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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 findAndGroupDataRefs(self, butler, dataRefs): 

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

109 

110 camera = butler.get('camera') 

111 

112 ccdIds = [] 

113 for detector in camera: 

114 ccdIds.append(detector.getId()) 

115 

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

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

118 # DM-13730. 

119 

120 nVisits = 0 

121 

122 groupedDataRefs = {} 

123 for dataRef in dataRefs: 

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

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

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

127 continue 

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

129 if self.config.checkAllCcds: 

130 if visit in groupedDataRefs: 

131 # We already have found this visit 

132 continue 

133 dataId = dataRef.dataId.copy() 

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

135 for ccdId in ccdIds: 

136 dataId[self.config.ccdDataRefName] = ccdId 

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

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

139 if visit in groupedDataRefs: 

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

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

142 groupedDataRefs[visit].append(goodDataRef) 

143 else: 

144 # This is a new visit 

145 nVisits += 1 

146 groupedDataRefs[visit] = [goodDataRef] 

147 else: 

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

149 # to check here. 

150 if visit in groupedDataRefs: 

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

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

153 groupedDataRefs[visit].append(dataRef) 

154 else: 

155 # This is a new visit 

156 nVisits += 1 

157 groupedDataRefs[visit] = [dataRef] 

158 

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

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

161 self.config.visitDataRefName)) 

162 

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

164 self.config.visitDataRefName)) 

165 

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

167 def ccdSorter(dataRef): 

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

169 if ccdId == self.config.referenceCCD: 

170 return -100 

171 else: 

172 return ccdId 

173 

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

175 if not self.config.checkAllCcds: 

176 for visit in groupedDataRefs: 

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

178 

179 return groupedDataRefs 

180 

181 def fgcmMakeAllStarObservations(self, groupedDataRefs, visitCat, 

182 calibFluxApertureRadius=None, 

183 visitCatDataRef=None, 

184 starObsDataRef=None, 

185 inStarObsCat=None): 

186 startTime = time.time() 

187 

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

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

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

191 # unintentional and we will warn. 

192 if (visitCatDataRef is not None and starObsDataRef is None or 

193 visitCatDataRef is None and starObsDataRef is not None): 

194 self.log.warn("Only one of visitCatDataRef and starObsDataRef are set, so " 

195 "no checkpoint files will be persisted.") 

196 

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

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

199 

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

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

202 sourceSchema = dataRef.get('src_schema', immediate=True).schema 

203 

204 # Construct a mapping from ccd number to index 

205 camera = dataRef.get('camera') 

206 ccdMapping = {} 

207 for ccdIndex, detector in enumerate(camera): 

208 ccdMapping[detector.getId()] = ccdIndex 

209 

210 approxPixelAreaFields = computeApproxPixelAreaFields(camera) 

211 

212 sourceMapper = self._makeSourceMapper(sourceSchema) 

213 

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

215 aperMapper = self._makeAperMapper(sourceSchema) 

216 

217 outputSchema = sourceMapper.getOutputSchema() 

218 

219 if inStarObsCat is not None: 

220 fullCatalog = inStarObsCat 

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

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

223 if not comp1 or not comp2: 

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

225 else: 

226 fullCatalog = afwTable.BaseCatalog(outputSchema) 

227 

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

229 

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

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

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

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

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

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

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

237 

238 # Prepare local background if desired 

239 if self.config.doSubtractLocalBackground: 

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

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

242 

243 aperOutputSchema = aperMapper.getOutputSchema() 

244 

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

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

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

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

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

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

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

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

253 

254 k = 2.5/np.log(10.) 

255 

256 # loop over visits 

257 for ctr, visit in enumerate(visitCat): 

258 if visit['sources_read']: 

259 continue 

260 

261 expTime = visit['exptime'] 

262 

263 nStarInVisit = 0 

264 

265 # Reset the aperture catalog (per visit) 

266 aperVisitCatalog = afwTable.BaseCatalog(aperOutputSchema) 

267 

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

269 

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

271 

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

273 goodSrc = self.sourceSelector.selectSources(sources) 

274 

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

276 # if necessary 

277 if self.config.doSubtractLocalBackground: 

278 localBackground = localBackgroundArea*sources[localBackgroundFluxKey] 

279 

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

281 goodSrc.selected[bad] = False 

282 

283 tempCat = afwTable.BaseCatalog(fullCatalog.schema) 

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

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

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

287 tempCat[ccdKey][:] = ccdId 

288 

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

290 scaledInstFlux = (sources[instFluxKey][goodSrc.selected] * 

291 visit['scaling'][ccdMapping[ccdId]]) 

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

293 

294 # Compute the change in magnitude from the background offset 

295 if self.config.doSubtractLocalBackground: 

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

297 # error by the background because the error on 

298 # base_LocalBackground_instFlux is the rms error in the 

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

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

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

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

303 # the annulus is sufficiently large such that these 

304 # additional errors are are negligibly small (much less 

305 # than a mmag in quadrature). 

306 

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

308 # and the mag without background correction. 

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

310 localBackground[goodSrc.selected]) - 

311 -2.5*np.log10(sources[instFluxKey][goodSrc.selected])) 

312 else: 

313 tempCat[deltaMagBkgKey][:] = 0.0 

314 

315 # Compute instMagErr from instFluxErr/instFlux, any scaling 

316 # will cancel out. 

317 

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

319 sources[instFluxKey][goodSrc.selected]) 

320 

321 # Compute the jacobian from an approximate PixelAreaBoundedField 

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

323 tempCat['y']) 

324 

325 # Apply the jacobian if configured 

326 if self.config.doApplyWcsJacobian: 

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

328 

329 fullCatalog.extend(tempCat) 

330 

331 # And the aperture information 

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

333 tempAperCat = afwTable.BaseCatalog(aperVisitCatalog.schema) 

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

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

336 

337 with np.warnings.catch_warnings(): 

338 # Ignore warnings, we will filter infinities and 

339 # nans below. 

340 np.warnings.simplefilter("ignore") 

341 

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

343 sources[instFluxAperInKey][goodSrc.selected]) 

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

345 sources[instFluxErrAperInKey][goodSrc.selected] / 

346 sources[instFluxAperInKey][goodSrc.selected]) 

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

348 sources[instFluxAperOutKey][goodSrc.selected]) 

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

350 sources[instFluxErrAperOutKey][goodSrc.selected] / 

351 sources[instFluxAperOutKey][goodSrc.selected]) 

352 

353 aperVisitCatalog.extend(tempAperCat) 

354 

355 nStarInVisit += len(tempCat) 

356 

357 # Compute the median delta-aper 

358 if not aperVisitCatalog.isContiguous(): 

359 aperVisitCatalog = aperVisitCatalog.copy(deep=True) 

360 

361 instMagIn = aperVisitCatalog[instMagInKey] 

362 instMagErrIn = aperVisitCatalog[instMagErrInKey] 

363 instMagOut = aperVisitCatalog[instMagOutKey] 

364 instMagErrOut = aperVisitCatalog[instMagErrOutKey] 

365 

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

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

368 

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

370 visit['sources_read'] = True 

371 

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

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

374 

375 if ((ctr % self.config.nVisitsPerCheckpoint) == 0 and 

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

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

378 # additional metadata from each visit. 

379 starObsDataRef.put(fullCatalog) 

380 visitCatDataRef.put(visitCat) 

381 

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

383 (time.time() - startTime)) 

384 

385 return fullCatalog 

386 

387 def _makeAperMapper(self, sourceSchema): 

388 """ 

389 Make a schema mapper for fgcm aperture measurements 

390 

391 Parameters 

392 ---------- 

393 sourceSchema: `afwTable.Schema` 

394 Default source schema from the butler 

395 

396 Returns 

397 ------- 

398 aperMapper: `afwTable.schemaMapper` 

399 Mapper to the FGCM aperture schema 

400 """ 

401 

402 aperMapper = afwTable.SchemaMapper(sourceSchema) 

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

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

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

406 doc="Magnitude at inner aperture") 

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

408 doc="Magnitude error at inner aperture") 

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

410 doc="Magnitude at outer aperture") 

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

412 doc="Magnitude error at outer aperture") 

413 

414 return aperMapper