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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 use, = np.where(goodSrc.selected) 

224 

225 tempCat = afwTable.BaseCatalog(fullCatalog.schema) 

226 tempCat.resize(use.size) 

227 

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

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

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

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

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

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

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

235 

236 if self.config.doSubtractLocalBackground: 

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

238 # error by the background because the error on 

239 # base_LocalBackground_instFlux is the rms error in the 

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

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

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

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

244 # the annulus is sufficiently large such that these 

245 # additional errors are are negligibly small (much less 

246 # than a mmag in quadrature). 

247 

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

249 

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

251 # and the mag without local background correction. 

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

253 localBackground[use]) - 

254 -2.5*np.log10(df[self.config.instFluxField].values[use])) 

255 else: 

256 tempCat['deltaMagBkg'][:] = 0.0 

257 

258 # Need to loop over ccds here 

259 for detector in camera: 

260 ccdId = detector.getId() 

261 # used index for all observations with a given ccd 

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

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

264 tempCat['y'][use2]) 

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

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

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

268 

269 # Compute instMagErr from instFluxErr/instFlux, any scaling 

270 # will cancel out. 

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

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

273 

274 # Apply the jacobian if configured 

275 if self.config.doApplyWcsJacobian: 

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

277 

278 fullCatalog.extend(tempCat) 

279 

280 # Now do the aperture information 

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

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

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

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

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

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

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

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

289 

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

291 visit['sources_read'] = True 

292 

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

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

295 

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

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

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

299 # additional metadata from each visit. 

300 starObsDataRef.put(fullCatalog) 

301 visitCatDataRef.put(visitCat) 

302 

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

304 (time.time() - startTime)) 

305 

306 return fullCatalog 

307 

308 def _get_sourceTable_visit_columns(self): 

309 """ 

310 Get the sourceTable_visit columns from the config. 

311 

312 Returns 

313 ------- 

314 columns : `list` 

315 List of columns to read from sourceTable_visit 

316 """ 

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

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

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

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

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

322 if self.sourceSelector.config.doFlags: 

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

324 if self.sourceSelector.config.doUnresolved: 

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

326 if self.sourceSelector.config.doIsolated: 

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

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

329 if self.config.doSubtractLocalBackground: 

330 columns.append(self.config.localBackgroundFluxField) 

331 

332 return columns