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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 as np 

24 

25from lsst.coadd.utils.coaddDataIdContainer import ExistingCoaddDataIdContainer 

26from lsst.coadd.utils.getGen3CoaddExposureId import getGen3CoaddExposureId 

27from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner, 

28 PipelineTask, PipelineTaskConfig, PipelineTaskConnections) 

29import lsst.pipe.base.connectionTypes as cT 

30from lsst.pex.config import Config, Field, ConfigurableField 

31from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader 

32from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask 

33from lsst.meas.deblender import SourceDeblendTask 

34from lsst.meas.extensions.scarlet import ScarletDeblendTask 

35from lsst.pipe.tasks.coaddBase import getSkyInfo 

36from lsst.pipe.tasks.scaleVariance import ScaleVarianceTask 

37from lsst.meas.astrom import DirectMatchTask, denormalizeMatches 

38from lsst.pipe.tasks.fakes import BaseFakeSourcesTask 

39from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask 

40from lsst.pipe.tasks.propagateVisitFlags import PropagateVisitFlagsTask 

41import lsst.afw.image as afwImage 

42import lsst.afw.table as afwTable 

43import lsst.afw.math as afwMath 

44from lsst.daf.base import PropertyList 

45from lsst.skymap import BaseSkyMap 

46from lsst.obs.base import ExposureIdInfo 

47 

48# NOTE: these imports are a convenience so multiband users only have to import this file. 

49from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401 

50from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401 

51from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401 

52from .multiBandUtils import getInputSchema, readCatalog, _makeMakeIdFactory # noqa: F401 

53from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401 

54from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401 

55from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401 

56from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401 

57 

58 

59""" 

60New set types: 

61* deepCoadd_det: detections from what used to be processCoadd (tract, patch, filter) 

62* deepCoadd_mergeDet: merged detections (tract, patch) 

63* deepCoadd_meas: measurements of merged detections (tract, patch, filter) 

64* deepCoadd_ref: reference sources (tract, patch) 

65All of these have associated *_schema catalogs that require no data ID and hold no records. 

66 

67In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in 

68the mergeDet, meas, and ref dataset Footprints: 

69* deepCoadd_peak_schema 

70""" 

71 

72 

73############################################################################################################## 

74class DetectCoaddSourcesConnections(PipelineTaskConnections, 

75 dimensions=("tract", "patch", "band", "skymap"), 

76 defaultTemplates={"inputCoaddName": "deep", "outputCoaddName": "deep"}): 

77 detectionSchema = cT.InitOutput( 

78 doc="Schema of the detection catalog", 

79 name="{outputCoaddName}Coadd_det_schema", 

80 storageClass="SourceCatalog", 

81 ) 

82 exposure = cT.Input( 

83 doc="Exposure on which detections are to be performed", 

84 name="{inputCoaddName}Coadd", 

85 storageClass="ExposureF", 

86 dimensions=("tract", "patch", "band", "skymap") 

87 ) 

88 outputBackgrounds = cT.Output( 

89 doc="Output Backgrounds used in detection", 

90 name="{outputCoaddName}Coadd_calexp_background", 

91 storageClass="Background", 

92 dimensions=("tract", "patch", "band", "skymap") 

93 ) 

94 outputSources = cT.Output( 

95 doc="Detected sources catalog", 

96 name="{outputCoaddName}Coadd_det", 

97 storageClass="SourceCatalog", 

98 dimensions=("tract", "patch", "band", "skymap") 

99 ) 

100 outputExposure = cT.Output( 

101 doc="Exposure post detection", 

102 name="{outputCoaddName}Coadd_calexp", 

103 storageClass="ExposureF", 

104 dimensions=("tract", "patch", "band", "skymap") 

105 ) 

106 

107 

108class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections): 

109 """! 

110 @anchor DetectCoaddSourcesConfig_ 

111 

112 @brief Configuration parameters for the DetectCoaddSourcesTask 

113 """ 

114 doScaleVariance = Field(dtype=bool, default=True, doc="Scale variance plane using empirical noise?") 

115 scaleVariance = ConfigurableField(target=ScaleVarianceTask, doc="Variance rescaling") 

116 detection = ConfigurableField(target=DynamicDetectionTask, doc="Source detection") 

117 coaddName = Field(dtype=str, default="deep", doc="Name of coadd") 

118 doInsertFakes = Field(dtype=bool, default=False, 

119 doc="Run fake sources injection task") 

120 insertFakes = ConfigurableField(target=BaseFakeSourcesTask, 

121 doc="Injection of fake sources for testing " 

122 "purposes (must be retargeted)") 

123 hasFakes = Field( 

124 dtype=bool, 

125 default=False, 

126 doc="Should be set to True if fake sources have been inserted into the input data." 

127 ) 

128 

129 def setDefaults(self): 

130 super().setDefaults() 

131 self.detection.thresholdType = "pixel_stdev" 

132 self.detection.isotropicGrow = True 

133 # Coadds are made from background-subtracted CCDs, so any background subtraction should be very basic 

134 self.detection.reEstimateBackground = False 

135 self.detection.background.useApprox = False 

136 self.detection.background.binSize = 4096 

137 self.detection.background.undersampleStyle = 'REDUCE_INTERP_ORDER' 

138 self.detection.doTempWideBackground = True # Suppress large footprints that overwhelm the deblender 

139 

140## @addtogroup LSST_task_documentation 

141## @{ 

142## @page DetectCoaddSourcesTask 

143## @ref DetectCoaddSourcesTask_ "DetectCoaddSourcesTask" 

144## @copybrief DetectCoaddSourcesTask 

145## @} 

146 

147 

148class DetectCoaddSourcesTask(PipelineTask, CmdLineTask): 

149 r"""! 

150 @anchor DetectCoaddSourcesTask_ 

151 

152 @brief Detect sources on a coadd 

153 

154 @section pipe_tasks_multiBand_Contents Contents 

155 

156 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose 

157 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize 

158 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run 

159 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config 

160 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug 

161 - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example 

162 

163 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description 

164 

165 Command-line task that detects sources on a coadd of exposures obtained with a single filter. 

166 

167 Coadding individual visits requires each exposure to be warped. This introduces covariance in the noise 

168 properties across pixels. Before detection, we correct the coadd variance by scaling the variance plane 

169 in the coadd to match the observed variance. This is an approximate approach -- strictly, we should 

170 propagate the full covariance matrix -- but it is simple and works well in practice. 

171 

172 After scaling the variance plane, we detect sources and generate footprints by delegating to the @ref 

173 SourceDetectionTask_ "detection" subtask. 

174 

175 @par Inputs: 

176 deepCoadd{tract,patch,filter}: ExposureF 

177 @par Outputs: 

178 deepCoadd_det{tract,patch,filter}: SourceCatalog (only parent Footprints) 

179 @n deepCoadd_calexp{tract,patch,filter}: Variance scaled, background-subtracted input 

180 exposure (ExposureF) 

181 @n deepCoadd_calexp_background{tract,patch,filter}: BackgroundList 

182 @par Data Unit: 

183 tract, patch, filter 

184 

185 DetectCoaddSourcesTask delegates most of its work to the @ref SourceDetectionTask_ "detection" subtask. 

186 You can retarget this subtask if you wish. 

187 

188 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization 

189 

190 @copydoc \_\_init\_\_ 

191 

192 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task 

193 

194 @copydoc run 

195 

196 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters 

197 

198 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig" 

199 

200 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables 

201 

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

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

204 files. 

205 

206 DetectCoaddSourcesTask has no debug variables of its own because it relegates all the work to 

207 @ref SourceDetectionTask_ "SourceDetectionTask"; see the documetation for 

208 @ref SourceDetectionTask_ "SourceDetectionTask" for further information. 

209 

210 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example 

211 of using DetectCoaddSourcesTask 

212 

213 DetectCoaddSourcesTask is meant to be run after assembling a coadded image in a given band. The purpose of 

214 the task is to update the background, detect all sources in a single band and generate a set of parent 

215 footprints. Subsequent tasks in the multi-band processing procedure will merge sources across bands and, 

216 eventually, perform forced photometry. Command-line usage of DetectCoaddSourcesTask expects a data 

217 reference to the coadd to be processed. A list of the available optional arguments can be obtained by 

218 calling detectCoaddSources.py with the `--help` command line argument: 

219 @code 

220 detectCoaddSources.py --help 

221 @endcode 

222 

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

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

225 steps 1 - 4 at @ref pipeTasks_multiBand, one may detect all the sources in each coadd as follows: 

226 @code 

227 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I 

228 @endcode 

229 that will process the HSC-I band data. The results are written to 

230 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I`. 

231 

232 It is also necessary to run: 

233 @code 

234 detectCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R 

235 @endcode 

236 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band 

237 processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask". 

238 """ 

239 _DefaultName = "detectCoaddSources" 

240 ConfigClass = DetectCoaddSourcesConfig 

241 getSchemaCatalogs = _makeGetSchemaCatalogs("det") 

242 makeIdFactory = _makeMakeIdFactory("CoaddId") 

243 

244 @classmethod 

245 def _makeArgumentParser(cls): 

246 parser = ArgumentParser(name=cls._DefaultName) 

247 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2 filter=r", 

248 ContainerClass=ExistingCoaddDataIdContainer) 

249 return parser 

250 

251 def __init__(self, schema=None, **kwargs): 

252 """! 

253 @brief Initialize the task. Create the @ref SourceDetectionTask_ "detection" subtask. 

254 

255 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 

256 

257 @param[in] schema: initial schema for the output catalog, modified-in place to include all 

258 fields set by this task. If None, the source minimal schema will be used. 

259 @param[in] **kwargs: keyword arguments to be passed to lsst.pipe.base.task.Task.__init__ 

260 """ 

261 # N.B. Super is used here to handle the multiple inheritance of PipelineTasks, the init tree 

262 # call structure has been reviewed carefully to be sure super will work as intended. 

263 super().__init__(**kwargs) 

264 if schema is None: 264 ↛ 266line 264 didn't jump to line 266, because the condition on line 264 was never false

265 schema = afwTable.SourceTable.makeMinimalSchema() 

266 if self.config.doInsertFakes: 266 ↛ 267line 266 didn't jump to line 267, because the condition on line 266 was never true

267 self.makeSubtask("insertFakes") 

268 self.schema = schema 

269 self.makeSubtask("detection", schema=self.schema) 

270 if self.config.doScaleVariance: 270 ↛ 273line 270 didn't jump to line 273, because the condition on line 270 was never false

271 self.makeSubtask("scaleVariance") 

272 

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

274 

275 def runDataRef(self, patchRef): 

276 """! 

277 @brief Run detection on a coadd. 

278 

279 Invokes @ref run and then uses @ref write to output the 

280 results. 

281 

282 @param[in] patchRef: data reference for patch 

283 """ 

284 if self.config.hasFakes: 284 ↛ 285line 284 didn't jump to line 285, because the condition on line 284 was never true

285 exposure = patchRef.get("fakes_" + self.config.coaddName + "Coadd", immediate=True) 

286 else: 

287 exposure = patchRef.get(self.config.coaddName + "Coadd", immediate=True) 

288 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, log=self.log) 

289 results = self.run(exposure, self.makeIdFactory(patchRef), expId=expId) 

290 self.write(results, patchRef) 

291 return results 

292 

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

294 inputs = butlerQC.get(inputRefs) 

295 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch_band") 

296 inputs["idFactory"] = exposureIdInfo.makeSourceIdFactory() 

297 inputs["expId"] = exposureIdInfo.expId 

298 outputs = self.run(**inputs) 

299 butlerQC.put(outputs, outputRefs) 

300 

301 def run(self, exposure, idFactory, expId): 

302 """! 

303 @brief Run detection on an exposure. 

304 

305 First scale the variance plane to match the observed variance 

306 using @ref ScaleVarianceTask. Then invoke the @ref SourceDetectionTask_ "detection" subtask to 

307 detect sources. 

308 

309 @param[in,out] exposure: Exposure on which to detect (may be backround-subtracted and scaled, 

310 depending on configuration). 

311 @param[in] idFactory: IdFactory to set source identifiers 

312 @param[in] expId: Exposure identifier (integer) for RNG seed 

313 

314 @return a pipe.base.Struct with fields 

315 - sources: catalog of detections 

316 - backgrounds: list of backgrounds 

317 """ 

318 if self.config.doScaleVariance: 318 ↛ 321line 318 didn't jump to line 321, because the condition on line 318 was never false

319 varScale = self.scaleVariance.run(exposure.maskedImage) 

320 exposure.getMetadata().add("VARIANCE_SCALE", varScale) 

321 backgrounds = afwMath.BackgroundList() 

322 if self.config.doInsertFakes: 322 ↛ 323line 322 didn't jump to line 323, because the condition on line 322 was never true

323 self.insertFakes.run(exposure, background=backgrounds) 

324 table = afwTable.SourceTable.make(self.schema, idFactory) 

325 detections = self.detection.run(table, exposure, expId=expId) 

326 sources = detections.sources 

327 fpSets = detections.fpSets 

328 if hasattr(fpSets, "background") and fpSets.background: 328 ↛ 331line 328 didn't jump to line 331, because the condition on line 328 was never false

329 for bg in fpSets.background: 

330 backgrounds.append(bg) 

331 return Struct(outputSources=sources, outputBackgrounds=backgrounds, outputExposure=exposure) 

332 

333 def write(self, results, patchRef): 

334 """! 

335 @brief Write out results from runDetection. 

336 

337 @param[in] exposure: Exposure to write out 

338 @param[in] results: Struct returned from runDetection 

339 @param[in] patchRef: data reference for patch 

340 """ 

341 coaddName = self.config.coaddName + "Coadd" 

342 patchRef.put(results.outputBackgrounds, coaddName + "_calexp_background") 

343 patchRef.put(results.outputSources, coaddName + "_det") 

344 if self.config.hasFakes: 344 ↛ 345line 344 didn't jump to line 345, because the condition on line 344 was never true

345 patchRef.put(results.outputExposure, "fakes_" + coaddName + "_calexp") 

346 else: 

347 patchRef.put(results.outputExposure, coaddName + "_calexp") 

348 

349############################################################################################################## 

350 

351 

352class DeblendCoaddSourcesConfig(Config): 

353 """DeblendCoaddSourcesConfig 

354 

355 Configuration parameters for the `DeblendCoaddSourcesTask`. 

356 """ 

357 singleBandDeblend = ConfigurableField(target=SourceDeblendTask, 

358 doc="Deblend sources separately in each band") 

359 multiBandDeblend = ConfigurableField(target=ScarletDeblendTask, 

360 doc="Deblend sources simultaneously across bands") 

361 simultaneous = Field(dtype=bool, 

362 default=True, 

363 doc="Simultaneously deblend all bands? " 

364 "True uses `multibandDeblend` while False uses `singleBandDeblend`") 

365 coaddName = Field(dtype=str, default="deep", doc="Name of coadd") 

366 hasFakes = Field(dtype=bool, 

367 default=False, 

368 doc="Should be set to True if fake sources have been inserted into the input data.") 

369 

370 def setDefaults(self): 

371 Config.setDefaults(self) 

372 self.singleBandDeblend.propagateAllPeaks = True 

373 

374 

375class DeblendCoaddSourcesRunner(MergeSourcesRunner): 

376 """Task runner for the `MergeSourcesTask` 

377 

378 Required because the run method requires a list of 

379 dataRefs rather than a single dataRef. 

380 """ 

381 @staticmethod 

382 def getTargetList(parsedCmd, **kwargs): 

383 """Provide a list of patch references for each patch, tract, filter combo. 

384 

385 Parameters 

386 ---------- 

387 parsedCmd: 

388 The parsed command 

389 kwargs: 

390 Keyword arguments passed to the task 

391 

392 Returns 

393 ------- 

394 targetList: list 

395 List of tuples, where each tuple is a (dataRef, kwargs) pair. 

396 """ 

397 refDict = MergeSourcesRunner.buildRefDict(parsedCmd) 

398 kwargs["psfCache"] = parsedCmd.psfCache 

399 return [(list(p.values()), kwargs) for t in refDict.values() for p in t.values()] 

400 

401 

402class DeblendCoaddSourcesTask(CmdLineTask): 

403 """Deblend the sources in a merged catalog 

404 

405 Deblend sources from master catalog in each coadd. 

406 This can either be done separately in each band using the HSC-SDSS deblender 

407 (`DeblendCoaddSourcesTask.config.simultaneous==False`) 

408 or use SCARLET to simultaneously fit the blend in all bands 

409 (`DeblendCoaddSourcesTask.config.simultaneous==True`). 

410 The task will set its own `self.schema` atribute to the `Schema` of the 

411 output deblended catalog. 

412 This will include all fields from the input `Schema`, as well as additional fields 

413 from the deblender. 

414 

415 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description 

416 --------------------------------------------------------- 

417 ` 

418 

419 Parameters 

420 ---------- 

421 butler: `Butler` 

422 Butler used to read the input schemas from disk or 

423 construct the reference catalog loader, if `schema` or `peakSchema` or 

424 schema: `Schema` 

425 The schema of the merged detection catalog as an input to this task. 

426 peakSchema: `Schema` 

427 The schema of the `PeakRecord`s in the `Footprint`s in the merged detection catalog 

428 """ 

429 ConfigClass = DeblendCoaddSourcesConfig 

430 RunnerClass = DeblendCoaddSourcesRunner 

431 _DefaultName = "deblendCoaddSources" 

432 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False) 

433 

434 @classmethod 

435 def _makeArgumentParser(cls): 

436 parser = ArgumentParser(name=cls._DefaultName) 

437 parser.add_id_argument("--id", "deepCoadd_calexp", 

438 help="data ID, e.g. --id tract=12345 patch=1,2 filter=g^r^i", 

439 ContainerClass=ExistingCoaddDataIdContainer) 

440 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache") 

441 return parser 

442 

443 def __init__(self, butler=None, schema=None, peakSchema=None, **kwargs): 

444 CmdLineTask.__init__(self, **kwargs) 

445 if schema is None: 445 ↛ 448line 445 didn't jump to line 448, because the condition on line 445 was never false

446 assert butler is not None, "Neither butler nor schema is defined" 

447 schema = butler.get(self.config.coaddName + "Coadd_mergeDet_schema", immediate=True).schema 

448 self.schemaMapper = afwTable.SchemaMapper(schema) 

449 self.schemaMapper.addMinimalSchema(schema) 

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

451 if peakSchema is None: 451 ↛ 455line 451 didn't jump to line 455, because the condition on line 451 was never false

452 assert butler is not None, "Neither butler nor peakSchema is defined" 

453 peakSchema = butler.get(self.config.coaddName + "Coadd_peak_schema", immediate=True).schema 

454 

455 if self.config.simultaneous: 455 ↛ 458line 455 didn't jump to line 458, because the condition on line 455 was never false

456 self.makeSubtask("multiBandDeblend", schema=self.schema, peakSchema=peakSchema) 

457 else: 

458 self.makeSubtask("singleBandDeblend", schema=self.schema, peakSchema=peakSchema) 

459 

460 def getSchemaCatalogs(self): 

461 """Return a dict of empty catalogs for each catalog dataset produced by this task. 

462 

463 Returns 

464 ------- 

465 result: dict 

466 Dictionary of empty catalogs, with catalog names as keys. 

467 """ 

468 catalog = afwTable.SourceCatalog(self.schema) 

469 return {self.config.coaddName + "Coadd_deblendedFlux": catalog, 

470 self.config.coaddName + "Coadd_deblendedModel": catalog} 

471 

472 def runDataRef(self, patchRefList, psfCache=100): 

473 """Deblend the patch 

474 

475 Deblend each source simultaneously or separately 

476 (depending on `DeblendCoaddSourcesTask.config.simultaneous`). 

477 Set `is-primary` and related flags. 

478 Propagate flags from individual visits. 

479 Write the deblended sources out. 

480 

481 Parameters 

482 ---------- 

483 patchRefList: list 

484 List of data references for each filter 

485 """ 

486 

487 if self.config.hasFakes: 487 ↛ 488line 487 didn't jump to line 488, because the condition on line 487 was never true

488 coaddType = "fakes_" + self.config.coaddName 

489 else: 

490 coaddType = self.config.coaddName 

491 

492 if self.config.simultaneous: 492 ↛ 515line 492 didn't jump to line 515, because the condition on line 492 was never false

493 # Use SCARLET to simultaneously deblend across filters 

494 filters = [] 

495 exposures = [] 

496 for patchRef in patchRefList: 

497 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True) 

498 filter = patchRef.get(coaddType + "Coadd_filterLabel", immediate=True) 

499 filters.append(filter.bandLabel) 

500 exposures.append(exposure) 

501 # Sort inputs by band to match Gen3 order of inputs 

502 exposures = [exposure for _, exposure in sorted(zip(filters, exposures))] 

503 patchRefList = [patchRef for _, patchRef in sorted(zip(filters, patchRefList))] 

504 filters.sort() 

505 # The input sources are the same for all bands, since it is a merged catalog 

506 sources = self.readSources(patchRef) 

507 exposure = afwImage.MultibandExposure.fromExposures(filters, exposures) 

508 templateCatalogs, fluxCatalogs = self.multiBandDeblend.run(exposure, sources) 

509 for n in range(len(patchRefList)): 

510 self.write(patchRefList[n], templateCatalogs[filters[n]], "Model") 

511 if filters[n] in fluxCatalogs: 511 ↛ 509line 511 didn't jump to line 509, because the condition on line 511 was never false

512 self.write(patchRefList[n], fluxCatalogs[filters[n]], "Flux") 

513 else: 

514 # Use the singeband deblender to deblend each band separately 

515 for patchRef in patchRefList: 

516 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True) 

517 exposure.getPsf().setCacheCapacity(psfCache) 

518 sources = self.readSources(patchRef) 

519 self.singleBandDeblend.run(exposure, sources) 

520 self.write(patchRef, sources) 

521 

522 def readSources(self, dataRef): 

523 """Read merged catalog 

524 

525 Read the catalog of merged detections and create a catalog 

526 in a single band. 

527 

528 Parameters 

529 ---------- 

530 dataRef: data reference 

531 Data reference for catalog of merged detections 

532 

533 Returns 

534 ------- 

535 sources: `SourceCatalog` 

536 List of sources in merged catalog 

537 

538 We also need to add columns to hold the measurements we're about to make 

539 so we can measure in-place. 

540 """ 

541 merged = dataRef.get(self.config.coaddName + "Coadd_mergeDet", immediate=True) 

542 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId) 

543 idFactory = self.makeIdFactory(dataRef) 

544 # There may be gaps in the mergeDet catalog, which will cause the 

545 # source ids to be inconsistent. So we update the id factory 

546 # with the largest id already in the catalog. 

547 maxId = np.max(merged["id"]) 

548 idFactory.notify(maxId) 

549 table = afwTable.SourceTable.make(self.schema, idFactory) 

550 sources = afwTable.SourceCatalog(table) 

551 sources.extend(merged, self.schemaMapper) 

552 return sources 

553 

554 def write(self, dataRef, sources, catalogType): 

555 """Write the source catalog(s) 

556 

557 Parameters 

558 ---------- 

559 dataRef: Data Reference 

560 Reference to the output catalog. 

561 sources: `SourceCatalog` 

562 Flux conserved sources to write to file. 

563 If using the single band deblender, this is the catalog 

564 generated. 

565 template_sources: `SourceCatalog` 

566 Source catalog using the multiband template models 

567 as footprints. 

568 """ 

569 dataRef.put(sources, self.config.coaddName + f"Coadd_deblended{catalogType}") 

570 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId) 

571 

572 def writeMetadata(self, dataRefList): 

573 """Write the metadata produced from processing the data. 

574 Parameters 

575 ---------- 

576 dataRefList 

577 List of Butler data references used to write the metadata. 

578 The metadata is written to dataset type `CmdLineTask._getMetadataName`. 

579 """ 

580 for dataRef in dataRefList: 

581 try: 

582 metadataName = self._getMetadataName() 

583 if metadataName is not None: 

584 dataRef.put(self.getFullMetadata(), metadataName) 

585 except Exception as e: 

586 self.log.warning("Could not persist metadata for dataId=%s: %s", dataRef.dataId, e) 

587 

588 

589class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections, 

590 dimensions=("tract", "patch", "band", "skymap"), 

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

592 "outputCoaddName": "deep"}): 

593 inputSchema = cT.InitInput( 

594 doc="Input schema for measure merged task produced by a deblender or detection task", 

595 name="{inputCoaddName}Coadd_deblendedFlux_schema", 

596 storageClass="SourceCatalog" 

597 ) 

598 outputSchema = cT.InitOutput( 

599 doc="Output schema after all new fields are added by task", 

600 name="{inputCoaddName}Coadd_meas_schema", 

601 storageClass="SourceCatalog" 

602 ) 

603 refCat = cT.PrerequisiteInput( 

604 doc="Reference catalog used to match measured sources against known sources", 

605 name="ref_cat", 

606 storageClass="SimpleCatalog", 

607 dimensions=("skypix",), 

608 deferLoad=True, 

609 multiple=True 

610 ) 

611 exposure = cT.Input( 

612 doc="Input coadd image", 

613 name="{inputCoaddName}Coadd_calexp", 

614 storageClass="ExposureF", 

615 dimensions=("tract", "patch", "band", "skymap") 

616 ) 

617 skyMap = cT.Input( 

618 doc="SkyMap to use in processing", 

619 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME, 

620 storageClass="SkyMap", 

621 dimensions=("skymap",), 

622 ) 

623 visitCatalogs = cT.Input( 

624 doc="Source catalogs for visits which overlap input tract, patch, band. Will be " 

625 "further filtered in the task for the purpose of propagating flags from image calibration " 

626 "and characterization to codd objects", 

627 name="src", 

628 dimensions=("instrument", "visit", "detector"), 

629 storageClass="SourceCatalog", 

630 multiple=True 

631 ) 

632 inputCatalog = cT.Input( 

633 doc=("Name of the input catalog to use." 

634 "If the single band deblender was used this should be 'deblendedFlux." 

635 "If the multi-band deblender was used this should be 'deblendedModel, " 

636 "or deblendedFlux if the multiband deblender was configured to output " 

637 "deblended flux catalogs. If no deblending was performed this should " 

638 "be 'mergeDet'"), 

639 name="{inputCoaddName}Coadd_deblendedFlux", 

640 storageClass="SourceCatalog", 

641 dimensions=("tract", "patch", "band", "skymap"), 

642 ) 

643 outputSources = cT.Output( 

644 doc="Source catalog containing all the measurement information generated in this task", 

645 name="{outputCoaddName}Coadd_meas", 

646 dimensions=("tract", "patch", "band", "skymap"), 

647 storageClass="SourceCatalog", 

648 ) 

649 matchResult = cT.Output( 

650 doc="Match catalog produced by configured matcher, optional on doMatchSources", 

651 name="{outputCoaddName}Coadd_measMatch", 

652 dimensions=("tract", "patch", "band", "skymap"), 

653 storageClass="Catalog", 

654 ) 

655 denormMatches = cT.Output( 

656 doc="Denormalized Match catalog produced by configured matcher, optional on " 

657 "doWriteMatchesDenormalized", 

658 name="{outputCoaddName}Coadd_measMatchFull", 

659 dimensions=("tract", "patch", "band", "skymap"), 

660 storageClass="Catalog", 

661 ) 

662 

663 def __init__(self, *, config=None): 

664 super().__init__(config=config) 

665 if config.doPropagateFlags is False: 

666 self.inputs -= set(("visitCatalogs",)) 

667 

668 if config.doMatchSources is False: 

669 self.outputs -= set(("matchResult",)) 

670 

671 if config.doWriteMatchesDenormalized is False: 

672 self.outputs -= set(("denormMatches",)) 

673 

674 

675class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig, 

676 pipelineConnections=MeasureMergedCoaddSourcesConnections): 

677 """! 

678 @anchor MeasureMergedCoaddSourcesConfig_ 

679 

680 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask 

681 """ 

682 inputCatalog = Field(dtype=str, default="deblendedFlux", 

683 doc=("Name of the input catalog to use." 

684 "If the single band deblender was used this should be 'deblendedFlux." 

685 "If the multi-band deblender was used this should be 'deblendedModel." 

686 "If no deblending was performed this should be 'mergeDet'")) 

687 measurement = ConfigurableField(target=SingleFrameMeasurementTask, doc="Source measurement") 

688 setPrimaryFlags = ConfigurableField(target=SetPrimaryFlagsTask, doc="Set flags for primary tract/patch") 

689 doPropagateFlags = Field( 

690 dtype=bool, default=True, 

691 doc="Whether to match sources to CCD catalogs to propagate flags (to e.g. identify PSF stars)" 

692 ) 

693 propagateFlags = ConfigurableField(target=PropagateVisitFlagsTask, doc="Propagate visit flags to coadd") 

694 doMatchSources = Field(dtype=bool, default=True, doc="Match sources to reference catalog?") 

695 match = ConfigurableField(target=DirectMatchTask, doc="Matching to reference catalog") 

696 doWriteMatchesDenormalized = Field( 

697 dtype=bool, 

698 default=False, 

699 doc=("Write reference matches in denormalized format? " 

700 "This format uses more disk space, but is more convenient to read."), 

701 ) 

702 coaddName = Field(dtype=str, default="deep", doc="Name of coadd") 

703 psfCache = Field(dtype=int, default=100, doc="Size of psfCache") 

704 checkUnitsParseStrict = Field( 

705 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'", 

706 dtype=str, 

707 default="raise", 

708 ) 

709 doApCorr = Field( 

710 dtype=bool, 

711 default=True, 

712 doc="Apply aperture corrections" 

713 ) 

714 applyApCorr = ConfigurableField( 

715 target=ApplyApCorrTask, 

716 doc="Subtask to apply aperture corrections" 

717 ) 

718 doRunCatalogCalculation = Field( 

719 dtype=bool, 

720 default=True, 

721 doc='Run catalogCalculation task' 

722 ) 

723 catalogCalculation = ConfigurableField( 

724 target=CatalogCalculationTask, 

725 doc="Subtask to run catalogCalculation plugins on catalog" 

726 ) 

727 

728 hasFakes = Field( 

729 dtype=bool, 

730 default=False, 

731 doc="Should be set to True if fake sources have been inserted into the input data." 

732 ) 

733 

734 @property 

735 def refObjLoader(self): 

736 return self.match.refObjLoader 

737 

738 def setDefaults(self): 

739 super().setDefaults() 

740 self.measurement.plugins.names |= ['base_InputCount', 

741 'base_Variance', 

742 'base_LocalPhotoCalib', 

743 'base_LocalWcs'] 

744 self.measurement.plugins['base_PixelFlags'].masksFpAnywhere = ['CLIPPED', 'SENSOR_EDGE', 

745 'INEXACT_PSF'] 

746 self.measurement.plugins['base_PixelFlags'].masksFpCenter = ['CLIPPED', 'SENSOR_EDGE', 

747 'INEXACT_PSF'] 

748 

749 def validate(self): 

750 super().validate() 

751 refCatGen2 = getattr(self.refObjLoader, "ref_dataset_name", None) 

752 if refCatGen2 is not None and refCatGen2 != self.connections.refCat: 

753 raise ValueError( 

754 f"Gen2 ({refCatGen2}) and Gen3 ({self.connections.refCat}) reference catalogs " 

755 f"are different. These options must be kept in sync until Gen2 is retired." 

756 ) 

757 

758 

759## @addtogroup LSST_task_documentation 

760## @{ 

761## @page MeasureMergedCoaddSourcesTask 

762## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask" 

763## @copybrief MeasureMergedCoaddSourcesTask 

764## @} 

765 

766 

767class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner): 

768 """Get the psfCache setting into MeasureMergedCoaddSourcesTask""" 

769 @staticmethod 

770 def getTargetList(parsedCmd, **kwargs): 

771 return ButlerInitializedTaskRunner.getTargetList(parsedCmd, psfCache=parsedCmd.psfCache) 

772 

773 

774class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask): 

775 r"""! 

776 @anchor MeasureMergedCoaddSourcesTask_ 

777 

778 @brief Deblend sources from master catalog in each coadd seperately and measure. 

779 

780 @section pipe_tasks_multiBand_Contents Contents 

781 

782 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose 

783 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize 

784 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run 

785 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config 

786 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug 

787 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example 

788 

789 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description 

790 

791 Command-line task that uses peaks and footprints from a master catalog to perform deblending and 

792 measurement in each coadd. 

793 

794 Given a master input catalog of sources (peaks and footprints) or deblender outputs 

795 (including a HeavyFootprint in each band), measure each source on the 

796 coadd. Repeating this procedure with the same master catalog across multiple coadds will generate a 

797 consistent set of child sources. 

798 

799 The deblender retains all peaks and deblends any missing peaks (dropouts in that band) as PSFs. Source 

800 properties are measured and the @c is-primary flag (indicating sources with no children) is set. Visit 

801 flags are propagated to the coadd sources. 

802 

803 Optionally, we can match the coadd sources to an external reference catalog. 

804 

805 @par Inputs: 

806 deepCoadd_mergeDet{tract,patch} or deepCoadd_deblend{tract,patch}: SourceCatalog 

807 @n deepCoadd_calexp{tract,patch,filter}: ExposureF 

808 @par Outputs: 

809 deepCoadd_meas{tract,patch,filter}: SourceCatalog 

810 @par Data Unit: 

811 tract, patch, filter 

812 

813 MeasureMergedCoaddSourcesTask delegates most of its work to a set of sub-tasks: 

814 

815 <DL> 

816 <DT> @ref SingleFrameMeasurementTask_ "measurement" 

817 <DD> Measure source properties of deblended sources.</DD> 

818 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags" 

819 <DD> Set flag 'is-primary' as well as related flags on sources. 'is-primary' is set for sources that are 

820 not at the edge of the field and that have either not been deblended or are the children of deblended 

821 sources</DD> 

822 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags" 

823 <DD> Propagate flags set in individual visits to the coadd.</DD> 

824 <DT> @ref DirectMatchTask_ "match" 

825 <DD> Match input sources to a reference catalog (optional). 

826 </DD> 

827 </DL> 

828 These subtasks may be retargeted as required. 

829 

830 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization 

831 

832 @copydoc \_\_init\_\_ 

833 

834 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task 

835 

836 @copydoc run 

837 

838 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters 

839 

840 See @ref MeasureMergedCoaddSourcesConfig_ 

841 

842 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables 

843 

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

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

846 files. 

847 

848 MeasureMergedCoaddSourcesTask has no debug variables of its own because it delegates all the work to 

849 the various sub-tasks. See the documetation for individual sub-tasks for more information. 

850 

851 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using 

852 MeasureMergedCoaddSourcesTask 

853 

854 After MeasureMergedCoaddSourcesTask has been run on multiple coadds, we have a set of per-band catalogs. 

855 The next stage in the multi-band processing procedure will merge these measurements into a suitable 

856 catalog for driving forced photometry. 

857 

858 Command-line usage of MeasureMergedCoaddSourcesTask expects a data reference to the coadds 

859 to be processed. 

860 A list of the available optional arguments can be obtained by calling measureCoaddSources.py with the 

861 `--help` command line argument: 

862 @code 

863 measureCoaddSources.py --help 

864 @endcode 

865 

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

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

868 step 6 at @ref pipeTasks_multiBand, one may perform deblending and measure sources in the HSC-I band 

869 coadd as follows: 

870 @code 

871 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I 

872 @endcode 

873 This will process the HSC-I band data. The results are written in 

874 `$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I/0/5,4/meas-HSC-I-0-5,4.fits 

875 

876 It is also necessary to run 

877 @code 

878 measureCoaddSources.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R 

879 @endcode 

880 to generate the sources catalogs for the HSC-R band required by the next step in the multi-band 

881 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask". 

882 """ 

883 _DefaultName = "measureCoaddSources" 

884 ConfigClass = MeasureMergedCoaddSourcesConfig 

885 RunnerClass = MeasureMergedCoaddSourcesRunner 

886 getSchemaCatalogs = _makeGetSchemaCatalogs("meas") 

887 # The IDs we already have are of this type 

888 makeIdFactory = _makeMakeIdFactory("MergedCoaddId", includeBand=False) 

889 

890 @classmethod 

891 def _makeArgumentParser(cls): 

892 parser = ArgumentParser(name=cls._DefaultName) 

893 parser.add_id_argument("--id", "deepCoadd_calexp", 

894 help="data ID, e.g. --id tract=12345 patch=1,2 filter=r", 

895 ContainerClass=ExistingCoaddDataIdContainer) 

896 parser.add_argument("--psfCache", type=int, default=100, help="Size of CoaddPsf cache") 

897 return parser 

898 

899 def __init__(self, butler=None, schema=None, peakSchema=None, refObjLoader=None, initInputs=None, 

900 **kwargs): 

901 """! 

902 @brief Initialize the task. 

903 

904 Keyword arguments (in addition to those forwarded to CmdLineTask.__init__): 

905 @param[in] schema: the schema of the merged detection catalog used as input to this one 

906 @param[in] peakSchema: the schema of the PeakRecords in the Footprints in the merged detection catalog 

907 @param[in] refObjLoader: an instance of LoadReferenceObjectsTasks that supplies an external reference 

908 catalog. May be None if the loader can be constructed from the butler argument or all steps 

909 requiring a reference catalog are disabled. 

910 @param[in] butler: a butler used to read the input schemas from disk or construct the reference 

911 catalog loader, if schema or peakSchema or refObjLoader is None 

912 

913 The task will set its own self.schema attribute to the schema of the output measurement catalog. 

914 This will include all fields from the input schema, as well as additional fields for all the 

915 measurements. 

916 """ 

917 super().__init__(**kwargs) 

918 self.deblended = self.config.inputCatalog.startswith("deblended") 

919 self.inputCatalog = "Coadd_" + self.config.inputCatalog 

920 if initInputs is not None: 920 ↛ 921line 920 didn't jump to line 921, because the condition on line 920 was never true

921 schema = initInputs['inputSchema'].schema 

922 if schema is None: 922 ↛ 925line 922 didn't jump to line 925, because the condition on line 922 was never false

923 assert butler is not None, "Neither butler nor schema is defined" 

924 schema = butler.get(self.config.coaddName + self.inputCatalog + "_schema", immediate=True).schema 

925 self.schemaMapper = afwTable.SchemaMapper(schema) 

926 self.schemaMapper.addMinimalSchema(schema) 

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

928 self.algMetadata = PropertyList() 

929 self.makeSubtask("measurement", schema=self.schema, algMetadata=self.algMetadata) 

930 self.makeSubtask("setPrimaryFlags", schema=self.schema) 

931 if self.config.doMatchSources: 931 ↛ 932line 931 didn't jump to line 932, because the condition on line 931 was never true

932 self.makeSubtask("match", butler=butler, refObjLoader=refObjLoader) 

933 if self.config.doPropagateFlags: 933 ↛ 935line 933 didn't jump to line 935, because the condition on line 933 was never false

934 self.makeSubtask("propagateFlags", schema=self.schema) 

935 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict) 

936 if self.config.doApCorr: 936 ↛ 938line 936 didn't jump to line 938, because the condition on line 936 was never false

937 self.makeSubtask("applyApCorr", schema=self.schema) 

938 if self.config.doRunCatalogCalculation: 938 ↛ 941line 938 didn't jump to line 941, because the condition on line 938 was never false

939 self.makeSubtask("catalogCalculation", schema=self.schema) 

940 

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

942 

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

944 inputs = butlerQC.get(inputRefs) 

945 

946 refObjLoader = ReferenceObjectLoader([ref.datasetRef.dataId for ref in inputRefs.refCat], 

947 inputs.pop('refCat'), config=self.config.refObjLoader, 

948 log=self.log) 

949 self.match.setRefObjLoader(refObjLoader) 

950 

951 # Set psfcache 

952 # move this to run after gen2 deprecation 

953 inputs['exposure'].getPsf().setCacheCapacity(self.config.psfCache) 

954 

955 # Get unique integer ID for IdFactory and RNG seeds 

956 exposureIdInfo = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "tract_patch") 

957 inputs['exposureId'] = exposureIdInfo.expId 

958 idFactory = exposureIdInfo.makeSourceIdFactory() 

959 # Transform inputCatalog 

960 table = afwTable.SourceTable.make(self.schema, idFactory) 

961 sources = afwTable.SourceCatalog(table) 

962 sources.extend(inputs.pop('inputCatalog'), self.schemaMapper) 

963 table = sources.getTable() 

964 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog. 

965 inputs['sources'] = sources 

966 

967 skyMap = inputs.pop('skyMap') 

968 tractNumber = inputRefs.inputCatalog.dataId['tract'] 

969 tractInfo = skyMap[tractNumber] 

970 patchInfo = tractInfo.getPatchInfo(inputRefs.inputCatalog.dataId['patch']) 

971 skyInfo = Struct( 

972 skyMap=skyMap, 

973 tractInfo=tractInfo, 

974 patchInfo=patchInfo, 

975 wcs=tractInfo.getWcs(), 

976 bbox=patchInfo.getOuterBBox() 

977 ) 

978 inputs['skyInfo'] = skyInfo 

979 

980 if self.config.doPropagateFlags: 

981 # Filter out any visit catalog that is not coadd inputs 

982 ccdInputs = inputs['exposure'].getInfo().getCoaddInputs().ccds 

983 visitKey = ccdInputs.schema.find("visit").key 

984 ccdKey = ccdInputs.schema.find("ccd").key 

985 inputVisitIds = set() 

986 ccdRecordsWcs = {} 

987 for ccdRecord in ccdInputs: 

988 visit = ccdRecord.get(visitKey) 

989 ccd = ccdRecord.get(ccdKey) 

990 inputVisitIds.add((visit, ccd)) 

991 ccdRecordsWcs[(visit, ccd)] = ccdRecord.getWcs() 

992 

993 inputCatalogsToKeep = [] 

994 inputCatalogWcsUpdate = [] 

995 for i, dataRef in enumerate(inputRefs.visitCatalogs): 

996 key = (dataRef.dataId['visit'], dataRef.dataId['detector']) 

997 if key in inputVisitIds: 

998 inputCatalogsToKeep.append(inputs['visitCatalogs'][i]) 

999 inputCatalogWcsUpdate.append(ccdRecordsWcs[key]) 

1000 inputs['visitCatalogs'] = inputCatalogsToKeep 

1001 inputs['wcsUpdates'] = inputCatalogWcsUpdate 

1002 inputs['ccdInputs'] = ccdInputs 

1003 

1004 outputs = self.run(**inputs) 

1005 butlerQC.put(outputs, outputRefs) 

1006 

1007 def runDataRef(self, patchRef, psfCache=100): 

1008 """! 

1009 @brief Deblend and measure. 

1010 

1011 @param[in] patchRef: Patch reference. 

1012 

1013 Set 'is-primary' and related flags. Propagate flags 

1014 from individual visits. Optionally match the sources to a reference catalog and write the matches. 

1015 Finally, write the deblended sources and measurements out. 

1016 """ 

1017 if self.config.hasFakes: 1017 ↛ 1018line 1017 didn't jump to line 1018, because the condition on line 1017 was never true

1018 coaddType = "fakes_" + self.config.coaddName 

1019 else: 

1020 coaddType = self.config.coaddName 

1021 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True) 

1022 exposure.getPsf().setCacheCapacity(psfCache) 

1023 sources = self.readSources(patchRef) 

1024 table = sources.getTable() 

1025 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog. 

1026 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef) 

1027 

1028 if self.config.doPropagateFlags: 1028 ↛ 1031line 1028 didn't jump to line 1031, because the condition on line 1028 was never false

1029 ccdInputs = self.propagateFlags.getCcdInputs(exposure) 

1030 else: 

1031 ccdInputs = None 

1032 

1033 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=False, 

1034 log=self.log) 

1035 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId, 

1036 ccdInputs=ccdInputs, butler=patchRef.getButler()) 

1037 

1038 if self.config.doMatchSources: 1038 ↛ 1039line 1038 didn't jump to line 1039, because the condition on line 1038 was never true

1039 self.writeMatches(patchRef, results) 

1040 self.write(patchRef, results.outputSources) 

1041 

1042 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None, 

1043 butler=None): 

1044 """Run measurement algorithms on the input exposure, and optionally populate the 

1045 resulting catalog with extra information. 

1046 

1047 Parameters 

1048 ---------- 

1049 exposure : `lsst.afw.exposure.Exposure` 

1050 The input exposure on which measurements are to be performed 

1051 sources : `lsst.afw.table.SourceCatalog` 

1052 A catalog built from the results of merged detections, or 

1053 deblender outputs. 

1054 skyInfo : `lsst.pipe.base.Struct` 

1055 A struct containing information about the position of the input exposure within 

1056 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box 

1057 exposureId : `int` or `bytes` 

1058 packed unique number or bytes unique to the input exposure 

1059 ccdInputs : `lsst.afw.table.ExposureCatalog` 

1060 Catalog containing information on the individual visits which went into making 

1061 the exposure 

1062 visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None` 

1063 A list of source catalogs corresponding to measurements made on the individual 

1064 visits which went into the input exposure. If None and butler is `None` then 

1065 the task cannot propagate visit flags to the output catalog. 

1066 wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None` 

1067 If visitCatalogs is not `None` this should be a list of wcs objects which correspond 

1068 to the input visits. Used to put all coordinates to common system. If `None` and 

1069 butler is `None` then the task cannot propagate visit flags to the output catalog. 

1070 butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler` 

1071 Either a gen2 or gen3 butler used to load visit catalogs 

1072 

1073 Returns 

1074 ------- 

1075 results : `lsst.pipe.base.Struct` 

1076 Results of running measurement task. Will contain the catalog in the 

1077 sources attribute. Optionally will have results of matching to a 

1078 reference catalog in the matchResults attribute, and denormalized 

1079 matches in the denormMatches attribute. 

1080 """ 

1081 self.measurement.run(sources, exposure, exposureId=exposureId) 

1082 

1083 if self.config.doApCorr: 1083 ↛ 1093line 1083 didn't jump to line 1093, because the condition on line 1083 was never false

1084 self.applyApCorr.run( 

1085 catalog=sources, 

1086 apCorrMap=exposure.getInfo().getApCorrMap() 

1087 ) 

1088 

1089 # TODO DM-11568: this contiguous check-and-copy could go away if we 

1090 # reserve enough space during SourceDetection and/or SourceDeblend. 

1091 # NOTE: sourceSelectors require contiguous catalogs, so ensure 

1092 # contiguity now, so views are preserved from here on. 

1093 if not sources.isContiguous(): 1093 ↛ 1094line 1093 didn't jump to line 1094, because the condition on line 1093 was never true

1094 sources = sources.copy(deep=True) 

1095 

1096 if self.config.doRunCatalogCalculation: 1096 ↛ 1099line 1096 didn't jump to line 1099, because the condition on line 1096 was never false

1097 self.catalogCalculation.run(sources) 

1098 

1099 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo, 

1100 patchInfo=skyInfo.patchInfo) 

1101 if self.config.doPropagateFlags: 1101 ↛ 1104line 1101 didn't jump to line 1104, because the condition on line 1101 was never false

1102 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates) 

1103 

1104 results = Struct() 

1105 

1106 if self.config.doMatchSources: 1106 ↛ 1107line 1106 didn't jump to line 1107, because the condition on line 1106 was never true

1107 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel) 

1108 matches = afwTable.packMatches(matchResult.matches) 

1109 matches.table.setMetadata(matchResult.matchMeta) 

1110 results.matchResult = matches 

1111 if self.config.doWriteMatchesDenormalized: 

1112 if matchResult.matches: 

1113 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta) 

1114 else: 

1115 self.log.warning("No matches, so generating dummy denormalized matches file") 

1116 denormMatches = afwTable.BaseCatalog(afwTable.Schema()) 

1117 denormMatches.setMetadata(PropertyList()) 

1118 denormMatches.getMetadata().add("COMMENT", 

1119 "This catalog is empty because no matches were found.") 

1120 results.denormMatches = denormMatches 

1121 results.denormMatches = denormMatches 

1122 

1123 results.outputSources = sources 

1124 return results 

1125 

1126 def readSources(self, dataRef): 

1127 """! 

1128 @brief Read input sources. 

1129 

1130 @param[in] dataRef: Data reference for catalog of merged detections 

1131 @return List of sources in merged catalog 

1132 

1133 We also need to add columns to hold the measurements we're about to make 

1134 so we can measure in-place. 

1135 """ 

1136 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True) 

1137 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId) 

1138 idFactory = self.makeIdFactory(dataRef) 

1139 for s in merged: 

1140 idFactory.notify(s.getId()) 

1141 table = afwTable.SourceTable.make(self.schema, idFactory) 

1142 sources = afwTable.SourceCatalog(table) 

1143 sources.extend(merged, self.schemaMapper) 

1144 return sources 

1145 

1146 def writeMatches(self, dataRef, results): 

1147 """! 

1148 @brief Write matches of the sources to the astrometric reference catalog. 

1149 

1150 @param[in] dataRef: data reference 

1151 @param[in] results: results struct from run method 

1152 """ 

1153 if hasattr(results, "matchResult"): 

1154 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch") 

1155 if hasattr(results, "denormMatches"): 

1156 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull") 

1157 

1158 def write(self, dataRef, sources): 

1159 """! 

1160 @brief Write the source catalog. 

1161 

1162 @param[in] dataRef: data reference 

1163 @param[in] sources: source catalog 

1164 """ 

1165 dataRef.put(sources, self.config.coaddName + "Coadd_meas") 

1166 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)