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
41import lsst.geom
43__all__ = ['FgcmLoadReferenceCatalogConfig', 'FgcmLoadReferenceCatalogTask']
46class FgcmLoadReferenceCatalogConfig(pexConfig.Config):
47 """Config for FgcmLoadReferenceCatalogTask"""
49 refObjLoader = pexConfig.ConfigurableField(
50 target=LoadIndexedReferenceObjectsTask,
51 doc="Reference object loader for photometry",
52 )
53 refFilterMap = pexConfig.DictField(
54 doc="Mapping from camera 'filterName' to reference filter name.",
55 keytype=str,
56 itemtype=str,
57 default={},
58 )
59 applyColorTerms = pexConfig.Field(
60 doc=("Apply photometric color terms to reference stars?"
61 "Requires that colorterms be set to a ColorTermLibrary"),
62 dtype=bool,
63 default=True
64 )
65 colorterms = pexConfig.ConfigField(
66 doc="Library of photometric reference catalog name to color term dict.",
67 dtype=ColortermLibrary,
68 )
69 referenceSelector = pexConfig.ConfigurableField(
70 target=ReferenceSourceSelectorTask,
71 doc="Selection of reference sources",
72 )
74 def validate(self):
75 super().validate()
76 if not self.refFilterMap:
77 msg = 'Must set refFilterMap'
78 raise pexConfig.FieldValidationError(FgcmLoadReferenceCatalogConfig.refFilterMap, self, msg)
79 if self.applyColorTerms and len(self.colorterms.data) == 0:
80 msg = "applyColorTerms=True requires the `colorterms` field be set to a ColortermLibrary."
81 raise pexConfig.FieldValidationError(FgcmLoadReferenceCatalogConfig.colorterms, self, msg)
84class FgcmLoadReferenceCatalogTask(pipeBase.Task):
85 """
86 Load multi-band reference objects from a reference catalog.
88 Parameters
89 ----------
90 butler: `lsst.daf.persistence.Butler`
91 Data butler for reading catalogs
92 """
93 ConfigClass = FgcmLoadReferenceCatalogConfig
94 _DefaultName = 'fgcmLoadReferenceCatalog'
96 def __init__(self, butler, *args, **kwargs):
97 """Construct an FgcmLoadReferenceCatalogTask
99 Parameters
100 ----------
101 butler: `lsst.daf.persistence.Buter`
102 Data butler for reading catalogs.
103 """
104 pipeBase.Task.__init__(self, *args, **kwargs)
105 self.butler = butler
106 self.makeSubtask('refObjLoader', butler=butler)
107 self.makeSubtask('referenceSelector')
108 self._fluxFilters = None
109 self._fluxFields = None
110 self._referenceFilter = None
112 def getFgcmReferenceStarsHealpix(self, nside, pixel, filterList, nest=False):
113 """
114 Get a reference catalog that overlaps a healpix pixel, using multiple
115 filters. In addition, apply colorterms if available.
117 Return format is a numpy recarray for use with fgcm, with the format:
119 dtype = ([('ra', `np.float64`),
120 ('dec', `np.float64`),
121 ('refMag', `np.float32`, len(filterList)),
122 ('refMagErr', `np.float32`, len(filterList)])
124 Reference magnitudes (AB) will be 99 for non-detections.
126 Parameters
127 ----------
128 nside: `int`
129 Healpix nside of pixel to load
130 pixel: `int`
131 Healpix pixel of pixel to load
132 filterList: `list`
133 list of `str` of camera filter names.
134 nest: `bool`, optional
135 Is the pixel in nest format? Default is False.
137 Returns
138 -------
139 fgcmRefCat: `np.recarray`
140 """
142 # Determine the size of the sky circle to load
143 theta, phi = hp.pix2ang(nside, pixel, nest=nest)
144 center = lsst.geom.SpherePoint(phi * lsst.geom.radians, (np.pi/2. - theta) * lsst.geom.radians)
146 corners = hp.boundaries(nside, pixel, step=1, nest=nest)
147 theta_phi = hp.vec2ang(np.transpose(corners))
149 radius = 0.0 * lsst.geom.radians
150 for ctheta, cphi in zip(*theta_phi):
151 rad = center.separation(lsst.geom.SpherePoint(cphi * lsst.geom.radians,
152 (np.pi/2. - ctheta) * lsst.geom.radians))
153 if (rad > radius):
154 radius = rad
156 # Load the fgcm-format reference catalog
157 fgcmRefCat = self.getFgcmReferenceStarsSkyCircle(center.getRa().asDegrees(),
158 center.getDec().asDegrees(),
159 radius.asDegrees(),
160 filterList)
161 catPix = hp.ang2pix(nside, np.radians(90.0 - fgcmRefCat['dec']),
162 np.radians(fgcmRefCat['ra']), nest=nest)
164 inPix, = np.where(catPix == pixel)
166 return fgcmRefCat[inPix]
168 def getFgcmReferenceStarsSkyCircle(self, ra, dec, radius, filterList):
169 """
170 Get a reference catalog that overlaps a circular sky region, using
171 multiple filters. In addition, apply colorterms if available.
173 Return format is a numpy recarray for use with fgcm.
175 dtype = ([('ra', `np.float64`),
176 ('dec', `np.float64`),
177 ('refMag', `np.float32`, len(filterList)),
178 ('refMagErr', `np.float32`, len(filterList)])
180 Reference magnitudes (AB) will be 99 for non-detections.
182 Parameters
183 ----------
184 ra: `float`
185 ICRS right ascension, degrees.
186 dec: `float`
187 ICRS declination, degrees.
188 radius: `float`
189 Radius to search, degrees.
190 filterList: `list`
191 list of `str` of camera filter names.
193 Returns
194 -------
195 fgcmRefCat: `np.recarray`
196 """
198 center = lsst.geom.SpherePoint(ra * lsst.geom.degrees, dec * lsst.geom.degrees)
200 # Check if we haev previously cached values for the fluxFields
201 if self._fluxFilters is None or self._fluxFilters != filterList:
202 self._determine_flux_fields(center, filterList)
204 skyCircle = self.refObjLoader.loadSkyCircle(center,
205 radius * lsst.geom.degrees,
206 self._referenceFilter)
208 if not skyCircle.refCat.isContiguous():
209 refCat = skyCircle.refCat.copy(deep=True)
210 else:
211 refCat = skyCircle.refCat
213 # Select on raw (uncorrected) catalog, where the errors should make more sense
214 goodSources = self.referenceSelector.selectSources(refCat)
215 selected = goodSources.selected
217 fgcmRefCat = np.zeros(np.sum(selected), dtype=[('ra', 'f8'),
218 ('dec', 'f8'),
219 ('refMag', 'f4', len(filterList)),
220 ('refMagErr', 'f4', len(filterList))])
221 if fgcmRefCat.size == 0:
222 # Return an empty catalog if we don't have any selected sources
223 return fgcmRefCat
225 # The ra/dec native Angle format is radians
226 # We determine the conversion from the native units (typically
227 # radians) to degrees for the first observation. This allows us
228 # to treate ra/dec as numpy arrays rather than Angles, which would
229 # be approximately 600x slower.
231 conv = refCat[0]['coord_ra'].asDegrees() / float(refCat[0]['coord_ra'])
232 fgcmRefCat['ra'] = refCat['coord_ra'][selected] * conv
233 fgcmRefCat['dec'] = refCat['coord_dec'][selected] * conv
235 # Default (unset) values are 99.0
236 fgcmRefCat['refMag'][:, :] = 99.0
237 fgcmRefCat['refMagErr'][:, :] = 99.0
239 if self.config.applyColorTerms:
240 try:
241 refCatName = self.refObjLoader.ref_dataset_name
242 except AttributeError:
243 # NOTE: we need this try:except: block in place until we've
244 # completely removed a.net support
245 raise RuntimeError("Cannot perform colorterm corrections with a.net refcats.")
247 for i, (filterName, fluxField) in enumerate(zip(self._fluxFilters, self._fluxFields)):
248 if fluxField is None:
249 continue
251 self.log.debug("Applying color terms for filtername=%r" % (filterName))
253 colorterm = self.config.colorterms.getColorterm(
254 filterName=filterName, photoCatName=refCatName, doRaise=True)
256 refMag, refMagErr = colorterm.getCorrectedMagnitudes(refCat, filterName)
258 # nan_to_num replaces nans with zeros, and this ensures that we select
259 # magnitudes that both filter out nans and are not very large (corresponding
260 # to very small fluxes), as "99" is a common sentinel for illegal magnitudes.
262 good, = np.where((np.nan_to_num(refMag[selected]) < 90.0) &
263 (np.nan_to_num(refMagErr[selected]) < 90.0) &
264 (np.nan_to_num(refMagErr[selected]) > 0.0))
266 fgcmRefCat['refMag'][good, i] = refMag[selected][good]
267 fgcmRefCat['refMagErr'][good, i] = refMagErr[selected][good]
269 else:
270 # No colorterms
272 # TODO: need to use Jy here until RFC-549 is completed and refcats return nanojansky
274 for i, (filterName, fluxField) in enumerate(zip(self._fluxFilters, self._fluxFields)):
275 # nan_to_num replaces nans with zeros, and this ensures that we select
276 # fluxes that both filter out nans and are positive.
277 good, = np.where((np.nan_to_num(refCat[fluxField][selected]) > 0.0) &
278 (np.nan_to_num(refCat[fluxField+'Err'][selected]) > 0.0))
279 refMag = (refCat[fluxField][selected][good] * units.Jy).to_value(units.ABmag)
280 refMagErr = abMagErrFromFluxErr(refCat[fluxField+'Err'][selected][good],
281 refCat[fluxField][selected][good])
282 fgcmRefCat['refMag'][good, i] = refMag
283 fgcmRefCat['refMagErr'][good, i] = refMagErr
285 return fgcmRefCat
287 def _determine_flux_fields(self, center, filterList):
288 """
289 Determine the flux field names for a reference catalog.
291 Will set self._fluxFields, self._referenceFilter.
293 Parameters
294 ----------
295 center: `lsst.geom.SpherePoint`
296 The center around which to load test sources.
297 filterList: `list`
298 list of `str` of camera filter names.
299 """
301 # Record self._fluxFilters for checks on subsequent calls
302 self._fluxFilters = filterList
304 # Search for a good filter to use to load the reference catalog
305 # via the refObjLoader task which requires a valid filterName
306 foundReferenceFilter = False
307 for filterName in filterList:
308 refFilterName = self.config.refFilterMap.get(filterName)
309 if refFilterName is None:
310 continue
312 try:
313 results = self.refObjLoader.loadSkyCircle(center,
314 0.05 * lsst.geom.degrees,
315 refFilterName)
316 foundReferenceFilter = True
317 self._referenceFilter = refFilterName
318 break
319 except RuntimeError:
320 # This just means that the filterName wasn't listed
321 # in the reference catalog. This is okay.
322 pass
324 if not foundReferenceFilter:
325 raise RuntimeError("Could not find any valid flux field(s) %s" %
326 (", ".join(filterList)))
328 # Retrieve all the fluxField names
329 self._fluxFields = []
330 for filterName in filterList:
331 fluxField = None
333 refFilterName = self.config.refFilterMap.get(filterName)
335 if refFilterName is not None:
336 try:
337 fluxField = getRefFluxField(results.refCat.schema, filterName=refFilterName)
338 except RuntimeError:
339 # This flux field isn't available. Set to None
340 fluxField = None
342 if fluxField is None:
343 self.log.warn(f'No reference flux field for camera filter {filterName}')
345 self._fluxFields.append(fluxField)