms.loadReferenceObjects._FilterCatalog
Definition: loadReferenceObjects.py:151
lsst::meas::algorithms.loadReferenceObjects._FilterCatalog.region
region
Definition: loadReferenceObjects.py:162
lsst::afw::table
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.loadPixelBox
def loadPixelBox(self, bbox, wcs, filterName=None, epoch=None, photoCalib=None, bboxPadding=100)
Definition: loadReferenceObjects.py:255
lsst::meas::algorithms.loadReferenceObjects.getRefFluxKeys
def getRefFluxKeys(schema, filterName=None)
Definition: loadReferenceObjects.py:732
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.log
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Definition: loadReferenceObjects.py:222
lsst::geom
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.joinMatchListWithCatalog
def joinMatchListWithCatalog(self, matchCat, sourceCat)
Definition: loadReferenceObjects.py:1338
lsst::daf::base
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.applyProperMotions
def applyProperMotions(self, catalog, epoch)
Definition: loadReferenceObjects.py:1365
lsst::meas::algorithms.loadReferenceObjects._FilterCatalog.__init__
def __init__(self, region)
Definition: loadReferenceObjects.py:161
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.loadSkyCircle
def loadSkyCircle(self, ctrCoord, radius, filterName=None, epoch=None, centroids=False)
Definition: loadReferenceObjects.py:965
lsst::afw::table::Field
Point< int, 2 >
lsst::afw::table::SimpleTable::makeMinimalSchema
static Schema makeMinimalSchema()
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.loadPixelBox
def loadPixelBox(self, bbox, wcs, filterName=None, photoCalib=None, epoch=None)
Definition: loadReferenceObjects.py:904
lsst::pex::exceptions
lsst::geom::SpherePoint
lsst::meas::algorithms.loadReferenceObjects.hasNanojanskyFluxUnits
def hasNanojanskyFluxUnits(schema)
Definition: loadReferenceObjects.py:57
lsst::geom::Box2D
lsst::pipe::base
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.remapReferenceCatalogSchema
def remapReferenceCatalogSchema(refCat, *filterNameList=None, position=False, photometric=False)
Definition: loadReferenceObjects.py:633
lsst::meas::algorithms.loadReferenceObjects.ReferenceObjectLoader.getMetadataBox
def getMetadataBox(cls, bbox, wcs, filterName=None, photoCalib=None, epoch=None, bboxPadding=100)
Definition: loadReferenceObjects.py:504
lsst::meas::algorithms.loadReferenceObjects.LoadReferenceObjectsTask.makeMinimalSchema
def makeMinimalSchema(filterNameList, *addCentroid=False, addIsPhotometric=False, addIsResolved=False, addIsVariable=False, coordErrDim=2, addProperMotion=False, properMotionErrDim=2, addParallax=False)
Definition: loadReferenceObjects.py:1086
lsst::log
Extent< double, 2 >
lsst::afw::table::SortedCatalogT
lsst::meas::algorithms.loadReferenceObjects._FilterCatalog.__call__
def __call__(self, refCat, catRegion)
Definition: loadReferenceObjects.py:164