Coverage for python/lsst/pipe/tasks/multiBand.py: 29%

Shortcuts on this page

r m x p   toggle line displays

j k   next/prev highlighted chunk

0   (zero) top of page

1   (one) first highlighted chunk

400 statements  

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 page_DetectCoaddSourcesTask 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 command line task 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: 

265 schema = afwTable.SourceTable.makeMinimalSchema() 

266 if self.config.doInsertFakes: 

267 self.makeSubtask("insertFakes") 

268 self.schema = schema 

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

270 if self.config.doScaleVariance: 

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: 

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: 

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

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

321 backgrounds = afwMath.BackgroundList() 

322 if self.config.doInsertFakes: 

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: 

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: 

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: 

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: 

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: 

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: 

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

489 else: 

490 coaddType = self.config.coaddName 

491 

492 if self.config.simultaneous: 

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: 

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 "deblendedCatalog": "deblendedFlux"}): 

594 inputSchema = cT.InitInput( 

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

596 name="{inputCoaddName}Coadd_deblendedFlux_schema", 

597 storageClass="SourceCatalog" 

598 ) 

599 outputSchema = cT.InitOutput( 

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

601 name="{inputCoaddName}Coadd_meas_schema", 

602 storageClass="SourceCatalog" 

603 ) 

604 refCat = cT.PrerequisiteInput( 

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

606 name="ref_cat", 

607 storageClass="SimpleCatalog", 

608 dimensions=("skypix",), 

609 deferLoad=True, 

610 multiple=True 

611 ) 

612 exposure = cT.Input( 

613 doc="Input coadd image", 

614 name="{inputCoaddName}Coadd_calexp", 

615 storageClass="ExposureF", 

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

617 ) 

618 skyMap = cT.Input( 

619 doc="SkyMap to use in processing", 

620 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME, 

621 storageClass="SkyMap", 

622 dimensions=("skymap",), 

623 ) 

624 visitCatalogs = cT.Input( 

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

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

627 "and characterization to codd objects", 

628 name="src", 

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

630 storageClass="SourceCatalog", 

631 multiple=True 

632 ) 

633 inputCatalog = cT.Input( 

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

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

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

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

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

639 "be 'mergeDet'"), 

640 name="{inputCoaddName}Coadd_{deblendedCatalog}", 

641 storageClass="SourceCatalog", 

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

643 ) 

644 outputSources = cT.Output( 

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

646 name="{outputCoaddName}Coadd_meas", 

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

648 storageClass="SourceCatalog", 

649 ) 

650 matchResult = cT.Output( 

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

652 name="{outputCoaddName}Coadd_measMatch", 

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

654 storageClass="Catalog", 

655 ) 

656 denormMatches = cT.Output( 

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

658 "doWriteMatchesDenormalized", 

659 name="{outputCoaddName}Coadd_measMatchFull", 

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

661 storageClass="Catalog", 

662 ) 

663 

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

665 super().__init__(config=config) 

666 if config.doPropagateFlags is False: 

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

668 

669 if config.doMatchSources is False: 

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

671 

672 if config.doWriteMatchesDenormalized is False: 

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

674 

675 

676class MeasureMergedCoaddSourcesConfig(PipelineTaskConfig, 

677 pipelineConnections=MeasureMergedCoaddSourcesConnections): 

678 """! 

679 @anchor MeasureMergedCoaddSourcesConfig_ 

680 

681 @brief Configuration parameters for the MeasureMergedCoaddSourcesTask 

682 """ 

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

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

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

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

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

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

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

690 doPropagateFlags = Field( 

691 dtype=bool, default=True, 

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

693 ) 

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

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

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

697 doWriteMatchesDenormalized = Field( 

698 dtype=bool, 

699 default=False, 

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

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

702 ) 

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

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

705 checkUnitsParseStrict = Field( 

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

707 dtype=str, 

708 default="raise", 

709 ) 

710 doApCorr = Field( 

711 dtype=bool, 

712 default=True, 

713 doc="Apply aperture corrections" 

714 ) 

715 applyApCorr = ConfigurableField( 

716 target=ApplyApCorrTask, 

717 doc="Subtask to apply aperture corrections" 

718 ) 

719 doRunCatalogCalculation = Field( 

720 dtype=bool, 

721 default=True, 

722 doc='Run catalogCalculation task' 

723 ) 

724 catalogCalculation = ConfigurableField( 

725 target=CatalogCalculationTask, 

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

727 ) 

728 

729 hasFakes = Field( 

730 dtype=bool, 

731 default=False, 

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

733 ) 

734 

735 @property 

736 def refObjLoader(self): 

737 return self.match.refObjLoader 

738 

739 def setDefaults(self): 

740 super().setDefaults() 

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

742 'base_Variance', 

743 'base_LocalPhotoCalib', 

744 'base_LocalWcs'] 

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

746 'INEXACT_PSF'] 

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

748 'INEXACT_PSF'] 

749 

750 def validate(self): 

751 super().validate() 

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

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

754 raise ValueError( 

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

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

757 ) 

758 

759 

760## @addtogroup LSST_task_documentation 

761## @{ 

762## @page page_MeasureMergedCoaddSourcesTask MeasureMergedCoaddSourcesTask 

763## @ref MeasureMergedCoaddSourcesTask_ "MeasureMergedCoaddSourcesTask" 

764## @copybrief MeasureMergedCoaddSourcesTask 

765## @} 

766 

767 

768class MeasureMergedCoaddSourcesRunner(ButlerInitializedTaskRunner): 

769 """Get the psfCache setting into MeasureMergedCoaddSourcesTask""" 

770 @staticmethod 

771 def getTargetList(parsedCmd, **kwargs): 

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

773 

774 

775class MeasureMergedCoaddSourcesTask(PipelineTask, CmdLineTask): 

776 r"""! 

777 @anchor MeasureMergedCoaddSourcesTask_ 

778 

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

780 

781 @section pipe_tasks_multiBand_Contents Contents 

782 

783 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose 

784 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize 

785 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run 

786 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config 

787 - @ref pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug 

788 - @ref pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example 

789 

790 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Purpose Description 

791 

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

793 measurement in each coadd. 

794 

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

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

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

798 consistent set of child sources. 

799 

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

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

802 flags are propagated to the coadd sources. 

803 

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

805 

806 @par Inputs: 

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

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

809 @par Outputs: 

810 deepCoadd_meas{tract,patch,filter}: SourceCatalog 

811 @par Data Unit: 

812 tract, patch, filter 

813 

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

815 

816 <DL> 

817 <DT> @ref SingleFrameMeasurementTask_ "measurement" 

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

819 <DT> @ref SetPrimaryFlagsTask_ "setPrimaryFlags" 

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

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

822 sources</DD> 

823 <DT> @ref PropagateVisitFlagsTask_ "propagateFlags" 

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

825 <DT> @ref DirectMatchTask_ "match" 

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

827 </DD> 

828 </DL> 

829 These subtasks may be retargeted as required. 

830 

831 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Initialize Task initialization 

832 

833 @copydoc \_\_init\_\_ 

834 

835 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Run Invoking the Task 

836 

837 @copydoc run 

838 

839 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Config Configuration parameters 

840 

841 See @ref MeasureMergedCoaddSourcesConfig_ 

842 

843 @section pipe_tasks_multiBand_MeasureMergedCoaddSourcesTask_Debug Debug variables 

844 

845 The command line task interface supports a 

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

847 files. 

848 

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

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

851 

852 @section pipe_tasks_multiband_MeasureMergedCoaddSourcesTask_Example A complete example of using 

853 MeasureMergedCoaddSourcesTask 

854 

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

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

857 catalog for driving forced photometry. 

858 

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

860 to be processed. 

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

862 `--help` command line argument: 

863 @code 

864 measureCoaddSources.py --help 

865 @endcode 

866 

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

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

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

870 coadd as follows: 

871 @code 

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

873 @endcode 

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

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

876 

877 It is also necessary to run 

878 @code 

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

880 @endcode 

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

882 procedure: @ref MergeMeasurementsTask_ "MergeMeasurementsTask". 

883 """ 

884 _DefaultName = "measureCoaddSources" 

885 ConfigClass = MeasureMergedCoaddSourcesConfig 

886 RunnerClass = MeasureMergedCoaddSourcesRunner 

887 getSchemaCatalogs = _makeGetSchemaCatalogs("meas") 

888 # The IDs we already have are of this type 

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

890 

891 @classmethod 

892 def _makeArgumentParser(cls): 

893 parser = ArgumentParser(name=cls._DefaultName) 

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

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

896 ContainerClass=ExistingCoaddDataIdContainer) 

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

898 return parser 

899 

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

901 **kwargs): 

902 """! 

903 @brief Initialize the task. 

904 

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

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

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

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

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

910 requiring a reference catalog are disabled. 

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

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

913 

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

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

916 measurements. 

917 """ 

918 super().__init__(**kwargs) 

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

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

921 if initInputs is not None: 

922 schema = initInputs['inputSchema'].schema 

923 if schema is None: 

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

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

926 self.schemaMapper = afwTable.SchemaMapper(schema) 

927 self.schemaMapper.addMinimalSchema(schema) 

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

929 self.algMetadata = PropertyList() 

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

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

932 if self.config.doMatchSources: 

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

934 if self.config.doPropagateFlags: 

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

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

937 if self.config.doApCorr: 

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

939 if self.config.doRunCatalogCalculation: 

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

941 

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

943 

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

945 inputs = butlerQC.get(inputRefs) 

946 

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

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

949 log=self.log) 

950 self.match.setRefObjLoader(refObjLoader) 

951 

952 # Set psfcache 

953 # move this to run after gen2 deprecation 

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

955 

956 # Get unique integer ID for IdFactory and RNG seeds 

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

958 inputs['exposureId'] = exposureIdInfo.expId 

959 idFactory = exposureIdInfo.makeSourceIdFactory() 

960 # Transform inputCatalog 

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

962 sources = afwTable.SourceCatalog(table) 

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

964 table = sources.getTable() 

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

966 inputs['sources'] = sources 

967 

968 skyMap = inputs.pop('skyMap') 

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

970 tractInfo = skyMap[tractNumber] 

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

972 skyInfo = Struct( 

973 skyMap=skyMap, 

974 tractInfo=tractInfo, 

975 patchInfo=patchInfo, 

976 wcs=tractInfo.getWcs(), 

977 bbox=patchInfo.getOuterBBox() 

978 ) 

979 inputs['skyInfo'] = skyInfo 

980 

981 if self.config.doPropagateFlags: 

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

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

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

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

986 inputVisitIds = set() 

987 ccdRecordsWcs = {} 

988 for ccdRecord in ccdInputs: 

989 visit = ccdRecord.get(visitKey) 

990 ccd = ccdRecord.get(ccdKey) 

991 inputVisitIds.add((visit, ccd)) 

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

993 

994 inputCatalogsToKeep = [] 

995 inputCatalogWcsUpdate = [] 

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

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

998 if key in inputVisitIds: 

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

1000 inputCatalogWcsUpdate.append(ccdRecordsWcs[key]) 

1001 inputs['visitCatalogs'] = inputCatalogsToKeep 

1002 inputs['wcsUpdates'] = inputCatalogWcsUpdate 

1003 inputs['ccdInputs'] = ccdInputs 

1004 

1005 outputs = self.run(**inputs) 

1006 butlerQC.put(outputs, outputRefs) 

1007 

1008 def runDataRef(self, patchRef, psfCache=100): 

1009 """! 

1010 @brief Deblend and measure. 

1011 

1012 @param[in] patchRef: Patch reference. 

1013 

1014 Set 'is-primary' and related flags. Propagate flags 

1015 from individual visits. Optionally match the sources to a reference catalog and write the matches. 

1016 Finally, write the deblended sources and measurements out. 

1017 """ 

1018 if self.config.hasFakes: 

1019 coaddType = "fakes_" + self.config.coaddName 

1020 else: 

1021 coaddType = self.config.coaddName 

1022 exposure = patchRef.get(coaddType + "Coadd_calexp", immediate=True) 

1023 exposure.getPsf().setCacheCapacity(psfCache) 

1024 sources = self.readSources(patchRef) 

1025 table = sources.getTable() 

1026 table.setMetadata(self.algMetadata) # Capture algorithm metadata to write out to the source catalog. 

1027 skyInfo = getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef) 

1028 

1029 if self.config.doPropagateFlags: 

1030 ccdInputs = self.propagateFlags.getCcdInputs(exposure) 

1031 else: 

1032 ccdInputs = None 

1033 

1034 expId = getGen3CoaddExposureId(patchRef, coaddName=self.config.coaddName, includeBand=False, 

1035 log=self.log) 

1036 results = self.run(exposure=exposure, sources=sources, skyInfo=skyInfo, exposureId=expId, 

1037 ccdInputs=ccdInputs, butler=patchRef.getButler()) 

1038 

1039 if self.config.doMatchSources: 

1040 self.writeMatches(patchRef, results) 

1041 self.write(patchRef, results.outputSources) 

1042 

1043 def run(self, exposure, sources, skyInfo, exposureId, ccdInputs=None, visitCatalogs=None, wcsUpdates=None, 

1044 butler=None): 

1045 """Run measurement algorithms on the input exposure, and optionally populate the 

1046 resulting catalog with extra information. 

1047 

1048 Parameters 

1049 ---------- 

1050 exposure : `lsst.afw.exposure.Exposure` 

1051 The input exposure on which measurements are to be performed 

1052 sources : `lsst.afw.table.SourceCatalog` 

1053 A catalog built from the results of merged detections, or 

1054 deblender outputs. 

1055 skyInfo : `lsst.pipe.base.Struct` 

1056 A struct containing information about the position of the input exposure within 

1057 a `SkyMap`, the `SkyMap`, its `Wcs`, and its bounding box 

1058 exposureId : `int` or `bytes` 

1059 packed unique number or bytes unique to the input exposure 

1060 ccdInputs : `lsst.afw.table.ExposureCatalog` 

1061 Catalog containing information on the individual visits which went into making 

1062 the exposure 

1063 visitCatalogs : list of `lsst.afw.table.SourceCatalogs` or `None` 

1064 A list of source catalogs corresponding to measurements made on the individual 

1065 visits which went into the input exposure. If None and butler is `None` then 

1066 the task cannot propagate visit flags to the output catalog. 

1067 wcsUpdates : list of `lsst.afw.geom.SkyWcs` or `None` 

1068 If visitCatalogs is not `None` this should be a list of wcs objects which correspond 

1069 to the input visits. Used to put all coordinates to common system. If `None` and 

1070 butler is `None` then the task cannot propagate visit flags to the output catalog. 

1071 butler : `lsst.daf.butler.Butler` or `lsst.daf.persistence.Butler` 

1072 Either a gen2 or gen3 butler used to load visit catalogs 

1073 

1074 Returns 

1075 ------- 

1076 results : `lsst.pipe.base.Struct` 

1077 Results of running measurement task. Will contain the catalog in the 

1078 sources attribute. Optionally will have results of matching to a 

1079 reference catalog in the matchResults attribute, and denormalized 

1080 matches in the denormMatches attribute. 

1081 """ 

1082 self.measurement.run(sources, exposure, exposureId=exposureId) 

1083 

1084 if self.config.doApCorr: 

1085 self.applyApCorr.run( 

1086 catalog=sources, 

1087 apCorrMap=exposure.getInfo().getApCorrMap() 

1088 ) 

1089 

1090 # TODO DM-11568: this contiguous check-and-copy could go away if we 

1091 # reserve enough space during SourceDetection and/or SourceDeblend. 

1092 # NOTE: sourceSelectors require contiguous catalogs, so ensure 

1093 # contiguity now, so views are preserved from here on. 

1094 if not sources.isContiguous(): 

1095 sources = sources.copy(deep=True) 

1096 

1097 if self.config.doRunCatalogCalculation: 

1098 self.catalogCalculation.run(sources) 

1099 

1100 self.setPrimaryFlags.run(sources, skyMap=skyInfo.skyMap, tractInfo=skyInfo.tractInfo, 

1101 patchInfo=skyInfo.patchInfo) 

1102 if self.config.doPropagateFlags: 

1103 self.propagateFlags.run(butler, sources, ccdInputs, exposure.getWcs(), visitCatalogs, wcsUpdates) 

1104 

1105 results = Struct() 

1106 

1107 if self.config.doMatchSources: 

1108 matchResult = self.match.run(sources, exposure.getInfo().getFilterLabel().bandLabel) 

1109 matches = afwTable.packMatches(matchResult.matches) 

1110 matches.table.setMetadata(matchResult.matchMeta) 

1111 results.matchResult = matches 

1112 if self.config.doWriteMatchesDenormalized: 

1113 if matchResult.matches: 

1114 denormMatches = denormalizeMatches(matchResult.matches, matchResult.matchMeta) 

1115 else: 

1116 self.log.warning("No matches, so generating dummy denormalized matches file") 

1117 denormMatches = afwTable.BaseCatalog(afwTable.Schema()) 

1118 denormMatches.setMetadata(PropertyList()) 

1119 denormMatches.getMetadata().add("COMMENT", 

1120 "This catalog is empty because no matches were found.") 

1121 results.denormMatches = denormMatches 

1122 results.denormMatches = denormMatches 

1123 

1124 results.outputSources = sources 

1125 return results 

1126 

1127 def readSources(self, dataRef): 

1128 """! 

1129 @brief Read input sources. 

1130 

1131 @param[in] dataRef: Data reference for catalog of merged detections 

1132 @return List of sources in merged catalog 

1133 

1134 We also need to add columns to hold the measurements we're about to make 

1135 so we can measure in-place. 

1136 """ 

1137 merged = dataRef.get(self.config.coaddName + self.inputCatalog, immediate=True) 

1138 self.log.info("Read %d detections: %s", len(merged), dataRef.dataId) 

1139 idFactory = self.makeIdFactory(dataRef) 

1140 for s in merged: 

1141 idFactory.notify(s.getId()) 

1142 table = afwTable.SourceTable.make(self.schema, idFactory) 

1143 sources = afwTable.SourceCatalog(table) 

1144 sources.extend(merged, self.schemaMapper) 

1145 return sources 

1146 

1147 def writeMatches(self, dataRef, results): 

1148 """! 

1149 @brief Write matches of the sources to the astrometric reference catalog. 

1150 

1151 @param[in] dataRef: data reference 

1152 @param[in] results: results struct from run method 

1153 """ 

1154 if hasattr(results, "matchResult"): 

1155 dataRef.put(results.matchResult, self.config.coaddName + "Coadd_measMatch") 

1156 if hasattr(results, "denormMatches"): 

1157 dataRef.put(results.denormMatches, self.config.coaddName + "Coadd_measMatchFull") 

1158 

1159 def write(self, dataRef, sources): 

1160 """! 

1161 @brief Write the source catalog. 

1162 

1163 @param[in] dataRef: data reference 

1164 @param[in] sources: source catalog 

1165 """ 

1166 dataRef.put(sources, self.config.coaddName + "Coadd_meas") 

1167 self.log.info("Wrote %d sources: %s", len(sources), dataRef.dataId)