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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 using sourceTable_visit. 

24 

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

26subset based on command line parameters) and extracts all the potential 

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

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

29input catalog as possible. 

30""" 

31 

32import time 

33 

34import numpy as np 

35import collections 

36 

37import lsst.pex.config as pexConfig 

38import lsst.pipe.base as pipeBase 

39import lsst.afw.table as afwTable 

40 

41from .fgcmBuildStarsBase import FgcmBuildStarsConfigBase, FgcmBuildStarsRunner, FgcmBuildStarsBaseTask 

42from .utilities import computeApproxPixelAreaFields 

43 

44__all__ = ['FgcmBuildStarsTableConfig', 'FgcmBuildStarsTableTask'] 

45 

46 

47class FgcmBuildStarsTableConfig(FgcmBuildStarsConfigBase): 

48 """Config for FgcmBuildStarsTableTask""" 

49 

50 referenceCCD = pexConfig.Field( 

51 doc="Reference CCD for checking PSF and background", 

52 dtype=int, 

53 default=40, 

54 ) 

55 

56 def setDefaults(self): 

57 super().setDefaults() 

58 

59 # The names here correspond to the post-transformed 

60 # sourceTable_visit catalogs, which differ from the raw src 

61 # catalogs. Therefore, all field and flag names cannot 

62 # be derived from the base config class. 

63 self.instFluxField = 'ApFlux_12_0_instFlux' 

64 self.localBackgroundFluxField = 'LocalBackground_instFlux' 

65 self.apertureInnerInstFluxField = 'ApFlux_12_0_instFlux' 

66 self.apertureOuterInstFluxField = 'ApFlux_17_0_instFlux' 

67 self.psfCandidateName = 'Calib_psf_candidate' 

68 

69 sourceSelector = self.sourceSelector["science"] 

70 

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

72 

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

74 'PixelFlags_interpolatedCenter', 

75 'PixelFlags_saturatedCenter', 

76 'PixelFlags_crCenter', 

77 'PixelFlags_bad', 

78 'PixelFlags_interpolated', 

79 'PixelFlags_saturated', 

80 '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 sourceSelector.isolated.parentName = 'parentSourceId' 

91 sourceSelector.isolated.nChildName = 'Deblend_nChild' 

92 

93 sourceSelector.unresolved.name = 'extendedness' 

94 

95 

96class FgcmBuildStarsTableTask(FgcmBuildStarsBaseTask): 

97 """ 

98 Build stars for the FGCM global calibration, using sourceTable_visit catalogs. 

99 """ 

100 ConfigClass = FgcmBuildStarsTableConfig 

101 RunnerClass = FgcmBuildStarsRunner 

102 _DefaultName = "fgcmBuildStarsTable" 

103 

104 @classmethod 

105 def _makeArgumentParser(cls): 

106 """Create an argument parser""" 

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

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

109 

110 return parser 

111 

112 def findAndGroupDataRefs(self, butler, dataRefs): 

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

114 

115 camera = butler.get('camera') 

116 

117 ccdIds = [] 

118 for detector in camera: 

119 ccdIds.append(detector.getId()) 

120 # Insert our preferred referenceCCD first: 

121 # It is fine that this is listed twice, because we only need 

122 # the first calexp that is found. 

123 ccdIds.insert(0, self.config.referenceCCD) 

124 

125 # The visitTable building code expects a dictionary of groupedDataRefs 

126 # keyed by visit, the first element as the "primary" calexp dataRef. 

127 # We then append the sourceTable_visit dataRef at the end for the 

128 # code which does the data reading (fgcmMakeAllStarObservations). 

129 

130 groupedDataRefs = collections.defaultdict(list) 

131 for dataRef in dataRefs: 

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

133 

134 # Find an existing calexp (we need for psf and metadata) 

135 # and make the relevant dataRef 

136 for ccdId in ccdIds: 

137 try: 

138 calexpRef = butler.dataRef('calexp', dataId={self.config.visitDataRefName: visit, 

139 self.config.ccdDataRefName: ccdId}) 

140 except RuntimeError: 

141 # Not found 

142 continue 

143 # It was found. Add and quit out, since we only 

144 # need one calexp per visit. 

145 groupedDataRefs[visit].append(calexpRef) 

146 break 

147 

148 # And append this dataRef 

149 groupedDataRefs[visit].append(dataRef) 

150 

151 return groupedDataRefs 

152 

153 def fgcmMakeAllStarObservations(self, groupedDataRefs, visitCat, 

154 calibFluxApertureRadius=None, 

155 visitCatDataRef=None, 

156 starObsDataRef=None, 

157 inStarObsCat=None): 

158 startTime = time.time() 

159 

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

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

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

163 # unintentional and we will warn. 

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

165 visitCatDataRef is None and starObsDataRef is not None): 

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

167 "no checkpoint files will be persisted.") 

168 

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

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

171 

172 # To get the correct output schema, we use similar code as fgcmBuildStarsTask 

173 # We are not actually using this mapper, except to grab the outputSchema 

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

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

176 sourceMapper = self._makeSourceMapper(sourceSchema) 

177 outputSchema = sourceMapper.getOutputSchema() 

178 

179 # Construct mapping from ccd number to index 

180 camera = dataRef.get('camera') 

181 ccdMapping = {} 

182 for ccdIndex, detector in enumerate(camera): 

183 ccdMapping[detector.getId()] = ccdIndex 

184 

185 approxPixelAreaFields = computeApproxPixelAreaFields(camera) 

186 

187 if inStarObsCat is not None: 

188 fullCatalog = inStarObsCat 

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

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

191 if not comp1 or not comp2: 

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

193 else: 

194 fullCatalog = afwTable.BaseCatalog(outputSchema) 

195 

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

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

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

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

200 

201 # Prepare local background if desired 

202 if self.config.doSubtractLocalBackground: 

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

204 

205 # Determine which columns we need from the sourceTable_visit catalogs 

206 columns = self._get_sourceTable_visit_columns() 

207 

208 k = 2.5/np.log(10.) 

209 

210 for counter, visit in enumerate(visitCat): 

211 # Check if these sources have already been read and stored in the checkpoint file 

212 if visit['sources_read']: 

213 continue 

214 

215 expTime = visit['exptime'] 

216 

217 dataRef = groupedDataRefs[visit['visit']][-1] 

218 srcTable = dataRef.get() 

219 

220 df = srcTable.toDataFrame(columns) 

221 

222 goodSrc = self.sourceSelector.selectSources(df) 

223 

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

225 # if necessary 

226 if self.config.doSubtractLocalBackground: 

227 localBackground = localBackgroundArea*df[self.config.localBackgroundFluxField].values 

228 use, = np.where((goodSrc.selected) & 

229 ((df[self.config.instFluxField].values - localBackground) > 0.0)) 

230 else: 

231 use, = np.where(goodSrc.selected) 

232 

233 tempCat = afwTable.BaseCatalog(fullCatalog.schema) 

234 tempCat.resize(use.size) 

235 

236 tempCat['ra'][:] = np.deg2rad(df['ra'].values[use]) 

237 tempCat['dec'][:] = np.deg2rad(df['decl'].values[use]) 

238 tempCat['x'][:] = df['x'].values[use] 

239 tempCat['y'][:] = df['y'].values[use] 

240 tempCat[visitKey][:] = df[self.config.visitDataRefName].values[use] 

241 tempCat[ccdKey][:] = df[self.config.ccdDataRefName].values[use] 

242 tempCat['psf_candidate'] = df['Calib_psf_candidate'].values[use] 

243 

244 if self.config.doSubtractLocalBackground: 

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

246 # error by the background because the error on 

247 # base_LocalBackground_instFlux is the rms error in the 

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

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

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

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

252 # the annulus is sufficiently large such that these 

253 # additional errors are are negligibly small (much less 

254 # than a mmag in quadrature). 

255 

256 # This is the difference between the mag with local background correction 

257 # and the mag without local background correction. 

258 tempCat['deltaMagBkg'] = (-2.5*np.log10(df[self.config.instFluxField].values[use] - 

259 localBackground[use]) - 

260 -2.5*np.log10(df[self.config.instFluxField].values[use])) 

261 else: 

262 tempCat['deltaMagBkg'][:] = 0.0 

263 

264 # Need to loop over ccds here 

265 for detector in camera: 

266 ccdId = detector.getId() 

267 # used index for all observations with a given ccd 

268 use2 = (tempCat[ccdKey] == ccdId) 

269 tempCat['jacobian'][use2] = approxPixelAreaFields[ccdId].evaluate(tempCat['x'][use2], 

270 tempCat['y'][use2]) 

271 scaledInstFlux = (df[self.config.instFluxField].values[use[use2]] * 

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

273 tempCat[instMagKey][use2] = (-2.5*np.log10(scaledInstFlux) + 2.5*np.log10(expTime)) 

274 

275 # Compute instMagErr from instFluxErr/instFlux, any scaling 

276 # will cancel out. 

277 tempCat[instMagErrKey][:] = k*(df[self.config.instFluxField + 'Err'].values[use] / 

278 df[self.config.instFluxField].values[use]) 

279 

280 # Apply the jacobian if configured 

281 if self.config.doApplyWcsJacobian: 

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

283 

284 fullCatalog.extend(tempCat) 

285 

286 # Now do the aperture information 

287 with np.warnings.catch_warnings(): 

288 # Ignore warnings, we will filter infinites and nans below 

289 np.warnings.simplefilter("ignore") 

290 

291 instMagIn = -2.5*np.log10(df[self.config.apertureInnerInstFluxField].values[use]) 

292 instMagErrIn = k*(df[self.config.apertureInnerInstFluxField + 'Err'].values[use] / 

293 df[self.config.apertureInnerInstFluxField].values[use]) 

294 instMagOut = -2.5*np.log10(df[self.config.apertureOuterInstFluxField].values[use]) 

295 instMagErrOut = k*(df[self.config.apertureOuterInstFluxField + 'Err'].values[use] / 

296 df[self.config.apertureOuterInstFluxField].values[use]) 

297 

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

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

300 

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

302 visit['sources_read'] = True 

303 

304 self.log.info(" Found %d good stars in visit %d (deltaAper = %0.3f)", 

305 use.size, visit['visit'], visit['deltaAper']) 

306 

307 if ((counter % self.config.nVisitsPerCheckpoint) == 0 and 

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

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

310 # additional metadata from each visit. 

311 starObsDataRef.put(fullCatalog) 

312 visitCatDataRef.put(visitCat) 

313 

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

315 (time.time() - startTime)) 

316 

317 return fullCatalog 

318 

319 def _get_sourceTable_visit_columns(self): 

320 """ 

321 Get the sourceTable_visit columns from the config. 

322 

323 Returns 

324 ------- 

325 columns : `list` 

326 List of columns to read from sourceTable_visit 

327 """ 

328 columns = [self.config.visitDataRefName, self.config.ccdDataRefName, 

329 'ra', 'decl', 'x', 'y', self.config.psfCandidateName, 

330 self.config.instFluxField, self.config.instFluxField + 'Err', 

331 self.config.apertureInnerInstFluxField, self.config.apertureInnerInstFluxField + 'Err', 

332 self.config.apertureOuterInstFluxField, self.config.apertureOuterInstFluxField + 'Err'] 

333 if self.sourceSelector.config.doFlags: 

334 columns.extend(self.sourceSelector.config.flags.bad) 

335 if self.sourceSelector.config.doUnresolved: 

336 columns.append(self.sourceSelector.config.unresolved.name) 

337 if self.sourceSelector.config.doIsolated: 

338 columns.append(self.sourceSelector.config.isolated.parentName) 

339 columns.append(self.sourceSelector.config.isolated.nChildName) 

340 if self.config.doSubtractLocalBackground: 

341 columns.append(self.config.localBackgroundFluxField) 

342 

343 return columns