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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 else: 

205 localBackground = 0.0 

206 

207 # Determine which columns we need from the sourceTable_visit catalogs 

208 columns = self._get_sourceTable_visit_columns() 

209 

210 k = 2.5/np.log(10.) 

211 

212 for counter, visit in enumerate(visitCat): 

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

214 if visit['sources_read']: 

215 continue 

216 

217 expTime = visit['exptime'] 

218 

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

220 srcTable = dataRef.get() 

221 

222 df = srcTable.toDataFrame(columns) 

223 

224 if self.config.doSubtractLocalBackground: 

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

226 df[self.config.instFluxField] -= localBackground 

227 

228 goodSrc = self.sourceSelector.selectSources(df) 

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

230 

231 tempCat = afwTable.BaseCatalog(fullCatalog.schema) 

232 tempCat.resize(use.size) 

233 

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

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

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

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

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

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

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

241 

242 # Need to loop over ccds here 

243 for detector in camera: 

244 ccdId = detector.getId() 

245 # used index for all observations with a given ccd 

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

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

248 tempCat['y'][use2]) 

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

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

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

252 

253 # Compute instMagErr from instFluxErr/instFlux, any scaling 

254 # will cancel out. 

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

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

257 

258 # Apply the jacobian if configured 

259 if self.config.doApplyWcsJacobian: 

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

261 

262 fullCatalog.extend(tempCat) 

263 

264 # Now do the aperture information 

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

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

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

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

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

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

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

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

273 

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

275 visit['sources_read'] = True 

276 

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

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

279 

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

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

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

283 # additional metadata from each visit. 

284 starObsDataRef.put(fullCatalog) 

285 visitCatDataRef.put(visitCat) 

286 

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

288 (time.time() - startTime)) 

289 

290 return fullCatalog 

291 

292 def _get_sourceTable_visit_columns(self): 

293 """ 

294 Get the sourceTable_visit columns from the config. 

295 

296 Returns 

297 ------- 

298 columns : `list` 

299 List of columns to read from sourceTable_visit 

300 """ 

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

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

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

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

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

306 if self.sourceSelector.config.doFlags: 

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

308 if self.sourceSelector.config.doUnresolved: 

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

310 if self.sourceSelector.config.doIsolated: 

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

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

313 if self.config.doSubtractLocalBackground: 

314 columns.append(self.config.localBackgroundFluxField) 

315 

316 return columns