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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# 

23from lsst.coadd.utils.coaddDataIdContainer import ExistingCoaddDataIdContainer 

24from lsst.pipe.base import (CmdLineTask, Struct, ArgumentParser, ButlerInitializedTaskRunner, 

25 PipelineTask, PipelineTaskConfig, PipelineTaskConnections) 

26import lsst.pipe.base.connectionTypes as cT 

27from lsst.pex.config import Config, Field, ConfigurableField 

28from lsst.meas.algorithms import DynamicDetectionTask, ReferenceObjectLoader 

29from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask 

30from lsst.meas.deblender import SourceDeblendTask 

31from lsst.meas.extensions.scarlet import ScarletDeblendTask 

32from lsst.pipe.tasks.coaddBase import getSkyInfo 

33from lsst.pipe.tasks.scaleVariance import ScaleVarianceTask 

34from lsst.meas.astrom import DirectMatchTask, denormalizeMatches 

35from lsst.pipe.tasks.fakes import BaseFakeSourcesTask 

36from lsst.pipe.tasks.setPrimaryFlags import SetPrimaryFlagsTask 

37from lsst.pipe.tasks.propagateVisitFlags import PropagateVisitFlagsTask 

38import lsst.afw.image as afwImage 

39import lsst.afw.table as afwTable 

40import lsst.afw.math as afwMath 

41from lsst.daf.base import PropertyList 

42from lsst.skymap import BaseSkyMap 

43 

44from .mergeDetections import MergeDetectionsConfig, MergeDetectionsTask # noqa: F401 

45from .mergeMeasurements import MergeMeasurementsConfig, MergeMeasurementsTask # noqa: F401 

46from .multiBandUtils import MergeSourcesRunner, CullPeaksConfig, _makeGetSchemaCatalogs # noqa: F401 

47from .multiBandUtils import getInputSchema, getShortFilterName, readCatalog, _makeMakeIdFactory # noqa: F401 

48from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleConfig # noqa: F401 

49from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesSingleTask # noqa: F401 

50from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiConfig # noqa: F401 

51from .deblendCoaddSourcesPipeline import DeblendCoaddSourcesMultiTask # noqa: F401 

52 

53 

54""" 

55New set types: 

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

57* deepCoadd_mergeDet: merged detections (tract, patch) 

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

59* deepCoadd_ref: reference sources (tract, patch) 

60All of these have associated *_schema catalogs that require no data ID and hold no records. 

61 

62In addition, we have a schema-only dataset, which saves the schema for the PeakRecords in 

63the mergeDet, meas, and ref dataset Footprints: 

64* deepCoadd_peak_schema 

65""" 

66 

67 

68############################################################################################################## 

69class DetectCoaddSourcesConnections(PipelineTaskConnections, 

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

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

72 detectionSchema = cT.InitOutput( 

73 doc="Schema of the detection catalog", 

74 name="{outputCoaddName}Coadd_det_schema", 

75 storageClass="SourceCatalog", 

76 ) 

77 exposure = cT.Input( 

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

79 name="{inputCoaddName}Coadd", 

80 storageClass="ExposureF", 

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

82 ) 

83 outputBackgrounds = cT.Output( 

84 doc="Output Backgrounds used in detection", 

85 name="{outputCoaddName}Coadd_calexp_background", 

86 storageClass="Background", 

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

88 ) 

89 outputSources = cT.Output( 

90 doc="Detected sources catalog", 

91 name="{outputCoaddName}Coadd_det", 

92 storageClass="SourceCatalog", 

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

94 ) 

95 outputExposure = cT.Output( 

96 doc="Exposure post detection", 

97 name="{outputCoaddName}Coadd_calexp", 

98 storageClass="ExposureF", 

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

100 ) 

101 

102 

103class DetectCoaddSourcesConfig(PipelineTaskConfig, pipelineConnections=DetectCoaddSourcesConnections): 

104 """! 

105 @anchor DetectCoaddSourcesConfig_ 

106 

107 @brief Configuration parameters for the DetectCoaddSourcesTask 

108 """ 

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

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

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

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

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

114 doc="Run fake sources injection task") 

115 insertFakes = ConfigurableField(target=BaseFakeSourcesTask, 

116 doc="Injection of fake sources for testing " 

117 "purposes (must be retargeted)") 

118 hasFakes = Field( 

119 dtype=bool, 

120 default=False, 

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

122 ) 

123 

124 def setDefaults(self): 

125 super().setDefaults() 

126 self.detection.thresholdType = "pixel_stdev" 

127 self.detection.isotropicGrow = True 

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

129 self.detection.reEstimateBackground = False 

130 self.detection.background.useApprox = False 

131 self.detection.background.binSize = 4096 

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

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

134 

135## @addtogroup LSST_task_documentation 

136## @{ 

137## @page DetectCoaddSourcesTask 

138## @ref DetectCoaddSourcesTask_ "DetectCoaddSourcesTask" 

139## @copybrief DetectCoaddSourcesTask 

140## @} 

141 

142 

143class DetectCoaddSourcesTask(PipelineTask, CmdLineTask): 

144 r"""! 

145 @anchor DetectCoaddSourcesTask_ 

146 

147 @brief Detect sources on a coadd 

148 

149 @section pipe_tasks_multiBand_Contents Contents 

150 

151 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose 

152 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize 

153 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Run 

154 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Config 

155 - @ref pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug 

156 - @ref pipe_tasks_multiband_DetectCoaddSourcesTask_Example 

157 

158 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Purpose Description 

159 

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

161 

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

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

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

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

166 

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

168 SourceDetectionTask_ "detection" subtask. 

169 

170 @par Inputs: 

171 deepCoadd{tract,patch,filter}: ExposureF 

172 @par Outputs: 

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

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

175 exposure (ExposureF) 

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

177 @par Data Unit: 

178 tract, patch, filter 

179 

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

181 You can retarget this subtask if you wish. 

182 

183 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Initialize Task initialization 

184 

185 @copydoc \_\_init\_\_ 

186 

187 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Run Invoking the Task 

188 

189 @copydoc run 

190 

191 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Config Configuration parameters 

192 

193 See @ref DetectCoaddSourcesConfig_ "DetectSourcesConfig" 

194 

195 @section pipe_tasks_multiBand_DetectCoaddSourcesTask_Debug Debug variables 

196 

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

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

199 files. 

200 

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

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

203 @ref SourceDetectionTask_ "SourceDetectionTask" for further information. 

204 

205 @section pipe_tasks_multiband_DetectCoaddSourcesTask_Example A complete example 

206 of using DetectCoaddSourcesTask 

207 

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

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

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

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

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

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

214 @code 

215 detectCoaddSources.py --help 

216 @endcode 

217 

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

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

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

221 @code 

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

223 @endcode 

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

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

226 

227 It is also necessary to run: 

228 @code 

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

230 @endcode 

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

232 processing procedure: @ref MergeDetectionsTask_ "MergeDetectionsTask". 

233 """ 

234 _DefaultName = "detectCoaddSources" 

235 ConfigClass = DetectCoaddSourcesConfig 

236 getSchemaCatalogs = _makeGetSchemaCatalogs("det") 

237 makeIdFactory = _makeMakeIdFactory("CoaddId") 

238 

239 @classmethod 

240 def _makeArgumentParser(cls): 

241 parser = ArgumentParser(name=cls._DefaultName) 

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

243 ContainerClass=ExistingCoaddDataIdContainer) 

244 return parser 

245 

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

247 """! 

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

249 

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

251 

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

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

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

255 """ 

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

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

258 super().__init__(**kwargs) 

259 if schema is None: 

260 schema = afwTable.SourceTable.makeMinimalSchema() 

261 if self.config.doInsertFakes: 

262 self.makeSubtask("insertFakes") 

263 self.schema = schema 

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

265 if self.config.doScaleVariance: 

266 self.makeSubtask("scaleVariance") 

267 

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

269 

270 def runDataRef(self, patchRef): 

271 """! 

272 @brief Run detection on a coadd. 

273 

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

275 results. 

276 

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

278 """ 

279 if self.config.hasFakes: 

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

281 else: 

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

283 expId = int(patchRef.get(self.config.coaddName + "CoaddId")) 

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

285 self.write(results, patchRef) 

286 return results 

287 

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

289 inputs = butlerQC.get(inputRefs) 

290 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch_band", returnMaxBits=True) 

291 inputs["idFactory"] = afwTable.IdFactory.makeSource(packedId, 64 - maxBits) 

292 inputs["expId"] = packedId 

293 outputs = self.run(**inputs) 

294 butlerQC.put(outputs, outputRefs) 

295 

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

297 """! 

298 @brief Run detection on an exposure. 

299 

300 First scale the variance plane to match the observed variance 

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

302 detect sources. 

303 

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

305 depending on configuration). 

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

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

308 

309 @return a pipe.base.Struct with fields 

310 - sources: catalog of detections 

311 - backgrounds: list of backgrounds 

312 """ 

313 if self.config.doScaleVariance: 

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

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

316 backgrounds = afwMath.BackgroundList() 

317 if self.config.doInsertFakes: 

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

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

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

321 sources = detections.sources 

322 fpSets = detections.fpSets 

323 if hasattr(fpSets, "background") and fpSets.background: 

324 for bg in fpSets.background: 

325 backgrounds.append(bg) 

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

327 

328 def write(self, results, patchRef): 

329 """! 

330 @brief Write out results from runDetection. 

331 

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

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

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

335 """ 

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

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

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

339 if self.config.hasFakes: 

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

341 else: 

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

343 

344############################################################################################################## 

345 

346 

347class DeblendCoaddSourcesConfig(Config): 

348 """DeblendCoaddSourcesConfig 

349 

350 Configuration parameters for the `DeblendCoaddSourcesTask`. 

351 """ 

352 singleBandDeblend = ConfigurableField(target=SourceDeblendTask, 

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

354 multiBandDeblend = ConfigurableField(target=ScarletDeblendTask, 

355 doc="Deblend sources simultaneously across bands") 

356 simultaneous = Field(dtype=bool, default=False, doc="Simultaneously deblend all bands?") 

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

358 hasFakes = Field(dtype=bool, 

359 default=False, 

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

361 

362 def setDefaults(self): 

363 Config.setDefaults(self) 

364 self.singleBandDeblend.propagateAllPeaks = True 

365 

366 

367class DeblendCoaddSourcesRunner(MergeSourcesRunner): 

368 """Task runner for the `MergeSourcesTask` 

369 

370 Required because the run method requires a list of 

371 dataRefs rather than a single dataRef. 

372 """ 

373 @staticmethod 

374 def getTargetList(parsedCmd, **kwargs): 

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

376 

377 Parameters 

378 ---------- 

379 parsedCmd: 

380 The parsed command 

381 kwargs: 

382 Keyword arguments passed to the task 

383 

384 Returns 

385 ------- 

386 targetList: list 

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

388 """ 

389 refDict = MergeSourcesRunner.buildRefDict(parsedCmd) 

390 kwargs["psfCache"] = parsedCmd.psfCache 

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

392 

393 

394class DeblendCoaddSourcesTask(CmdLineTask): 

395 """Deblend the sources in a merged catalog 

396 

397 Deblend sources from master catalog in each coadd. 

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

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

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

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

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

403 output deblended catalog. 

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

405 from the deblender. 

406 

407 `pipe.tasks.multiband.DeblendCoaddSourcesTask Description 

408 --------------------------------------------------------- 

409 ` 

410 

411 Parameters 

412 ---------- 

413 butler: `Butler` 

414 Butler used to read the input schemas from disk or 

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

416 schema: `Schema` 

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

418 peakSchema: `Schema` 

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

420 """ 

421 ConfigClass = DeblendCoaddSourcesConfig 

422 RunnerClass = DeblendCoaddSourcesRunner 

423 _DefaultName = "deblendCoaddSources" 

424 makeIdFactory = _makeMakeIdFactory("MergedCoaddId") 

425 

426 @classmethod 

427 def _makeArgumentParser(cls): 

428 parser = ArgumentParser(name=cls._DefaultName) 

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

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

431 ContainerClass=ExistingCoaddDataIdContainer) 

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

433 return parser 

434 

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

436 CmdLineTask.__init__(self, **kwargs) 

437 if schema is None: 

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

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

440 self.schemaMapper = afwTable.SchemaMapper(schema) 

441 self.schemaMapper.addMinimalSchema(schema) 

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

443 if peakSchema is None: 

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

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

446 

447 if self.config.simultaneous: 

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

449 else: 

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

451 

452 def getSchemaCatalogs(self): 

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

454 

455 Returns 

456 ------- 

457 result: dict 

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

459 """ 

460 catalog = afwTable.SourceCatalog(self.schema) 

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

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

463 

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

465 """Deblend the patch 

466 

467 Deblend each source simultaneously or separately 

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

469 Set `is-primary` and related flags. 

470 Propagate flags from individual visits. 

471 Write the deblended sources out. 

472 

473 Parameters 

474 ---------- 

475 patchRefList: list 

476 List of data references for each filter 

477 """ 

478 

479 if self.config.hasFakes: 

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

481 else: 

482 coaddType = self.config.coaddName 

483 

484 if self.config.simultaneous: 

485 # Use SCARLET to simultaneously deblend across filters 

486 filters = [] 

487 exposures = [] 

488 for patchRef in patchRefList: 

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

490 filters.append(patchRef.dataId["filter"]) 

491 exposures.append(exposure) 

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

493 sources = self.readSources(patchRef) 

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

495 templateCatalogs = self.multiBandDeblend.run(exposure, sources) 

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

497 self.write(patchRefList[n], templateCatalogs[filters[n]]) 

498 else: 

499 # Use the singeband deblender to deblend each band separately 

500 for patchRef in patchRefList: 

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

502 exposure.getPsf().setCacheCapacity(psfCache) 

503 sources = self.readSources(patchRef) 

504 self.singleBandDeblend.run(exposure, sources) 

505 self.write(patchRef, sources) 

506 

507 def readSources(self, dataRef): 

508 """Read merged catalog 

509 

510 Read the catalog of merged detections and create a catalog 

511 in a single band. 

512 

513 Parameters 

514 ---------- 

515 dataRef: data reference 

516 Data reference for catalog of merged detections 

517 

518 Returns 

519 ------- 

520 sources: `SourceCatalog` 

521 List of sources in merged catalog 

522 

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

524 so we can measure in-place. 

525 """ 

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

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

528 idFactory = self.makeIdFactory(dataRef) 

529 for s in merged: 

530 idFactory.notify(s.getId()) 

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

532 sources = afwTable.SourceCatalog(table) 

533 sources.extend(merged, self.schemaMapper) 

534 return sources 

535 

536 def write(self, dataRef, sources): 

537 """Write the source catalog(s) 

538 

539 Parameters 

540 ---------- 

541 dataRef: Data Reference 

542 Reference to the output catalog. 

543 sources: `SourceCatalog` 

544 Flux conserved sources to write to file. 

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

546 generated. 

547 template_sources: `SourceCatalog` 

548 Source catalog using the multiband template models 

549 as footprints. 

550 """ 

551 dataRef.put(sources, self.config.coaddName + "Coadd_deblendedFlux") 

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

553 

554 def writeMetadata(self, dataRefList): 

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

556 Parameters 

557 ---------- 

558 dataRefList 

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

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

561 """ 

562 for dataRef in dataRefList: 

563 try: 

564 metadataName = self._getMetadataName() 

565 if metadataName is not None: 

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

567 except Exception as e: 

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

569 

570 def getExposureId(self, dataRef): 

571 """Get the ExposureId from a data reference 

572 """ 

573 return int(dataRef.get(self.config.coaddName + "CoaddId")) 

574 

575 

576class MeasureMergedCoaddSourcesConnections(PipelineTaskConnections, 

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

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

579 "outputCoaddName": "deep"}): 

580 inputSchema = cT.InitInput( 

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

582 name="{inputCoaddName}Coadd_deblendedFlux_schema", 

583 storageClass="SourceCatalog" 

584 ) 

585 outputSchema = cT.InitOutput( 

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

587 name="{inputCoaddName}Coadd_meas_schema", 

588 storageClass="SourceCatalog" 

589 ) 

590 refCat = cT.PrerequisiteInput( 

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

592 name="ref_cat", 

593 storageClass="SimpleCatalog", 

594 dimensions=("skypix",), 

595 deferLoad=True, 

596 multiple=True 

597 ) 

598 exposure = cT.Input( 

599 doc="Input coadd image", 

600 name="{inputCoaddName}Coadd_calexp", 

601 storageClass="ExposureF", 

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

603 ) 

604 skyMap = cT.Input( 

605 doc="SkyMap to use in processing", 

606 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME, 

607 storageClass="SkyMap", 

608 dimensions=("skymap",), 

609 ) 

610 visitCatalogs = cT.Input( 

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

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

613 "and characterization to codd objects", 

614 name="src", 

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

616 storageClass="SourceCatalog", 

617 multiple=True 

618 ) 

619 inputCatalog = cT.Input( 

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

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

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

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

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

625 "be 'mergeDet'"), 

626 name="{inputCoaddName}Coadd_deblendedFlux", 

627 storageClass="SourceCatalog", 

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

629 ) 

630 outputSources = cT.Output( 

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

632 name="{outputCoaddName}Coadd_meas", 

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

634 storageClass="SourceCatalog", 

635 ) 

636 matchResult = cT.Output( 

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

638 name="{outputCoaddName}Coadd_measMatch", 

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

640 storageClass="Catalog", 

641 ) 

642 denormMatches = cT.Output( 

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

644 "doWriteMatchesDenormalized", 

645 name="{outputCoaddName}Coadd_measMatchFull", 

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

647 storageClass="Catalog", 

648 ) 

649 

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

651 super().__init__(config=config) 

652 if config.doPropagateFlags is False: 

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

654 

655 if config.doMatchSources is False: 

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

657 

658 if config.doWriteMatchesDenormalized is False: 

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

660 

661 

662class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig, 

663 pipelineConnections=MeasureMergedCoaddSourcesConnections): 

664 """! 

665 @anchor MeasureMergedCoaddSourcesConfig_ 

666 

667 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask 

668 """ 

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

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

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

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

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

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

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

676 doPropagateFlags = Field( 

677 dtype=bool, default=True, 

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

679 ) 

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

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

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

683 doWriteMatchesDenormalized = Field( 

684 dtype=bool, 

685 default=False, 

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

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

688 ) 

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

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

691 checkUnitsParseStrict = Field( 

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

693 dtype=str, 

694 default="raise", 

695 ) 

696 doApCorr = Field( 

697 dtype=bool, 

698 default=True, 

699 doc="Apply aperture corrections" 

700 ) 

701 applyApCorr = ConfigurableField( 

702 target=ApplyApCorrTask, 

703 doc="Subtask to apply aperture corrections" 

704 ) 

705 doRunCatalogCalculation = Field( 

706 dtype=bool, 

707 default=True, 

708 doc='Run catalogCalculation task' 

709 ) 

710 catalogCalculation = ConfigurableField( 

711 target=CatalogCalculationTask, 

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

713 ) 

714 

715 hasFakes = Field( 

716 dtype=bool, 

717 default=False, 

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

719 ) 

720 

721 @property 

722 def refObjLoader(self): 

723 return self.match.refObjLoader 

724 

725 def setDefaults(self): 

726 super().setDefaults() 

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

728 'base_Variance', 

729 'base_LocalPhotoCalib', 

730 'base_LocalWcs'] 

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

732 'INEXACT_PSF'] 

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

734 'INEXACT_PSF'] 

735 

736 def validate(self): 

737 super().validate() 

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

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

740 raise ValueError( 

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

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

743 ) 

744 

745 

746## @addtogroup LSST_task_documentation 

747## @{ 

748## @page MeasureMergedCoaddSourcesTask 

749## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask" 

750## @copybrief MeasureMergedCoaddSourcesTask 

751## @} 

752 

753 

754class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner): 

755 """Get the psfCache setting into MeasureMergedCoaddSourcesTask""" 

756 @staticmethod 

757 def getTargetList(parsedCmd, **kwargs): 

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

759 

760 

761class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask): 

762 r"""! 

763 @anchor MeasureMergedCoaddSourcesTask_ 

764 

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

766 

767 @section pipe_tasks_multiBand_Contents Contents 

768 

769 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose 

770 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize 

771 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run 

772 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config 

773 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug 

774 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example 

775 

776 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description 

777 

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

779 measurement in each coadd. 

780 

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

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

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

784 consistent set of child sources. 

785 

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

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

788 flags are propagated to the coadd sources. 

789 

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

791 

792 @par Inputs: 

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

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

795 @par Outputs: 

796 deepCoadd_meas{tract,patch,filter}: SourceCatalog 

797 @par Data Unit: 

798 tract, patch, filter 

799 

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

801 

802 <DL> 

803 <DT> @ref SingleFrameMeasurementTask_ "measurement" 

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

805 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags" 

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

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

808 sources</DD> 

809 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags" 

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

811 <DT> @ref DirectMatchTask_ "match" 

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

813 </DD> 

814 </DL> 

815 These subtasks may be retargeted as required. 

816 

817 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization 

818 

819 @copydoc \_\_init\_\_ 

820 

821 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task 

822 

823 @copydoc run 

824 

825 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters 

826 

827 See @ref MeasureMergedCoaddSourcesConfig_ 

828 

829 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables 

830 

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

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

833 files. 

834 

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

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

837 

838 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using 

839 MeasureMergedCoaddSourcesTask 

840 

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

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

843 catalog for driving forced photometry. 

844 

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

846 to be processed. 

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

848 `--help` command line argument: 

849 @code 

850 measureCoaddSources.py --help 

851 @endcode 

852 

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

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

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

856 coadd as follows: 

857 @code 

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

859 @endcode 

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

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

862 

863 It is also necessary to run 

864 @code 

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

866 @endcode 

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

868 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask". 

869 """ 

870 _DefaultName = "measureCoaddSources" 

871 ConfigClass = MeasureMergedCoaddSourcesConfig 

872 RunnerClass = MeasureMergedCoaddSourcesRunner 

873 getSchemaCatalogs = _makeGetSchemaCatalogs("meas") 

874 makeIdFactory = _makeMakeIdFactory("MergedCoaddId") # The IDs we already have are of this type 

875 

876 @classmethod 

877 def _makeArgumentParser(cls): 

878 parser = ArgumentParser(name=cls._DefaultName) 

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

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

881 ContainerClass=ExistingCoaddDataIdContainer) 

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

883 return parser 

884 

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

886 **kwargs): 

887 """! 

888 @brief Initialize the task. 

889 

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

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

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

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

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

895 requiring a reference catalog are disabled. 

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

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

898 

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

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

901 measurements. 

902 """ 

903 super().__init__(**kwargs) 

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

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

906 if initInputs is not None: 

907 schema = initInputs['inputSchema'].schema 

908 if schema is None: 

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

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

911 self.schemaMapper = afwTable.SchemaMapper(schema) 

912 self.schemaMapper.addMinimalSchema(schema) 

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

914 self.algMetadata = PropertyList() 

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

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

917 if self.config.doMatchSources: 

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

919 if self.config.doPropagateFlags: 

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

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

922 if self.config.doApCorr: 

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

924 if self.config.doRunCatalogCalculation: 

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

926 

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

928 

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

930 inputs = butlerQC.get(inputRefs) 

931 

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

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

934 log=self.log) 

935 self.match.setRefObjLoader(refObjLoader) 

936 

937 # Set psfcache 

938 # move this to run after gen2 deprecation 

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

940 

941 # Get unique integer ID for IdFactory and RNG seeds 

942 packedId, maxBits = butlerQC.quantum.dataId.pack("tract_patch", returnMaxBits=True) 

943 inputs['exposureId'] = packedId 

944 idFactory = afwTable.IdFactory.makeSource(packedId, 64 - maxBits) 

945 # Transform inputCatalog 

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

947 sources = afwTable.SourceCatalog(table) 

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

949 table = sources.getTable() 

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

951 inputs['sources'] = sources 

952 

953 skyMap = inputs.pop('skyMap') 

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

955 tractInfo = skyMap[tractNumber] 

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

957 skyInfo = Struct( 

958 skyMap=skyMap, 

959 tractInfo=tractInfo, 

960 patchInfo=patchInfo, 

961 wcs=tractInfo.getWcs(), 

962 bbox=patchInfo.getOuterBBox() 

963 ) 

964 inputs['skyInfo'] = skyInfo 

965 

966 if self.config.doPropagateFlags: 

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

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

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

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

971 inputVisitIds = set() 

972 ccdRecordsWcs = {} 

973 for ccdRecord in ccdInputs: 

974 visit = ccdRecord.get(visitKey) 

975 ccd = ccdRecord.get(ccdKey) 

976 inputVisitIds.add((visit, ccd)) 

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

978 

979 inputCatalogsToKeep = [] 

980 inputCatalogWcsUpdate = [] 

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

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

983 if key in inputVisitIds: 

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

985 inputCatalogWcsUpdate.append(ccdRecordsWcs[key]) 

986 inputs['visitCatalogs'] = inputCatalogsToKeep 

987 inputs['wcsUpdates'] = inputCatalogWcsUpdate 

988 inputs['ccdInputs'] = ccdInputs 

989 

990 outputs = self.run(**inputs) 

991 butlerQC.put(outputs, outputRefs) 

992 

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

994 """! 

995 @brief Deblend and measure. 

996 

997 @param[in] patchRef: Patch reference. 

998 

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

1000 from individual visits. Optionally match the sources to a reference catalog and write the matches. 

1001 Finally, write the deblended sources and measurements out. 

1002 """ 

1003 if self.config.hasFakes: 

1004 coaddType = "fakes_" + self.config.coaddName 

1005 else: 

1006 coaddType = self.config.coaddName 

1007 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True) 

1008 exposure.getPsf().setCacheCapacity(psfCache) 

1009 sources = self.readSources(patchRef) 

1010 table = sources.getTable() 

1011 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog. 

1012 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef) 

1013 

1014 if self.config.doPropagateFlags: 

1015 ccdInputs = self.propagateFlags.getCcdInputs(exposure) 

1016 else: 

1017 ccdInputs = None 

1018 

1019 results = self.run(exposure=exposure, sources=sources, 

1020 ccdInputs=ccdInputs, 

1021 skyInfo=skyInfo, butler=patchRef.getButler(), 

1022 exposureId=self.getExposureId(patchRef)) 

1023 

1024 if self.config.doMatchSources: 

1025 self.writeMatches(patchRef, results) 

1026 self.write(patchRef, results.outputSources) 

1027 

1028 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None, 

1029 butler=None): 

1030 """Run measurement algorithms on the input exposure, and optionally populate the 

1031 resulting catalog with extra information. 

1032 

1033 Parameters 

1034 ---------- 

1035 exposure : `lsst.afw.exposure.Exposure` 

1036 The input exposure on which measurements are to be performed 

1037 sources : `lsst.afw.table.SourceCatalog` 

1038 A catalog built from the results of merged detections, or 

1039 deblender outputs. 

1040 skyInfo : `lsst.pipe.base.Struct` 

1041 A struct containing information about the position of the input exposure within 

1042 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box 

1043 exposureId : `int` or `bytes` 

1044 packed unique number or bytes unique to the input exposure 

1045 ccdInputs : `lsst.afw.table.ExposureCatalog` 

1046 Catalog containing information on the individual visits which went into making 

1047 the exposure 

1048 visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None` 

1049 A list of source catalogs corresponding to measurements made on the individual 

1050 visits which went into the input exposure. If None and butler is `None` then 

1051 the task cannot propagate visit flags to the output catalog. 

1052 wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None` 

1053 If visitCatalogs is not `None` this should be a list of wcs objects which correspond 

1054 to the input visits. Used to put all coordinates to common system. If `None` and 

1055 butler is `None` then the task cannot propagate visit flags to the output catalog. 

1056 butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler` 

1057 Either a gen2 or gen3 butler used to load visit catalogs 

1058 

1059 Returns 

1060 ------- 

1061 results : `lsst.pipe.base.Struct` 

1062 Results of running measurement task. Will contain the catalog in the 

1063 sources attribute. Optionally will have results of matching to a 

1064 reference catalog in the matchResults attribute, and denormalized 

1065 matches in the denormMatches attribute. 

1066 """ 

1067 self.measurement.run(sources, exposure, exposureId=exposureId) 

1068 

1069 if self.config.doApCorr: 

1070 self.applyApCorr.run( 

1071 catalog=sources, 

1072 apCorrMap=exposure.getInfo().getApCorrMap() 

1073 ) 

1074 

1075 # TODO DM-11568: this contiguous check-and-copy could go away if we 

1076 # reserve enough space during SourceDetection and/or SourceDeblend. 

1077 # NOTE: sourceSelectors require contiguous catalogs, so ensure 

1078 # contiguity now, so views are preserved from here on. 

1079 if not sources.isContiguous(): 

1080 sources = sources.copy(deep=True) 

1081 

1082 if self.config.doRunCatalogCalculation: 

1083 self.catalogCalculation.run(sources) 

1084 

1085 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo, 

1086 patchInfo=skyInfo.patchInfo, includeDeblend=self.deblended) 

1087 if self.config.doPropagateFlags: 

1088 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates) 

1089 

1090 results = Struct() 

1091 

1092 if self.config.doMatchSources: 

1093 matchResult = self.match.run(sources, exposure.getInfo().getFilter().getName()) 

1094 matches = afwTable.packMatches(matchResult.matches) 

1095 matches.table.setMetadata(matchResult.matchMeta) 

1096 results.matchResult = matches 

1097 if self.config.doWriteMatchesDenormalized: 

1098 if matchResult.matches: 

1099 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta) 

1100 else: 

1101 self.log.warn("No matches, so generating dummy denormalized matches file") 

1102 denormMatches = afwTable.BaseCatalog(afwTable.Schema()) 

1103 denormMatches.setMetadata(PropertyList()) 

1104 denormMatches.getMetadata().add("COMMENT", 

1105 "This catalog is empty because no matches were found.") 

1106 results.denormMatches = denormMatches 

1107 results.denormMatches = denormMatches 

1108 

1109 results.outputSources = sources 

1110 return results 

1111 

1112 def readSources(self, dataRef): 

1113 """! 

1114 @brief Read input sources. 

1115 

1116 @param[in] dataRef: Data reference for catalog of merged detections 

1117 @return List of sources in merged catalog 

1118 

1119 We also need to add columns to hold the measurements we're about to make 

1120 so we can measure in-place. 

1121 """ 

1122 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True) 

1123 self.log.info("Read %d detections: %s" % (len(merged), dataRef.dataId)) 

1124 idFactory = self.makeIdFactory(dataRef) 

1125 for s in merged: 

1126 idFactory.notify(s.getId()) 

1127 table = afwTable.SourceTable.make(self.schema, idFactory) 

1128 sources = afwTable.SourceCatalog(table) 

1129 sources.extend(merged, self.schemaMapper) 

1130 return sources 

1131 

1132 def writeMatches(self, dataRef, results): 

1133 """! 

1134 @brief Write matches of the sources to the astrometric reference catalog. 

1135 

1136 @param[in] dataRef: data reference 

1137 @param[in] results: results struct from run method 

1138 """ 

1139 if hasattr(results, "matchResult"): 

1140 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch") 

1141 if hasattr(results, "denormMatches"): 

1142 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull") 

1143 

1144 def write(self, dataRef, sources): 

1145 """! 

1146 @brief Write the source catalog. 

1147 

1148 @param[in] dataRef: data reference 

1149 @param[in] sources: source catalog 

1150 """ 

1151 dataRef.put(sources, self.config.coaddName + "Coadd_meas") 

1152 self.log.info("Wrote %d sources: %s" % (len(sources), dataRef.dataId)) 

1153 

1154 def getExposureId(self, dataRef): 

1155 return int(dataRef.get(self.config.coaddName + "CoaddId"))