Coverage for python/lsst/fgcmcal/fgcmLoadReferenceCatalog.py : 17%

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1# See COPYRIGHT file at the top of the source tree.
2#
3# This file is part of fgcmcal.
4#
5# Developed for the LSST Data Management System.
6# This product includes software developed by the LSST Project
7# (https://www.lsst.org).
8# See the COPYRIGHT file at the top-level directory of this distribution
9# for details of code ownership.
10#
11# This program is free software: you can redistribute it and/or modify
12# it under the terms of the GNU General Public License as published by
13# the Free Software Foundation, either version 3 of the License, or
14# (at your option) any later version.
15#
16# This program is distributed in the hope that it will be useful,
17# but WITHOUT ANY WARRANTY; without even the implied warranty of
18# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19# GNU General Public License for more details.
20#
21# You should have received a copy of the GNU General Public License
22# along with this program. If not, see <https://www.gnu.org/licenses/>.
23"""Load reference catalog objects for input to FGCM.
25This task will load multi-band reference objects and apply color terms (if
26configured). This wrapper around LoadReferenceObjects task also allows loading
27by healpix pixel (the native pixelization of fgcm), and is self-contained so
28the task can be called by third-party code.
29"""
31import numpy as np
32import healpy as hp
33from astropy import units
35import lsst.pex.config as pexConfig
36import lsst.pipe.base as pipeBase
37from lsst.meas.algorithms import LoadIndexedReferenceObjectsTask, ReferenceSourceSelectorTask
38from lsst.meas.algorithms import getRefFluxField
39from lsst.pipe.tasks.colorterms import ColortermLibrary
40from lsst.afw.image import abMagErrFromFluxErr
41from lsst.meas.algorithms import ReferenceObjectLoader
43import lsst.geom
45__all__ = ['FgcmLoadReferenceCatalogConfig', 'FgcmLoadReferenceCatalogTask']
48class FgcmLoadReferenceCatalogConfig(pexConfig.Config):
49 """Config for FgcmLoadReferenceCatalogTask"""
51 refObjLoader = pexConfig.ConfigurableField(
52 target=LoadIndexedReferenceObjectsTask,
53 doc="Reference object loader for photometry",
54 )
55 refFilterMap = pexConfig.DictField(
56 doc="Mapping from camera 'filterName' to reference filter name.",
57 keytype=str,
58 itemtype=str,
59 default={},
60 )
61 applyColorTerms = pexConfig.Field(
62 doc=("Apply photometric color terms to reference stars?"
63 "Requires that colorterms be set to a ColorTermLibrary"),
64 dtype=bool,
65 default=True
66 )
67 colorterms = pexConfig.ConfigField(
68 doc="Library of photometric reference catalog name to color term dict.",
69 dtype=ColortermLibrary,
70 )
71 referenceSelector = pexConfig.ConfigurableField(
72 target=ReferenceSourceSelectorTask,
73 doc="Selection of reference sources",
74 )
76 def validate(self):
77 super().validate()
78 if not self.refFilterMap:
79 msg = 'Must set refFilterMap'
80 raise pexConfig.FieldValidationError(FgcmLoadReferenceCatalogConfig.refFilterMap, self, msg)
81 if self.applyColorTerms and len(self.colorterms.data) == 0:
82 msg = "applyColorTerms=True requires the `colorterms` field be set to a ColortermLibrary."
83 raise pexConfig.FieldValidationError(FgcmLoadReferenceCatalogConfig.colorterms, self, msg)
86class FgcmLoadReferenceCatalogTask(pipeBase.Task):
87 """
88 Load multi-band reference objects from a reference catalog.
90 Parameters
91 ----------
92 butler: `lsst.daf.persistence.Butler`
93 Data butler for reading catalogs
94 """
95 ConfigClass = FgcmLoadReferenceCatalogConfig
96 _DefaultName = 'fgcmLoadReferenceCatalog'
98 def __init__(self, butler=None, refObjLoader=None, **kwargs):
99 """Construct an FgcmLoadReferenceCatalogTask
101 Parameters
102 ----------
103 butler: `lsst.daf.persistence.Buter`
104 Data butler for reading catalogs.
105 """
106 pipeBase.Task.__init__(self, **kwargs)
107 if refObjLoader is None and butler is not None:
108 self.makeSubtask('refObjLoader', butler=butler)
109 else:
110 self.refObjLoader = refObjLoader
112 self.makeSubtask('referenceSelector')
113 self._fluxFilters = None
114 self._fluxFields = None
115 self._referenceFilter = None
117 def getFgcmReferenceStarsHealpix(self, nside, pixel, filterList, nest=False):
118 """
119 Get a reference catalog that overlaps a healpix pixel, using multiple
120 filters. In addition, apply colorterms if available.
122 Return format is a numpy recarray for use with fgcm, with the format:
124 dtype = ([('ra', `np.float64`),
125 ('dec', `np.float64`),
126 ('refMag', `np.float32`, len(filterList)),
127 ('refMagErr', `np.float32`, len(filterList)])
129 Reference magnitudes (AB) will be 99 for non-detections.
131 Parameters
132 ----------
133 nside: `int`
134 Healpix nside of pixel to load
135 pixel: `int`
136 Healpix pixel of pixel to load
137 filterList: `list`
138 list of `str` of camera filter names.
139 nest: `bool`, optional
140 Is the pixel in nest format? Default is False.
142 Returns
143 -------
144 fgcmRefCat: `np.recarray`
145 """
147 # Determine the size of the sky circle to load
148 theta, phi = hp.pix2ang(nside, pixel, nest=nest)
149 center = lsst.geom.SpherePoint(phi * lsst.geom.radians, (np.pi/2. - theta) * lsst.geom.radians)
151 corners = hp.boundaries(nside, pixel, step=1, nest=nest)
152 theta_phi = hp.vec2ang(np.transpose(corners))
154 radius = 0.0 * lsst.geom.radians
155 for ctheta, cphi in zip(*theta_phi):
156 rad = center.separation(lsst.geom.SpherePoint(cphi * lsst.geom.radians,
157 (np.pi/2. - ctheta) * lsst.geom.radians))
158 if (rad > radius):
159 radius = rad
161 # Load the fgcm-format reference catalog
162 fgcmRefCat = self.getFgcmReferenceStarsSkyCircle(center.getRa().asDegrees(),
163 center.getDec().asDegrees(),
164 radius.asDegrees(),
165 filterList)
166 catPix = hp.ang2pix(nside, np.radians(90.0 - fgcmRefCat['dec']),
167 np.radians(fgcmRefCat['ra']), nest=nest)
169 inPix, = np.where(catPix == pixel)
171 return fgcmRefCat[inPix]
173 def getFgcmReferenceStarsSkyCircle(self, ra, dec, radius, filterList):
174 """
175 Get a reference catalog that overlaps a circular sky region, using
176 multiple filters. In addition, apply colorterms if available.
178 Return format is a numpy recarray for use with fgcm.
180 dtype = ([('ra', `np.float64`),
181 ('dec', `np.float64`),
182 ('refMag', `np.float32`, len(filterList)),
183 ('refMagErr', `np.float32`, len(filterList)])
185 Reference magnitudes (AB) will be 99 for non-detections.
187 Parameters
188 ----------
189 ra: `float`
190 ICRS right ascension, degrees.
191 dec: `float`
192 ICRS declination, degrees.
193 radius: `float`
194 Radius to search, degrees.
195 filterList: `list`
196 list of `str` of camera filter names.
198 Returns
199 -------
200 fgcmRefCat: `np.recarray`
201 """
203 center = lsst.geom.SpherePoint(ra * lsst.geom.degrees, dec * lsst.geom.degrees)
205 # Check if we haev previously cached values for the fluxFields
206 if self._fluxFilters is None or self._fluxFilters != filterList:
207 self._determine_flux_fields(center, filterList)
209 skyCircle = self.refObjLoader.loadSkyCircle(center,
210 radius * lsst.geom.degrees,
211 self._referenceFilter)
213 if not skyCircle.refCat.isContiguous():
214 refCat = skyCircle.refCat.copy(deep=True)
215 else:
216 refCat = skyCircle.refCat
218 # Select on raw (uncorrected) catalog, where the errors should make more sense
219 goodSources = self.referenceSelector.selectSources(refCat)
220 selected = goodSources.selected
222 fgcmRefCat = np.zeros(np.sum(selected), dtype=[('ra', 'f8'),
223 ('dec', 'f8'),
224 ('refMag', 'f4', len(filterList)),
225 ('refMagErr', 'f4', len(filterList))])
226 if fgcmRefCat.size == 0:
227 # Return an empty catalog if we don't have any selected sources
228 return fgcmRefCat
230 # The ra/dec native Angle format is radians
231 # We determine the conversion from the native units (typically
232 # radians) to degrees for the first observation. This allows us
233 # to treate ra/dec as numpy arrays rather than Angles, which would
234 # be approximately 600x slower.
236 conv = refCat[0]['coord_ra'].asDegrees() / float(refCat[0]['coord_ra'])
237 fgcmRefCat['ra'] = refCat['coord_ra'][selected] * conv
238 fgcmRefCat['dec'] = refCat['coord_dec'][selected] * conv
240 # Default (unset) values are 99.0
241 fgcmRefCat['refMag'][:, :] = 99.0
242 fgcmRefCat['refMagErr'][:, :] = 99.0
244 if self.config.applyColorTerms:
245 if isinstance(self.refObjLoader, ReferenceObjectLoader):
246 # Gen3
247 refCatName = self.refObjLoader.config.value.ref_dataset_name
248 else:
249 # Gen2
250 refCatName = self.refObjLoader.ref_dataset_name
252 for i, (filterName, fluxField) in enumerate(zip(self._fluxFilters, self._fluxFields)):
253 if fluxField is None:
254 continue
256 self.log.debug("Applying color terms for filtername=%r" % (filterName))
258 colorterm = self.config.colorterms.getColorterm(
259 filterName=filterName, photoCatName=refCatName, doRaise=True)
261 refMag, refMagErr = colorterm.getCorrectedMagnitudes(refCat, filterName)
263 # nan_to_num replaces nans with zeros, and this ensures that we select
264 # magnitudes that both filter out nans and are not very large (corresponding
265 # to very small fluxes), as "99" is a common sentinel for illegal magnitudes.
267 good, = np.where((np.nan_to_num(refMag[selected]) < 90.0)
268 & (np.nan_to_num(refMagErr[selected]) < 90.0)
269 & (np.nan_to_num(refMagErr[selected]) > 0.0))
271 fgcmRefCat['refMag'][good, i] = refMag[selected][good]
272 fgcmRefCat['refMagErr'][good, i] = refMagErr[selected][good]
274 else:
275 # No colorterms
277 for i, (filterName, fluxField) in enumerate(zip(self._fluxFilters, self._fluxFields)):
278 # nan_to_num replaces nans with zeros, and this ensures that we select
279 # fluxes that both filter out nans and are positive.
280 good, = np.where((np.nan_to_num(refCat[fluxField][selected]) > 0.0)
281 & (np.nan_to_num(refCat[fluxField+'Err'][selected]) > 0.0))
282 refMag = (refCat[fluxField][selected][good] * units.nJy).to_value(units.ABmag)
283 refMagErr = abMagErrFromFluxErr(refCat[fluxField+'Err'][selected][good],
284 refCat[fluxField][selected][good])
285 fgcmRefCat['refMag'][good, i] = refMag
286 fgcmRefCat['refMagErr'][good, i] = refMagErr
288 return fgcmRefCat
290 def _determine_flux_fields(self, center, filterList):
291 """
292 Determine the flux field names for a reference catalog.
294 Will set self._fluxFields, self._referenceFilter.
296 Parameters
297 ----------
298 center: `lsst.geom.SpherePoint`
299 The center around which to load test sources.
300 filterList: `list`
301 list of `str` of camera filter names.
302 """
304 # Record self._fluxFilters for checks on subsequent calls
305 self._fluxFilters = filterList
307 # Search for a good filter to use to load the reference catalog
308 # via the refObjLoader task which requires a valid filterName
309 foundReferenceFilter = False
310 for filterName in filterList:
311 refFilterName = self.config.refFilterMap.get(filterName)
312 if refFilterName is None:
313 continue
315 try:
316 results = self.refObjLoader.loadSkyCircle(center,
317 0.05 * lsst.geom.degrees,
318 refFilterName)
319 foundReferenceFilter = True
320 self._referenceFilter = refFilterName
321 break
322 except RuntimeError:
323 # This just means that the filterName wasn't listed
324 # in the reference catalog. This is okay.
325 pass
327 if not foundReferenceFilter:
328 raise RuntimeError("Could not find any valid flux field(s) %s" %
329 (", ".join(filterList)))
331 # Retrieve all the fluxField names
332 self._fluxFields = []
333 for filterName in filterList:
334 fluxField = None
336 refFilterName = self.config.refFilterMap.get(filterName)
338 if refFilterName is not None:
339 try:
340 fluxField = getRefFluxField(results.refCat.schema, filterName=refFilterName)
341 except RuntimeError:
342 # This flux field isn't available. Set to None
343 fluxField = None
345 if fluxField is None:
346 self.log.warn(f'No reference flux field for camera filter {filterName}')
348 self._fluxFields.append(fluxField)