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1#!/usr/bin/env python 

2# 

3# LSST Data Management System 

4# Copyright 2008-2015 AURA/LSST. 

5# 

6# This product includes software developed by the 

7# LSST Project (http://www.lsst.org/). 

8# 

9# This program is free software: you can redistribute it and/or modify 

10# it under the terms of the GNU General Public License as published by 

11# the Free Software Foundation, either version 3 of the License, or 

12# (at your option) any later version. 

13# 

14# This program is distributed in the hope that it will be useful, 

15# but WITHOUT ANY WARRANTY; without even the implied warranty of 

16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

17# GNU General Public License for more details. 

18# 

19# You should have received a copy of the LSST License Statement and 

20# the GNU General Public License along with this program. If not, 

21# see <https://www.lsstcorp.org/LegalNotices/>. 

22# 

23import numpy 

24 

25from .multiBandUtils import (MergeSourcesRunner, _makeGetSchemaCatalogs, makeMergeArgumentParser, 

26 getInputSchema, getShortFilterName, readCatalog) 

27 

28 

29import lsst.afw.table as afwTable 

30import lsst.pex.config as pexConfig 

31import lsst.pipe.base as pipeBase 

32 

33from lsst.pipe.base import PipelineTaskConnections, PipelineTaskConfig 

34import lsst.pipe.base.connectionTypes as cT 

35 

36 

37class MergeMeasurementsConnections(PipelineTaskConnections, 

38 dimensions=("skymap", "tract", "patch"), 

39 defaultTemplates={"inputCoaddName": "deep", 

40 "outputCoaddName": "deep"}): 

41 inputSchema = cT.InitInput( 

42 doc="Schema for the output merged measurement catalog.", 

43 name="{inputCoaddName}Coadd_meas_schema", 

44 storageClass="SourceCatalog", 

45 ) 

46 outputSchema = cT.InitOutput( 

47 doc="Schema for the output merged measurement catalog.", 

48 name="{outputCoaddName}Coadd_ref_schema", 

49 storageClass="SourceCatalog", 

50 ) 

51 catalogs = cT.Input( 

52 doc="Input catalogs to merge.", 

53 name="{inputCoaddName}Coadd_meas", 

54 multiple=True, 

55 storageClass="SourceCatalog", 

56 dimensions=["abstract_filter", "skymap", "tract", "patch"], 

57 ) 

58 mergedCatalog = cT.Output( 

59 doc="Output merged catalog.", 

60 name="{outputCoaddName}Coadd_ref", 

61 storageClass="SourceCatalog", 

62 dimensions=["skymap", "tract", "patch"], 

63 ) 

64 

65 

66class MergeMeasurementsConfig(PipelineTaskConfig, pipelineConnections=MergeMeasurementsConnections): 

67 """! 

68 @anchor MergeMeasurementsConfig_ 

69 

70 @brief Configuration parameters for the MergeMeasurementsTask 

71 """ 

72 pseudoFilterList = pexConfig.ListField( 

73 dtype=str, 

74 default=["sky"], 

75 doc="Names of filters which may have no associated detection\n" 

76 "(N.b. should include MergeDetectionsConfig.skyFilterName)" 

77 ) 

78 snName = pexConfig.Field( 

79 dtype=str, 

80 default="base_PsfFlux", 

81 doc="Name of flux measurement for calculating the S/N when choosing the reference band." 

82 ) 

83 minSN = pexConfig.Field( 

84 dtype=float, 

85 default=10., 

86 doc="If the S/N from the priority band is below this value (and the S/N " 

87 "is larger than minSNDiff compared to the priority band), use the band with " 

88 "the largest S/N as the reference band." 

89 ) 

90 minSNDiff = pexConfig.Field( 

91 dtype=float, 

92 default=3., 

93 doc="If the difference in S/N between another band and the priority band is larger " 

94 "than this value (and the S/N in the priority band is less than minSN) " 

95 "use the band with the largest S/N as the reference band" 

96 ) 

97 flags = pexConfig.ListField( 

98 dtype=str, 

99 doc="Require that these flags, if available, are not set", 

100 default=["base_PixelFlags_flag_interpolatedCenter", "base_PsfFlux_flag", 

101 "ext_photometryKron_KronFlux_flag", "modelfit_CModel_flag", ] 

102 ) 

103 priorityList = pexConfig.ListField( 

104 dtype=str, 

105 default=[], 

106 doc="Priority-ordered list of bands for the merge." 

107 ) 

108 coaddName = pexConfig.Field( 

109 dtype=str, 

110 default="deep", 

111 doc="Name of coadd" 

112 ) 

113 

114 def validate(self): 

115 super().validate() 

116 if len(self.priorityList) == 0: 

117 raise RuntimeError("No priority list provided") 

118 

119 

120## @addtogroup LSST_task_documentation 

121## @{ 

122## @page MergeMeasurementsTask 

123## @ref MergeMeasurementsTask_ "MergeMeasurementsTask" 

124## @copybrief MergeMeasurementsTask 

125## @} 

126 

127 

128class MergeMeasurementsTask(pipeBase.PipelineTask, pipeBase.CmdLineTask): 

129 r"""! 

130 @anchor MergeMeasurementsTask_ 

131 

132 @brief Merge measurements from multiple bands 

133 

134 @section pipe_tasks_multiBand_Contents Contents 

135 

136 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Purpose 

137 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Initialize 

138 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Run 

139 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Config 

140 - @ref pipe_tasks_multiBand_MergeMeasurementsTask_Debug 

141 - @ref pipe_tasks_multiband_MergeMeasurementsTask_Example 

142 

143 @section pipe_tasks_multiBand_MergeMeasurementsTask_Purpose Description 

144 

145 Command-line task that merges measurements from multiple bands. 

146 

147 Combines consistent (i.e. with the same peaks and footprints) catalogs of sources from multiple filter 

148 bands to construct a unified catalog that is suitable for driving forced photometry. Every source is 

149 required to have centroid, shape and flux measurements in each band. 

150 

151 @par Inputs: 

152 deepCoadd_meas{tract,patch,filter}: SourceCatalog 

153 @par Outputs: 

154 deepCoadd_ref{tract,patch}: SourceCatalog 

155 @par Data Unit: 

156 tract, patch 

157 

158 MergeMeasurementsTask subclasses @ref CmdLineTask_ "CmdLineTask". 

159 

160 @section pipe_tasks_multiBand_MergeMeasurementsTask_Initialize Task initialization 

161 

162 @copydoc \_\_init\_\_ 

163 

164 @section pipe_tasks_multiBand_MergeMeasurementsTask_Run Invoking the Task 

165 

166 @copydoc run 

167 

168 @section pipe_tasks_multiBand_MergeMeasurementsTask_Config Configuration parameters 

169 

170 See @ref MergeMeasurementsConfig_ 

171 

172 @section pipe_tasks_multiBand_MergeMeasurementsTask_Debug Debug variables 

173 

174 The @link lsst.pipe.base.cmdLineTask.CmdLineTask command line task@endlink interface supports a 

175 flag @c -d to import @b debug.py from your @c PYTHONPATH; see @ref baseDebug for more about @b debug.py 

176 files. 

177 

178 MergeMeasurementsTask has no debug variables. 

179 

180 @section pipe_tasks_multiband_MergeMeasurementsTask_Example A complete example 

181 of using MergeMeasurementsTask 

182 

183 MergeMeasurementsTask is meant to be run after deblending & measuring sources in every band. 

184 The purpose of the task is to generate a catalog of sources suitable for driving forced photometry in 

185 coadds and individual exposures. 

186 Command-line usage of MergeMeasurementsTask expects a data reference to the coadds to be processed. A list 

187 of the available optional arguments can be obtained by calling mergeCoaddMeasurements.py with the `--help` 

188 command line argument: 

189 @code 

190 mergeCoaddMeasurements.py --help 

191 @endcode 

192 

193 To demonstrate usage of the DetectCoaddSourcesTask in the larger context of multi-band processing, we 

194 will process HSC data in the [ci_hsc](https://github.com/lsst/ci_hsc) package. Assuming one has finished 

195 step 7 at @ref pipeTasks_multiBand, one may merge the catalogs generated after deblending and measuring 

196 as follows: 

197 @code 

198 mergeCoaddMeasurements.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I^HSC-R 

199 @endcode 

200 This will merge the HSC-I & HSC-R band catalogs. The results are written in 

201 `$CI_HSC_DIR/DATA/deepCoadd-results/`. 

202 """ 

203 _DefaultName = "mergeCoaddMeasurements" 

204 ConfigClass = MergeMeasurementsConfig 

205 RunnerClass = MergeSourcesRunner 

206 inputDataset = "meas" 

207 outputDataset = "ref" 

208 getSchemaCatalogs = _makeGetSchemaCatalogs("ref") 

209 

210 @classmethod 

211 def _makeArgumentParser(cls): 

212 return makeMergeArgumentParser(cls._DefaultName, cls.inputDataset) 

213 

214 def getInputSchema(self, butler=None, schema=None): 

215 return getInputSchema(self, butler, schema) 

216 

217 def runQuantum(self, butlerQC, inputRefs, outputRefs): 

218 inputs = butlerQC.get(inputRefs) 

219 dataIds = (ref.dataId for ref in inputRefs.catalogs) 

220 catalogDict = {dataId['abstract_filter']: cat for dataId, cat in zip(dataIds, 

221 inputs['catalogs'])} 

222 inputs['catalogs'] = catalogDict 

223 outputs = self.run(**inputs) 

224 butlerQC.put(outputs, outputRefs) 

225 

226 def __init__(self, butler=None, schema=None, initInputs=None, **kwargs): 

227 """! 

228 Initialize the task. 

229 

230 @param[in] schema: the schema of the detection catalogs used as input to this one 

231 @param[in] butler: a butler used to read the input schema from disk, if schema is None 

232 

233 The task will set its own self.schema attribute to the schema of the output merged catalog. 

234 """ 

235 super().__init__(**kwargs) 

236 

237 if initInputs is not None: 237 ↛ 238line 237 didn't jump to line 238, because the condition on line 237 was never true

238 inputSchema = initInputs['inputSchema'].schema 

239 else: 

240 inputSchema = self.getInputSchema(butler=butler, schema=schema) 

241 self.schemaMapper = afwTable.SchemaMapper(inputSchema, True) 

242 self.schemaMapper.addMinimalSchema(inputSchema, True) 

243 self.instFluxKey = inputSchema.find(self.config.snName + "_instFlux").getKey() 

244 self.instFluxErrKey = inputSchema.find(self.config.snName + "_instFluxErr").getKey() 

245 self.fluxFlagKey = inputSchema.find(self.config.snName + "_flag").getKey() 

246 

247 self.flagKeys = {} 

248 for band in self.config.priorityList: 

249 short = getShortFilterName(band) 

250 outputKey = self.schemaMapper.editOutputSchema().addField( 

251 "merge_measurement_%s" % short, 

252 type="Flag", 

253 doc="Flag field set if the measurements here are from the %s filter" % band 

254 ) 

255 peakKey = inputSchema.find("merge_peak_%s" % short).key 

256 footprintKey = inputSchema.find("merge_footprint_%s" % short).key 

257 self.flagKeys[band] = pipeBase.Struct(peak=peakKey, footprint=footprintKey, output=outputKey) 

258 self.schema = self.schemaMapper.getOutputSchema() 

259 

260 self.pseudoFilterKeys = [] 

261 for filt in self.config.pseudoFilterList: 

262 try: 

263 self.pseudoFilterKeys.append(self.schema.find("merge_peak_%s" % filt).getKey()) 

264 except Exception as e: 

265 self.log.warn("merge_peak is not set for pseudo-filter %s: %s" % (filt, e)) 

266 

267 self.badFlags = {} 

268 for flag in self.config.flags: 

269 try: 

270 self.badFlags[flag] = self.schema.find(flag).getKey() 

271 except KeyError as exc: 

272 self.log.warn("Can't find flag %s in schema: %s" % (flag, exc,)) 

273 self.outputSchema = afwTable.SourceCatalog(self.schema) 

274 

275 def runDataRef(self, patchRefList): 

276 """! 

277 @brief Merge coadd sources from multiple bands. Calls @ref `run`. 

278 @param[in] patchRefList list of data references for each filter 

279 """ 

280 catalogs = dict(readCatalog(self, patchRef) for patchRef in patchRefList) 

281 mergedCatalog = self.run(catalogs).mergedCatalog 

282 self.write(patchRefList[0], mergedCatalog) 

283 

284 def run(self, catalogs): 

285 """! 

286 Merge measurement catalogs to create a single reference catalog for forced photometry 

287 

288 @param[in] catalogs: the catalogs to be merged 

289 

290 For parent sources, we choose the first band in config.priorityList for which the 

291 merge_footprint flag for that band is is True. 

292 

293 For child sources, the logic is the same, except that we use the merge_peak flags. 

294 """ 

295 # Put catalogs, filters in priority order 

296 orderedCatalogs = [catalogs[band] for band in self.config.priorityList if band in catalogs.keys()] 

297 orderedKeys = [self.flagKeys[band] for band in self.config.priorityList if band in catalogs.keys()] 

298 

299 mergedCatalog = afwTable.SourceCatalog(self.schema) 

300 mergedCatalog.reserve(len(orderedCatalogs[0])) 

301 

302 idKey = orderedCatalogs[0].table.getIdKey() 

303 for catalog in orderedCatalogs[1:]: 303 ↛ 304line 303 didn't jump to line 304, because the loop on line 303 never started

304 if numpy.any(orderedCatalogs[0].get(idKey) != catalog.get(idKey)): 

305 raise ValueError("Error in inputs to MergeCoaddMeasurements: source IDs do not match") 

306 

307 # This first zip iterates over all the catalogs simultaneously, yielding a sequence of one 

308 # record for each band, in priority order. 

309 for orderedRecords in zip(*orderedCatalogs): 

310 

311 maxSNRecord = None 

312 maxSNFlagKeys = None 

313 maxSN = 0. 

314 priorityRecord = None 

315 priorityFlagKeys = None 

316 prioritySN = 0. 

317 hasPseudoFilter = False 

318 

319 # Now we iterate over those record-band pairs, keeping track of the priority and the 

320 # largest S/N band. 

321 for inputRecord, flagKeys in zip(orderedRecords, orderedKeys): 

322 parent = (inputRecord.getParent() == 0 and inputRecord.get(flagKeys.footprint)) 

323 child = (inputRecord.getParent() != 0 and inputRecord.get(flagKeys.peak)) 

324 

325 if not (parent or child): 

326 for pseudoFilterKey in self.pseudoFilterKeys: 326 ↛ 332line 326 didn't jump to line 332, because the loop on line 326 didn't complete

327 if inputRecord.get(pseudoFilterKey): 327 ↛ 326line 327 didn't jump to line 326, because the condition on line 327 was never false

328 hasPseudoFilter = True 

329 priorityRecord = inputRecord 

330 priorityFlagKeys = flagKeys 

331 break 

332 if hasPseudoFilter: 332 ↛ 335line 332 didn't jump to line 335, because the condition on line 332 was never false

333 break 

334 

335 isBad = any(inputRecord.get(flag) for flag in self.badFlags) 

336 if isBad or inputRecord.get(self.fluxFlagKey) or inputRecord.get(self.instFluxErrKey) == 0: 

337 sn = 0. 

338 else: 

339 sn = inputRecord.get(self.instFluxKey)/inputRecord.get(self.instFluxErrKey) 

340 if numpy.isnan(sn) or sn < 0.: 340 ↛ 341line 340 didn't jump to line 341, because the condition on line 340 was never true

341 sn = 0. 

342 if (parent or child) and priorityRecord is None: 342 ↛ 346line 342 didn't jump to line 346, because the condition on line 342 was never false

343 priorityRecord = inputRecord 

344 priorityFlagKeys = flagKeys 

345 prioritySN = sn 

346 if sn > maxSN: 

347 maxSNRecord = inputRecord 

348 maxSNFlagKeys = flagKeys 

349 maxSN = sn 

350 

351 # If the priority band has a low S/N we would like to choose the band with the highest S/N as 

352 # the reference band instead. However, we only want to choose the highest S/N band if it is 

353 # significantly better than the priority band. Therefore, to choose a band other than the 

354 # priority, we require that the priority S/N is below the minimum threshold and that the 

355 # difference between the priority and highest S/N is larger than the difference threshold. 

356 # 

357 # For pseudo code objects we always choose the first band in the priority list. 

358 bestRecord = None 

359 bestFlagKeys = None 

360 if hasPseudoFilter: 

361 bestRecord = priorityRecord 

362 bestFlagKeys = priorityFlagKeys 

363 elif (prioritySN < self.config.minSN and (maxSN - prioritySN) > self.config.minSNDiff 363 ↛ 365line 363 didn't jump to line 365, because the condition on line 363 was never true

364 and maxSNRecord is not None): 

365 bestRecord = maxSNRecord 

366 bestFlagKeys = maxSNFlagKeys 

367 elif priorityRecord is not None: 367 ↛ 371line 367 didn't jump to line 371, because the condition on line 367 was never false

368 bestRecord = priorityRecord 

369 bestFlagKeys = priorityFlagKeys 

370 

371 if bestRecord is not None and bestFlagKeys is not None: 371 ↛ 376line 371 didn't jump to line 376, because the condition on line 371 was never false

372 outputRecord = mergedCatalog.addNew() 

373 outputRecord.assign(bestRecord, self.schemaMapper) 

374 outputRecord.set(bestFlagKeys.output, True) 

375 else: # if we didn't find any records 

376 raise ValueError("Error in inputs to MergeCoaddMeasurements: no valid reference for %s" % 

377 inputRecord.getId()) 

378 

379 # more checking for sane inputs, since zip silently iterates over the smallest sequence 

380 for inputCatalog in orderedCatalogs: 

381 if len(mergedCatalog) != len(inputCatalog): 381 ↛ 382line 381 didn't jump to line 382, because the condition on line 381 was never true

382 raise ValueError("Mismatch between catalog sizes: %s != %s" % 

383 (len(mergedCatalog), len(orderedCatalogs))) 

384 

385 return pipeBase.Struct( 

386 mergedCatalog=mergedCatalog 

387 ) 

388 

389 def write(self, patchRef, catalog): 

390 """! 

391 @brief Write the output. 

392 

393 @param[in] patchRef data reference for patch 

394 @param[in] catalog catalog 

395 

396 We write as the dataset provided by the 'outputDataset' 

397 class variable. 

398 """ 

399 patchRef.put(catalog, self.config.coaddName + "Coadd_" + self.outputDataset) 

400 # since the filter isn't actually part of the data ID for the dataset we're saving, 

401 # it's confusing to see it in the log message, even if the butler simply ignores it. 

402 mergeDataId = patchRef.dataId.copy() 

403 del mergeDataId["filter"] 

404 self.log.info("Wrote merged catalog: %s" % (mergeDataId,)) 

405 

406 def writeMetadata(self, dataRefList): 

407 """! 

408 @brief No metadata to write, and not sure how to write it for a list of dataRefs. 

409 """ 

410 pass