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1# 

2# LSST Data Management System 

3# Copyright 2008-2015 AURA/LSST. 

4# 

5# This product includes software developed by the 

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

7# 

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

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

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

11# (at your option) any later version. 

12# 

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

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

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

16# GNU General Public License for more details. 

17# 

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

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

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

21# 

22import numpy as np 

23 

24from lsstDebug import getDebugFrame 

25import lsst.afw.table as afwTable 

26import lsst.pex.config as pexConfig 

27import lsst.pipe.base as pipeBase 

28import lsst.daf.base as dafBase 

29import lsst.pipe.base.connectionTypes as cT 

30from lsst.afw.math import BackgroundList 

31from lsst.afw.table import SourceTable, SourceCatalog 

32from lsst.meas.algorithms import SubtractBackgroundTask, SourceDetectionTask, MeasureApCorrTask 

33from lsst.meas.algorithms.installGaussianPsf import InstallGaussianPsfTask 

34from lsst.meas.astrom import RefMatchTask, displayAstrometry 

35from lsst.meas.algorithms import LoadIndexedReferenceObjectsTask 

36from lsst.obs.base import ExposureIdInfo 

37from lsst.meas.base import SingleFrameMeasurementTask, ApplyApCorrTask, CatalogCalculationTask 

38from lsst.meas.deblender import SourceDeblendTask 

39from .measurePsf import MeasurePsfTask 

40from .repair import RepairTask 

41from .computeExposureSummaryStats import ComputeExposureSummaryStatsTask 

42from lsst.pex.exceptions import LengthError 

43 

44__all__ = ["CharacterizeImageConfig", "CharacterizeImageTask"] 

45 

46 

47class CharacterizeImageConnections(pipeBase.PipelineTaskConnections, 

48 dimensions=("instrument", "visit", "detector")): 

49 exposure = cT.Input( 

50 doc="Input exposure data", 

51 name="postISRCCD", 

52 storageClass="Exposure", 

53 dimensions=["instrument", "exposure", "detector"], 

54 ) 

55 characterized = cT.Output( 

56 doc="Output characterized data.", 

57 name="icExp", 

58 storageClass="ExposureF", 

59 dimensions=["instrument", "visit", "detector"], 

60 ) 

61 sourceCat = cT.Output( 

62 doc="Output source catalog.", 

63 name="icSrc", 

64 storageClass="SourceCatalog", 

65 dimensions=["instrument", "visit", "detector"], 

66 ) 

67 backgroundModel = cT.Output( 

68 doc="Output background model.", 

69 name="icExpBackground", 

70 storageClass="Background", 

71 dimensions=["instrument", "visit", "detector"], 

72 ) 

73 outputSchema = cT.InitOutput( 

74 doc="Schema of the catalog produced by CharacterizeImage", 

75 name="icSrc_schema", 

76 storageClass="SourceCatalog", 

77 ) 

78 

79 def adjustQuantum(self, datasetRefMap: pipeBase.InputQuantizedConnection): 

80 # Docstring inherited from PipelineTaskConnections 

81 try: 

82 return super().adjustQuantum(datasetRefMap) 

83 except pipeBase.ScalarError as err: 

84 raise pipeBase.ScalarError( 

85 "CharacterizeImageTask can at present only be run on visits that are associated with " 

86 "exactly one exposure. Either this is not a valid exposure for this pipeline, or the " 

87 "snap-combination step you probably want hasn't been configured to run between ISR and " 

88 "this task (as of this writing, that would be because it hasn't been implemented yet)." 

89 ) from err 

90 

91 

92class CharacterizeImageConfig(pipeBase.PipelineTaskConfig, 

93 pipelineConnections=CharacterizeImageConnections): 

94 

95 """!Config for CharacterizeImageTask""" 

96 doMeasurePsf = pexConfig.Field( 

97 dtype=bool, 

98 default=True, 

99 doc="Measure PSF? If False then for all subsequent operations use either existing PSF " 

100 "model when present, or install simple PSF model when not (see installSimplePsf " 

101 "config options)" 

102 ) 

103 doWrite = pexConfig.Field( 

104 dtype=bool, 

105 default=True, 

106 doc="Persist results?", 

107 ) 

108 doWriteExposure = pexConfig.Field( 

109 dtype=bool, 

110 default=True, 

111 doc="Write icExp and icExpBackground in addition to icSrc? Ignored if doWrite False.", 

112 ) 

113 psfIterations = pexConfig.RangeField( 

114 dtype=int, 

115 default=2, 

116 min=1, 

117 doc="Number of iterations of detect sources, measure sources, " 

118 "estimate PSF. If useSimplePsf is True then 2 should be plenty; " 

119 "otherwise more may be wanted.", 

120 ) 

121 background = pexConfig.ConfigurableField( 

122 target=SubtractBackgroundTask, 

123 doc="Configuration for initial background estimation", 

124 ) 

125 detection = pexConfig.ConfigurableField( 

126 target=SourceDetectionTask, 

127 doc="Detect sources" 

128 ) 

129 doDeblend = pexConfig.Field( 

130 dtype=bool, 

131 default=True, 

132 doc="Run deblender input exposure" 

133 ) 

134 deblend = pexConfig.ConfigurableField( 

135 target=SourceDeblendTask, 

136 doc="Split blended source into their components" 

137 ) 

138 measurement = pexConfig.ConfigurableField( 

139 target=SingleFrameMeasurementTask, 

140 doc="Measure sources" 

141 ) 

142 doApCorr = pexConfig.Field( 

143 dtype=bool, 

144 default=True, 

145 doc="Run subtasks to measure and apply aperture corrections" 

146 ) 

147 measureApCorr = pexConfig.ConfigurableField( 

148 target=MeasureApCorrTask, 

149 doc="Subtask to measure aperture corrections" 

150 ) 

151 applyApCorr = pexConfig.ConfigurableField( 

152 target=ApplyApCorrTask, 

153 doc="Subtask to apply aperture corrections" 

154 ) 

155 # If doApCorr is False, and the exposure does not have apcorrections already applied, the 

156 # active plugins in catalogCalculation almost certainly should not contain the characterization plugin 

157 catalogCalculation = pexConfig.ConfigurableField( 

158 target=CatalogCalculationTask, 

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

160 ) 

161 doComputeSummaryStats = pexConfig.Field( 

162 dtype=bool, 

163 default=True, 

164 doc="Run subtask to measure exposure summary statistics" 

165 ) 

166 computeSummaryStats = pexConfig.ConfigurableField( 

167 target=ComputeExposureSummaryStatsTask, 

168 doc="Subtask to run computeSummaryStats on exposure" 

169 ) 

170 useSimplePsf = pexConfig.Field( 

171 dtype=bool, 

172 default=True, 

173 doc="Replace the existing PSF model with a simplified version that has the same sigma " 

174 "at the start of each PSF determination iteration? Doing so makes PSF determination " 

175 "converge more robustly and quickly.", 

176 ) 

177 installSimplePsf = pexConfig.ConfigurableField( 

178 target=InstallGaussianPsfTask, 

179 doc="Install a simple PSF model", 

180 ) 

181 refObjLoader = pexConfig.ConfigurableField( 

182 target=LoadIndexedReferenceObjectsTask, 

183 doc="reference object loader", 

184 ) 

185 ref_match = pexConfig.ConfigurableField( 

186 target=RefMatchTask, 

187 doc="Task to load and match reference objects. Only used if measurePsf can use matches. " 

188 "Warning: matching will only work well if the initial WCS is accurate enough " 

189 "to give good matches (roughly: good to 3 arcsec across the CCD).", 

190 ) 

191 measurePsf = pexConfig.ConfigurableField( 

192 target=MeasurePsfTask, 

193 doc="Measure PSF", 

194 ) 

195 repair = pexConfig.ConfigurableField( 

196 target=RepairTask, 

197 doc="Remove cosmic rays", 

198 ) 

199 requireCrForPsf = pexConfig.Field( 

200 dtype=bool, 

201 default=True, 

202 doc="Require cosmic ray detection and masking to run successfully before measuring the PSF." 

203 ) 

204 checkUnitsParseStrict = pexConfig.Field( 

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

206 dtype=str, 

207 default="raise", 

208 ) 

209 

210 def setDefaults(self): 

211 super().setDefaults() 

212 # just detect bright stars; includeThresholdMultipler=10 seems large, 

213 # but these are the values we have been using 

214 self.detection.thresholdValue = 5.0 

215 self.detection.includeThresholdMultiplier = 10.0 

216 self.detection.doTempLocalBackground = False 

217 # do not deblend, as it makes a mess 

218 self.doDeblend = False 

219 # measure and apply aperture correction; note: measuring and applying aperture 

220 # correction are disabled until the final measurement, after PSF is measured 

221 self.doApCorr = True 

222 # minimal set of measurements needed to determine PSF 

223 self.measurement.plugins.names = [ 

224 "base_PixelFlags", 

225 "base_SdssCentroid", 

226 "base_SdssShape", 

227 "base_GaussianFlux", 

228 "base_PsfFlux", 

229 "base_CircularApertureFlux", 

230 ] 

231 

232 def validate(self): 

233 if self.doApCorr and not self.measurePsf: 

234 raise RuntimeError("Must measure PSF to measure aperture correction, " 

235 "because flags determined by PSF measurement are used to identify " 

236 "sources used to measure aperture correction") 

237 

238## \addtogroup LSST_task_documentation 

239## \{ 

240## \page CharacterizeImageTask 

241## \ref CharacterizeImageTask_ "CharacterizeImageTask" 

242## \copybrief CharacterizeImageTask 

243## \} 

244 

245 

246class CharacterizeImageTask(pipeBase.PipelineTask, pipeBase.CmdLineTask): 

247 r"""!Measure bright sources and use this to estimate background and PSF of an exposure 

248 

249 @anchor CharacterizeImageTask_ 

250 

251 @section pipe_tasks_characterizeImage_Contents Contents 

252 

253 - @ref pipe_tasks_characterizeImage_Purpose 

254 - @ref pipe_tasks_characterizeImage_Initialize 

255 - @ref pipe_tasks_characterizeImage_IO 

256 - @ref pipe_tasks_characterizeImage_Config 

257 - @ref pipe_tasks_characterizeImage_Debug 

258 

259 

260 @section pipe_tasks_characterizeImage_Purpose Description 

261 

262 Given an exposure with defects repaired (masked and interpolated over, e.g. as output by IsrTask): 

263 - detect and measure bright sources 

264 - repair cosmic rays 

265 - measure and subtract background 

266 - measure PSF 

267 

268 @section pipe_tasks_characterizeImage_Initialize Task initialisation 

269 

270 @copydoc \_\_init\_\_ 

271 

272 @section pipe_tasks_characterizeImage_IO Invoking the Task 

273 

274 If you want this task to unpersist inputs or persist outputs, then call 

275 the `runDataRef` method (a thin wrapper around the `run` method). 

276 

277 If you already have the inputs unpersisted and do not want to persist the output 

278 then it is more direct to call the `run` method: 

279 

280 @section pipe_tasks_characterizeImage_Config Configuration parameters 

281 

282 See @ref CharacterizeImageConfig 

283 

284 @section pipe_tasks_characterizeImage_Debug Debug variables 

285 

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

287 `--debug` to import `debug.py` from your `$PYTHONPATH`; see @ref baseDebug for more about `debug.py`. 

288 

289 CharacterizeImageTask has a debug dictionary with the following keys: 

290 <dl> 

291 <dt>frame 

292 <dd>int: if specified, the frame of first debug image displayed (defaults to 1) 

293 <dt>repair_iter 

294 <dd>bool; if True display image after each repair in the measure PSF loop 

295 <dt>background_iter 

296 <dd>bool; if True display image after each background subtraction in the measure PSF loop 

297 <dt>measure_iter 

298 <dd>bool; if True display image and sources at the end of each iteration of the measure PSF loop 

299 See @ref lsst.meas.astrom.displayAstrometry for the meaning of the various symbols. 

300 <dt>psf 

301 <dd>bool; if True display image and sources after PSF is measured; 

302 this will be identical to the final image displayed by measure_iter if measure_iter is true 

303 <dt>repair 

304 <dd>bool; if True display image and sources after final repair 

305 <dt>measure 

306 <dd>bool; if True display image and sources after final measurement 

307 </dl> 

308 

309 For example, put something like: 

310 @code{.py} 

311 import lsstDebug 

312 def DebugInfo(name): 

313 di = lsstDebug.getInfo(name) # N.b. lsstDebug.Info(name) would call us recursively 

314 if name == "lsst.pipe.tasks.characterizeImage": 

315 di.display = dict( 

316 repair = True, 

317 ) 

318 

319 return di 

320 

321 lsstDebug.Info = DebugInfo 

322 @endcode 

323 into your `debug.py` file and run `calibrateTask.py` with the `--debug` flag. 

324 

325 Some subtasks may have their own debug variables; see individual Task documentation. 

326 """ 

327 

328 # Example description used to live here, removed 2-20-2017 by MSSG 

329 

330 ConfigClass = CharacterizeImageConfig 

331 _DefaultName = "characterizeImage" 

332 RunnerClass = pipeBase.ButlerInitializedTaskRunner 

333 

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

335 inputs = butlerQC.get(inputRefs) 

336 if 'exposureIdInfo' not in inputs.keys(): 

337 inputs['exposureIdInfo'] = ExposureIdInfo.fromDataId(butlerQC.quantum.dataId, "visit_detector") 

338 outputs = self.run(**inputs) 

339 butlerQC.put(outputs, outputRefs) 

340 

341 def __init__(self, butler=None, refObjLoader=None, schema=None, **kwargs): 

342 """!Construct a CharacterizeImageTask 

343 

344 @param[in] butler A butler object is passed to the refObjLoader constructor in case 

345 it is needed to load catalogs. May be None if a catalog-based star selector is 

346 not used, if the reference object loader constructor does not require a butler, 

347 or if a reference object loader is passed directly via the refObjLoader argument. 

348 @param[in] refObjLoader An instance of LoadReferenceObjectsTasks that supplies an 

349 external reference catalog to a catalog-based star selector. May be None if a 

350 catalog star selector is not used or the loader can be constructed from the 

351 butler argument. 

352 @param[in,out] schema initial schema (an lsst.afw.table.SourceTable), or None 

353 @param[in,out] kwargs other keyword arguments for lsst.pipe.base.CmdLineTask 

354 """ 

355 super().__init__(**kwargs) 

356 

357 if schema is None: 

358 schema = SourceTable.makeMinimalSchema() 

359 self.schema = schema 

360 self.makeSubtask("background") 

361 self.makeSubtask("installSimplePsf") 

362 self.makeSubtask("repair") 

363 self.makeSubtask("measurePsf", schema=self.schema) 

364 if self.config.doMeasurePsf and self.measurePsf.usesMatches: 

365 if not refObjLoader: 

366 self.makeSubtask('refObjLoader', butler=butler) 

367 refObjLoader = self.refObjLoader 

368 self.makeSubtask("ref_match", refObjLoader=refObjLoader) 

369 self.algMetadata = dafBase.PropertyList() 

370 self.makeSubtask('detection', schema=self.schema) 

371 if self.config.doDeblend: 

372 self.makeSubtask("deblend", schema=self.schema) 

373 self.makeSubtask('measurement', schema=self.schema, algMetadata=self.algMetadata) 

374 if self.config.doApCorr: 

375 self.makeSubtask('measureApCorr', schema=self.schema) 

376 self.makeSubtask('applyApCorr', schema=self.schema) 

377 self.makeSubtask('catalogCalculation', schema=self.schema) 

378 if self.config.doComputeSummaryStats: 

379 self.makeSubtask('computeSummaryStats') 

380 self._initialFrame = getDebugFrame(self._display, "frame") or 1 

381 self._frame = self._initialFrame 

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

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

384 

385 def getInitOutputDatasets(self): 

386 outputCatSchema = afwTable.SourceCatalog(self.schema) 

387 outputCatSchema.getTable().setMetadata(self.algMetadata) 

388 return {'outputSchema': outputCatSchema} 

389 

390 @pipeBase.timeMethod 

391 def runDataRef(self, dataRef, exposure=None, background=None, doUnpersist=True): 

392 """!Characterize a science image and, if wanted, persist the results 

393 

394 This simply unpacks the exposure and passes it to the characterize method to do the work. 

395 

396 @param[in] dataRef: butler data reference for science exposure 

397 @param[in,out] exposure exposure to characterize (an lsst.afw.image.ExposureF or similar). 

398 If None then unpersist from "postISRCCD". 

399 The following changes are made, depending on the config: 

400 - set psf to the measured PSF 

401 - set apCorrMap to the measured aperture correction 

402 - subtract background 

403 - interpolate over cosmic rays 

404 - update detection and cosmic ray mask planes 

405 @param[in,out] background initial model of background already subtracted from exposure 

406 (an lsst.afw.math.BackgroundList). May be None if no background has been subtracted, 

407 which is typical for image characterization. 

408 A refined background model is output. 

409 @param[in] doUnpersist if True the exposure is read from the repository 

410 and the exposure and background arguments must be None; 

411 if False the exposure must be provided. 

412 True is intended for running as a command-line task, False for running as a subtask 

413 

414 @return same data as the characterize method 

415 """ 

416 self._frame = self._initialFrame # reset debug display frame 

417 self.log.info("Processing %s" % (dataRef.dataId)) 

418 

419 if doUnpersist: 

420 if exposure is not None or background is not None: 

421 raise RuntimeError("doUnpersist true; exposure and background must be None") 

422 exposure = dataRef.get("postISRCCD", immediate=True) 

423 elif exposure is None: 

424 raise RuntimeError("doUnpersist false; exposure must be provided") 

425 

426 exposureIdInfo = dataRef.get("expIdInfo") 

427 

428 charRes = self.run( 

429 exposure=exposure, 

430 exposureIdInfo=exposureIdInfo, 

431 background=background, 

432 ) 

433 

434 if self.config.doWrite: 

435 dataRef.put(charRes.sourceCat, "icSrc") 

436 if self.config.doWriteExposure: 

437 dataRef.put(charRes.exposure, "icExp") 

438 dataRef.put(charRes.background, "icExpBackground") 

439 

440 return charRes 

441 

442 @pipeBase.timeMethod 

443 def run(self, exposure, exposureIdInfo=None, background=None): 

444 """!Characterize a science image 

445 

446 Peforms the following operations: 

447 - Iterate the following config.psfIterations times, or once if config.doMeasurePsf false: 

448 - detect and measure sources and estimate PSF (see detectMeasureAndEstimatePsf for details) 

449 - interpolate over cosmic rays 

450 - perform final measurement 

451 

452 @param[in,out] exposure exposure to characterize (an lsst.afw.image.ExposureF or similar). 

453 The following changes are made: 

454 - update or set psf 

455 - set apCorrMap 

456 - update detection and cosmic ray mask planes 

457 - subtract background and interpolate over cosmic rays 

458 @param[in] exposureIdInfo ID info for exposure (an lsst.obs.base.ExposureIdInfo). 

459 If not provided, returned SourceCatalog IDs will not be globally unique. 

460 @param[in,out] background initial model of background already subtracted from exposure 

461 (an lsst.afw.math.BackgroundList). May be None if no background has been subtracted, 

462 which is typical for image characterization. 

463 

464 @return pipe_base Struct containing these fields, all from the final iteration 

465 of detectMeasureAndEstimatePsf: 

466 - exposure: characterized exposure; image is repaired by interpolating over cosmic rays, 

467 mask is updated accordingly, and the PSF model is set 

468 - sourceCat: detected sources (an lsst.afw.table.SourceCatalog) 

469 - background: model of background subtracted from exposure (an lsst.afw.math.BackgroundList) 

470 - psfCellSet: spatial cells of PSF candidates (an lsst.afw.math.SpatialCellSet) 

471 """ 

472 self._frame = self._initialFrame # reset debug display frame 

473 

474 if not self.config.doMeasurePsf and not exposure.hasPsf(): 

475 self.log.warn("Source catalog detected and measured with placeholder or default PSF") 

476 self.installSimplePsf.run(exposure=exposure) 

477 

478 if exposureIdInfo is None: 

479 exposureIdInfo = ExposureIdInfo() 

480 

481 # subtract an initial estimate of background level 

482 background = self.background.run(exposure).background 

483 

484 psfIterations = self.config.psfIterations if self.config.doMeasurePsf else 1 

485 for i in range(psfIterations): 

486 dmeRes = self.detectMeasureAndEstimatePsf( 

487 exposure=exposure, 

488 exposureIdInfo=exposureIdInfo, 

489 background=background, 

490 ) 

491 

492 psf = dmeRes.exposure.getPsf() 

493 psfSigma = psf.computeShape().getDeterminantRadius() 

494 psfDimensions = psf.computeImage().getDimensions() 

495 medBackground = np.median(dmeRes.background.getImage().getArray()) 

496 self.log.info("iter %s; PSF sigma=%0.2f, dimensions=%s; median background=%0.2f" % 

497 (i + 1, psfSigma, psfDimensions, medBackground)) 

498 

499 self.display("psf", exposure=dmeRes.exposure, sourceCat=dmeRes.sourceCat) 

500 

501 # perform final repair with final PSF 

502 self.repair.run(exposure=dmeRes.exposure) 

503 self.display("repair", exposure=dmeRes.exposure, sourceCat=dmeRes.sourceCat) 

504 

505 # perform final measurement with final PSF, including measuring and applying aperture correction, 

506 # if wanted 

507 self.measurement.run(measCat=dmeRes.sourceCat, exposure=dmeRes.exposure, 

508 exposureId=exposureIdInfo.expId) 

509 if self.config.doApCorr: 

510 apCorrMap = self.measureApCorr.run(exposure=dmeRes.exposure, catalog=dmeRes.sourceCat).apCorrMap 

511 dmeRes.exposure.getInfo().setApCorrMap(apCorrMap) 

512 self.applyApCorr.run(catalog=dmeRes.sourceCat, apCorrMap=exposure.getInfo().getApCorrMap()) 

513 self.catalogCalculation.run(dmeRes.sourceCat) 

514 if self.config.doComputeSummaryStats: 

515 summary = self.computeSummaryStats.run(exposure=dmeRes.exposure, 

516 sources=dmeRes.sourceCat, 

517 background=dmeRes.background) 

518 dmeRes.exposure.getInfo().setSummaryStats(summary) 

519 

520 self.display("measure", exposure=dmeRes.exposure, sourceCat=dmeRes.sourceCat) 

521 

522 return pipeBase.Struct( 

523 exposure=dmeRes.exposure, 

524 sourceCat=dmeRes.sourceCat, 

525 background=dmeRes.background, 

526 psfCellSet=dmeRes.psfCellSet, 

527 

528 characterized=dmeRes.exposure, 

529 backgroundModel=dmeRes.background 

530 ) 

531 

532 @pipeBase.timeMethod 

533 def detectMeasureAndEstimatePsf(self, exposure, exposureIdInfo, background): 

534 """!Perform one iteration of detect, measure and estimate PSF 

535 

536 Performs the following operations: 

537 - if config.doMeasurePsf or not exposure.hasPsf(): 

538 - install a simple PSF model (replacing the existing one, if need be) 

539 - interpolate over cosmic rays with keepCRs=True 

540 - estimate background and subtract it from the exposure 

541 - detect, deblend and measure sources, and subtract a refined background model; 

542 - if config.doMeasurePsf: 

543 - measure PSF 

544 

545 @param[in,out] exposure exposure to characterize (an lsst.afw.image.ExposureF or similar) 

546 The following changes are made: 

547 - update or set psf 

548 - update detection and cosmic ray mask planes 

549 - subtract background 

550 @param[in] exposureIdInfo ID info for exposure (an lsst.obs_base.ExposureIdInfo) 

551 @param[in,out] background initial model of background already subtracted from exposure 

552 (an lsst.afw.math.BackgroundList). 

553 

554 @return pipe_base Struct containing these fields, all from the final iteration 

555 of detect sources, measure sources and estimate PSF: 

556 - exposure characterized exposure; image is repaired by interpolating over cosmic rays, 

557 mask is updated accordingly, and the PSF model is set 

558 - sourceCat detected sources (an lsst.afw.table.SourceCatalog) 

559 - background model of background subtracted from exposure (an lsst.afw.math.BackgroundList) 

560 - psfCellSet spatial cells of PSF candidates (an lsst.afw.math.SpatialCellSet) 

561 """ 

562 # install a simple PSF model, if needed or wanted 

563 if not exposure.hasPsf() or (self.config.doMeasurePsf and self.config.useSimplePsf): 

564 self.log.warn("Source catalog detected and measured with placeholder or default PSF") 

565 self.installSimplePsf.run(exposure=exposure) 

566 

567 # run repair, but do not interpolate over cosmic rays (do that elsewhere, with the final PSF model) 

568 if self.config.requireCrForPsf: 

569 self.repair.run(exposure=exposure, keepCRs=True) 

570 else: 

571 try: 

572 self.repair.run(exposure=exposure, keepCRs=True) 

573 except LengthError: 

574 self.log.warn("Skipping cosmic ray detection: Too many CR pixels (max %0.f)" % 

575 self.config.repair.cosmicray.nCrPixelMax) 

576 

577 self.display("repair_iter", exposure=exposure) 

578 

579 if background is None: 

580 background = BackgroundList() 

581 

582 sourceIdFactory = exposureIdInfo.makeSourceIdFactory() 

583 table = SourceTable.make(self.schema, sourceIdFactory) 

584 table.setMetadata(self.algMetadata) 

585 

586 detRes = self.detection.run(table=table, exposure=exposure, doSmooth=True) 

587 sourceCat = detRes.sources 

588 if detRes.fpSets.background: 

589 for bg in detRes.fpSets.background: 

590 background.append(bg) 

591 

592 if self.config.doDeblend: 

593 self.deblend.run(exposure=exposure, sources=sourceCat) 

594 

595 self.measurement.run(measCat=sourceCat, exposure=exposure, exposureId=exposureIdInfo.expId) 

596 

597 measPsfRes = pipeBase.Struct(cellSet=None) 

598 if self.config.doMeasurePsf: 

599 if self.measurePsf.usesMatches: 

600 matches = self.ref_match.loadAndMatch(exposure=exposure, sourceCat=sourceCat).matches 

601 else: 

602 matches = None 

603 measPsfRes = self.measurePsf.run(exposure=exposure, sources=sourceCat, matches=matches, 

604 expId=exposureIdInfo.expId) 

605 self.display("measure_iter", exposure=exposure, sourceCat=sourceCat) 

606 

607 return pipeBase.Struct( 

608 exposure=exposure, 

609 sourceCat=sourceCat, 

610 background=background, 

611 psfCellSet=measPsfRes.cellSet, 

612 ) 

613 

614 def getSchemaCatalogs(self): 

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

616 """ 

617 sourceCat = SourceCatalog(self.schema) 

618 sourceCat.getTable().setMetadata(self.algMetadata) 

619 return {"icSrc": sourceCat} 

620 

621 def display(self, itemName, exposure, sourceCat=None): 

622 """Display exposure and sources on next frame, if display of itemName has been requested 

623 

624 @param[in] itemName name of item in debugInfo 

625 @param[in] exposure exposure to display 

626 @param[in] sourceCat source catalog to display 

627 """ 

628 val = getDebugFrame(self._display, itemName) 

629 if not val: 

630 return 

631 

632 displayAstrometry(exposure=exposure, sourceCat=sourceCat, frame=self._frame, pause=False) 

633 self._frame += 1