Coverage for python/lsst/fgcmcal/fgcmBuildStars.py: 11%

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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"""Build star observations for input to FGCM. 

24 

25This task finds all the visits and calexps in a repository (or a subset 

26based on command line parameters) and extract all the potential calibration 

27stars for input into fgcm. This task additionally uses fgcm to match 

28star observations into unique stars, and performs as much cleaning of 

29the input catalog as possible. 

30""" 

31 

32import time 

33 

34import numpy as np 

35 

36import lsst.pex.config as pexConfig 

37import lsst.pipe.base as pipeBase 

38import lsst.afw.table as afwTable 

39 

40from .fgcmBuildStarsBase import FgcmBuildStarsConfigBase, FgcmBuildStarsRunner, FgcmBuildStarsBaseTask 

41from .utilities import computeApproxPixelAreaFields 

42 

43__all__ = ['FgcmBuildStarsConfig', 'FgcmBuildStarsTask'] 

44 

45 

46class FgcmBuildStarsConfig(FgcmBuildStarsConfigBase): 

47 """Config for FgcmBuildStarsTask""" 

48 

49 referenceCCD = pexConfig.Field( 

50 doc="Reference CCD for scanning visits", 

51 dtype=int, 

52 default=13, 

53 ) 

54 checkAllCcds = pexConfig.Field( 

55 doc=("Check repo for all CCDs for each visit specified. To be used when the " 

56 "full set of ids (visit/ccd) are not specified on the command line. For " 

57 "Gen2, specifying one ccd and setting checkAllCcds=True is significantly " 

58 "faster than the alternatives."), 

59 dtype=bool, 

60 default=True, 

61 ) 

62 

63 def setDefaults(self): 

64 super().setDefaults() 

65 

66 sourceSelector = self.sourceSelector["science"] 

67 

68 # The names here correspond to raw src catalogs, which differ 

69 # from the post-transformed sourceTable_visit catalogs. 

70 # Therefore, field and flag names cannot be easily 

71 # derived from the base config class. 

72 fluxFlagName = self.instFluxField[0: -len('instFlux')] + 'flag' 

73 sourceSelector.flags.bad = ['base_PixelFlags_flag_edge', 

74 'base_PixelFlags_flag_interpolatedCenter', 

75 'base_PixelFlags_flag_saturatedCenter', 

76 'base_PixelFlags_flag_crCenter', 

77 'base_PixelFlags_flag_bad', 

78 'base_PixelFlags_flag_interpolated', 

79 'base_PixelFlags_flag_saturated', 

80 'slot_Centroid_flag', 

81 fluxFlagName] 

82 

83 if self.doSubtractLocalBackground: 

84 localBackgroundFlagName = self.localBackgroundFluxField[0: -len('instFlux')] + 'flag' 

85 sourceSelector.flags.bad.append(localBackgroundFlagName) 

86 

87 sourceSelector.signalToNoise.fluxField = self.instFluxField 

88 sourceSelector.signalToNoise.errField = self.instFluxField + 'Err' 

89 

90 

91class FgcmBuildStarsTask(FgcmBuildStarsBaseTask): 

92 """ 

93 Build stars for the FGCM global calibration, using src catalogs. 

94 """ 

95 ConfigClass = FgcmBuildStarsConfig 

96 RunnerClass = FgcmBuildStarsRunner 

97 _DefaultName = "fgcmBuildStars" 

98 

99 @classmethod 

100 def _makeArgumentParser(cls): 

101 """Create an argument parser""" 

102 parser = pipeBase.ArgumentParser(name=cls._DefaultName) 

103 parser.add_id_argument("--id", "src", help="Data ID, e.g. --id visit=6789") 

104 

105 return parser 

106 

107 def _findAndGroupDataRefsGen2(self, butler, camera, dataRefs): 

108 self.log.info("Grouping dataRefs by %s" % (self.config.visitDataRefName)) 

109 

110 ccdIds = [] 

111 for detector in camera: 

112 ccdIds.append(detector.getId()) 

113 

114 # TODO: related to DM-13730, this dance of looking for source visits 

115 # will be unnecessary with Gen3 Butler. This should be part of 

116 # DM-13730. 

117 

118 nVisits = 0 

119 

120 groupedDataRefs = {} 

121 for dataRef in dataRefs: 

122 visit = dataRef.dataId[self.config.visitDataRefName] 

123 # If we don't have the dataset, just continue 

124 if not dataRef.datasetExists(datasetType='src'): 

125 continue 

126 # If we need to check all ccds, do it here 

127 if self.config.checkAllCcds: 

128 if visit in groupedDataRefs: 

129 # We already have found this visit 

130 continue 

131 dataId = dataRef.dataId.copy() 

132 # For each ccd we must check that a valid source catalog exists. 

133 for ccdId in ccdIds: 

134 dataId[self.config.ccdDataRefName] = ccdId 

135 if butler.datasetExists('src', dataId=dataId): 

136 goodDataRef = butler.dataRef('src', dataId=dataId) 

137 if visit in groupedDataRefs: 

138 if (goodDataRef.dataId[self.config.ccdDataRefName] not in 

139 [d.dataId[self.config.ccdDataRefName] for d in groupedDataRefs[visit]]): 

140 groupedDataRefs[visit].append(goodDataRef) 

141 else: 

142 # This is a new visit 

143 nVisits += 1 

144 groupedDataRefs[visit] = [goodDataRef] 

145 else: 

146 # We have already confirmed that the dataset exists, so no need 

147 # to check here. 

148 if visit in groupedDataRefs: 

149 if (dataRef.dataId[self.config.ccdDataRefName] not in 

150 [d.dataId[self.config.ccdDataRefName] for d in groupedDataRefs[visit]]): 

151 groupedDataRefs[visit].append(dataRef) 

152 else: 

153 # This is a new visit 

154 nVisits += 1 

155 groupedDataRefs[visit] = [dataRef] 

156 

157 if (nVisits % 100) == 0 and nVisits > 0: 

158 self.log.info("Found %d unique %ss..." % (nVisits, 

159 self.config.visitDataRefName)) 

160 

161 self.log.info("Found %d unique %ss total." % (nVisits, 

162 self.config.visitDataRefName)) 

163 

164 # Put them in ccd order, with the reference ccd first (if available) 

165 def ccdSorter(dataRef): 

166 ccdId = dataRef.dataId[self.config.ccdDataRefName] 

167 if ccdId == self.config.referenceCCD: 

168 return -100 

169 else: 

170 return ccdId 

171 

172 # If we did not check all ccds, put them in ccd order 

173 if not self.config.checkAllCcds: 

174 for visit in groupedDataRefs: 

175 groupedDataRefs[visit] = sorted(groupedDataRefs[visit], key=ccdSorter) 

176 

177 # This should be sorted by visit (the key) 

178 return dict(sorted(groupedDataRefs.items())) 

179 

180 def fgcmMakeAllStarObservations(self, groupedDataRefs, visitCat, 

181 sourceSchema, 

182 camera, 

183 calibFluxApertureRadius=None, 

184 visitCatDataRef=None, 

185 starObsDataRef=None, 

186 inStarObsCat=None): 

187 startTime = time.time() 

188 

189 # If both dataRefs are None, then we assume the caller does not 

190 # want to store checkpoint files. If both are set, we will 

191 # do checkpoint files. And if only one is set, this is potentially 

192 # unintentional and we will warn. 

193 if (visitCatDataRef is not None and starObsDataRef is None 

194 or visitCatDataRef is None and starObsDataRef is not None): 

195 self.log.warning("Only one of visitCatDataRef and starObsDataRef are set, so " 

196 "no checkpoint files will be persisted.") 

197 

198 if self.config.doSubtractLocalBackground and calibFluxApertureRadius is None: 

199 raise RuntimeError("Must set calibFluxApertureRadius if doSubtractLocalBackground is True.") 

200 

201 # create our source schema. Use the first valid dataRef 

202 dataRef = groupedDataRefs[list(groupedDataRefs.keys())[0]][0] 

203 

204 # Construct a mapping from ccd number to index 

205 ccdMapping = {} 

206 for ccdIndex, detector in enumerate(camera): 

207 ccdMapping[detector.getId()] = ccdIndex 

208 

209 approxPixelAreaFields = computeApproxPixelAreaFields(camera) 

210 

211 sourceMapper = self._makeSourceMapper(sourceSchema) 

212 

213 # We also have a temporary catalog that will accumulate aperture measurements 

214 aperMapper = self._makeAperMapper(sourceSchema) 

215 

216 outputSchema = sourceMapper.getOutputSchema() 

217 

218 if inStarObsCat is not None: 

219 fullCatalog = inStarObsCat 

220 comp1 = fullCatalog.schema.compare(outputSchema, outputSchema.EQUAL_KEYS) 

221 comp2 = fullCatalog.schema.compare(outputSchema, outputSchema.EQUAL_NAMES) 

222 if not comp1 or not comp2: 

223 raise RuntimeError("Existing fgcmStarObservations file found with mismatched schema.") 

224 else: 

225 fullCatalog = afwTable.BaseCatalog(outputSchema) 

226 

227 # FGCM will provide relative calibration for the flux in config.instFluxField 

228 

229 instFluxKey = sourceSchema[self.config.instFluxField].asKey() 

230 instFluxErrKey = sourceSchema[self.config.instFluxField + 'Err'].asKey() 

231 visitKey = outputSchema['visit'].asKey() 

232 ccdKey = outputSchema['ccd'].asKey() 

233 instMagKey = outputSchema['instMag'].asKey() 

234 instMagErrKey = outputSchema['instMagErr'].asKey() 

235 deltaMagBkgKey = outputSchema['deltaMagBkg'].asKey() 

236 

237 # Prepare local background if desired 

238 if self.config.doSubtractLocalBackground: 

239 localBackgroundFluxKey = sourceSchema[self.config.localBackgroundFluxField].asKey() 

240 localBackgroundArea = np.pi*calibFluxApertureRadius**2. 

241 

242 aperOutputSchema = aperMapper.getOutputSchema() 

243 

244 instFluxAperInKey = sourceSchema[self.config.apertureInnerInstFluxField].asKey() 

245 instFluxErrAperInKey = sourceSchema[self.config.apertureInnerInstFluxField + 'Err'].asKey() 

246 instFluxAperOutKey = sourceSchema[self.config.apertureOuterInstFluxField].asKey() 

247 instFluxErrAperOutKey = sourceSchema[self.config.apertureOuterInstFluxField + 'Err'].asKey() 

248 instMagInKey = aperOutputSchema['instMag_aper_inner'].asKey() 

249 instMagErrInKey = aperOutputSchema['instMagErr_aper_inner'].asKey() 

250 instMagOutKey = aperOutputSchema['instMag_aper_outer'].asKey() 

251 instMagErrOutKey = aperOutputSchema['instMagErr_aper_outer'].asKey() 

252 

253 k = 2.5/np.log(10.) 

254 

255 # loop over visits 

256 for ctr, visit in enumerate(visitCat): 

257 if visit['sources_read']: 

258 continue 

259 

260 expTime = visit['exptime'] 

261 

262 nStarInVisit = 0 

263 

264 # Reset the aperture catalog (per visit) 

265 aperVisitCatalog = afwTable.BaseCatalog(aperOutputSchema) 

266 

267 for dataRef in groupedDataRefs[visit['visit']]: 

268 

269 ccdId = dataRef.dataId[self.config.ccdDataRefName] 

270 

271 sources = dataRef.get(datasetType='src', flags=afwTable.SOURCE_IO_NO_FOOTPRINTS) 

272 goodSrc = self.sourceSelector.selectSources(sources) 

273 

274 # Need to add a selection based on the local background correction 

275 # if necessary 

276 if self.config.doSubtractLocalBackground: 

277 localBackground = localBackgroundArea*sources[localBackgroundFluxKey] 

278 

279 bad, = np.where((sources[instFluxKey] - localBackground) <= 0.0) 

280 goodSrc.selected[bad] = False 

281 

282 tempCat = afwTable.BaseCatalog(fullCatalog.schema) 

283 tempCat.reserve(goodSrc.selected.sum()) 

284 tempCat.extend(sources[goodSrc.selected], mapper=sourceMapper) 

285 tempCat[visitKey][:] = visit['visit'] 

286 tempCat[ccdKey][:] = ccdId 

287 

288 # Compute "instrumental magnitude" by scaling flux with exposure time. 

289 scaledInstFlux = (sources[instFluxKey][goodSrc.selected] 

290 * visit['scaling'][ccdMapping[ccdId]]) 

291 tempCat[instMagKey][:] = (-2.5*np.log10(scaledInstFlux) + 2.5*np.log10(expTime)) 

292 

293 # Compute the change in magnitude from the background offset 

294 if self.config.doSubtractLocalBackground: 

295 # At the moment we only adjust the flux and not the flux 

296 # error by the background because the error on 

297 # base_LocalBackground_instFlux is the rms error in the 

298 # background annulus, not the error on the mean in the 

299 # background estimate (which is much smaller, by sqrt(n) 

300 # pixels used to estimate the background, which we do not 

301 # have access to in this task). In the default settings, 

302 # the annulus is sufficiently large such that these 

303 # additional errors are are negligibly small (much less 

304 # than a mmag in quadrature). 

305 

306 # This is the difference between the mag with background correction 

307 # and the mag without background correction. 

308 tempCat[deltaMagBkgKey][:] = (-2.5*np.log10(sources[instFluxKey][goodSrc.selected] 

309 - localBackground[goodSrc.selected]) - 

310 -2.5*np.log10(sources[instFluxKey][goodSrc.selected])) 

311 else: 

312 tempCat[deltaMagBkgKey][:] = 0.0 

313 

314 # Compute instMagErr from instFluxErr/instFlux, any scaling 

315 # will cancel out. 

316 

317 tempCat[instMagErrKey][:] = k*(sources[instFluxErrKey][goodSrc.selected] 

318 / sources[instFluxKey][goodSrc.selected]) 

319 

320 # Compute the jacobian from an approximate PixelAreaBoundedField 

321 tempCat['jacobian'] = approxPixelAreaFields[ccdId].evaluate(tempCat['x'], 

322 tempCat['y']) 

323 

324 # Apply the jacobian if configured 

325 if self.config.doApplyWcsJacobian: 

326 tempCat[instMagKey][:] -= 2.5*np.log10(tempCat['jacobian'][:]) 

327 

328 fullCatalog.extend(tempCat) 

329 

330 # And the aperture information 

331 # This does not need the jacobian because it is all locally relative 

332 tempAperCat = afwTable.BaseCatalog(aperVisitCatalog.schema) 

333 tempAperCat.reserve(goodSrc.selected.sum()) 

334 tempAperCat.extend(sources[goodSrc.selected], mapper=aperMapper) 

335 

336 with np.warnings.catch_warnings(): 

337 # Ignore warnings, we will filter infinities and 

338 # nans below. 

339 np.warnings.simplefilter("ignore") 

340 

341 tempAperCat[instMagInKey][:] = -2.5*np.log10( 

342 sources[instFluxAperInKey][goodSrc.selected]) 

343 tempAperCat[instMagErrInKey][:] = k*( 

344 sources[instFluxErrAperInKey][goodSrc.selected] 

345 / sources[instFluxAperInKey][goodSrc.selected]) 

346 tempAperCat[instMagOutKey][:] = -2.5*np.log10( 

347 sources[instFluxAperOutKey][goodSrc.selected]) 

348 tempAperCat[instMagErrOutKey][:] = k*( 

349 sources[instFluxErrAperOutKey][goodSrc.selected] 

350 / sources[instFluxAperOutKey][goodSrc.selected]) 

351 

352 aperVisitCatalog.extend(tempAperCat) 

353 

354 nStarInVisit += len(tempCat) 

355 

356 # Compute the median delta-aper 

357 if not aperVisitCatalog.isContiguous(): 

358 aperVisitCatalog = aperVisitCatalog.copy(deep=True) 

359 

360 instMagIn = aperVisitCatalog[instMagInKey] 

361 instMagErrIn = aperVisitCatalog[instMagErrInKey] 

362 instMagOut = aperVisitCatalog[instMagOutKey] 

363 instMagErrOut = aperVisitCatalog[instMagErrOutKey] 

364 

365 ok = (np.isfinite(instMagIn) & np.isfinite(instMagErrIn) 

366 & np.isfinite(instMagOut) & np.isfinite(instMagErrOut)) 

367 

368 visit['deltaAper'] = np.median(instMagIn[ok] - instMagOut[ok]) 

369 visit['sources_read'] = True 

370 

371 self.log.info(" Found %d good stars in visit %d (deltaAper = %.3f)" % 

372 (nStarInVisit, visit['visit'], visit['deltaAper'])) 

373 

374 if ((ctr % self.config.nVisitsPerCheckpoint) == 0 

375 and starObsDataRef is not None and visitCatDataRef is not None): 

376 # We need to persist both the stars and the visit catalog which gets 

377 # additional metadata from each visit. 

378 starObsDataRef.put(fullCatalog) 

379 visitCatDataRef.put(visitCat) 

380 

381 self.log.info("Found all good star observations in %.2f s" % 

382 (time.time() - startTime)) 

383 

384 return fullCatalog 

385 

386 def _makeAperMapper(self, sourceSchema): 

387 """ 

388 Make a schema mapper for fgcm aperture measurements 

389 

390 Parameters 

391 ---------- 

392 sourceSchema: `afwTable.Schema` 

393 Default source schema from the butler 

394 

395 Returns 

396 ------- 

397 aperMapper: `afwTable.schemaMapper` 

398 Mapper to the FGCM aperture schema 

399 """ 

400 

401 aperMapper = afwTable.SchemaMapper(sourceSchema) 

402 aperMapper.addMapping(sourceSchema['coord_ra'].asKey(), 'ra') 

403 aperMapper.addMapping(sourceSchema['coord_dec'].asKey(), 'dec') 

404 aperMapper.editOutputSchema().addField('instMag_aper_inner', type=np.float64, 

405 doc="Magnitude at inner aperture") 

406 aperMapper.editOutputSchema().addField('instMagErr_aper_inner', type=np.float64, 

407 doc="Magnitude error at inner aperture") 

408 aperMapper.editOutputSchema().addField('instMag_aper_outer', type=np.float64, 

409 doc="Magnitude at outer aperture") 

410 aperMapper.editOutputSchema().addField('instMagErr_aper_outer', type=np.float64, 

411 doc="Magnitude error at outer aperture") 

412 

413 return aperMapper