Hide keyboard shortcuts

Hot-keys 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

1# This file is part of pipe_tasks. 

2# 

3# LSST Data Management System 

4# This product includes software developed by the 

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

6# See COPYRIGHT file at the top of the source tree. 

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 os 

23import copy 

24import numpy 

25import warnings 

26import logging 

27import lsst.pex.config as pexConfig 

28import lsst.pex.exceptions as pexExceptions 

29import lsst.geom as geom 

30import lsst.afw.geom as afwGeom 

31import lsst.afw.image as afwImage 

32import lsst.afw.math as afwMath 

33import lsst.afw.table as afwTable 

34import lsst.afw.detection as afwDet 

35import lsst.coadd.utils as coaddUtils 

36import lsst.pipe.base as pipeBase 

37import lsst.meas.algorithms as measAlg 

38import lsstDebug 

39import lsst.utils as utils 

40from lsst.skymap import BaseSkyMap 

41from .coaddBase import CoaddBaseTask, SelectDataIdContainer, makeSkyInfo, makeCoaddSuffix, reorderAndPadList 

42from .interpImage import InterpImageTask 

43from .scaleZeroPoint import ScaleZeroPointTask 

44from .coaddHelpers import groupPatchExposures, getGroupDataRef 

45from .scaleVariance import ScaleVarianceTask 

46from .maskStreaks import MaskStreaksTask 

47from .healSparseMapping import HealSparseInputMapTask 

48from lsst.meas.algorithms import SourceDetectionTask, AccumulatorMeanStack 

49from lsst.daf.butler import DeferredDatasetHandle 

50 

51__all__ = ["AssembleCoaddTask", "AssembleCoaddConnections", "AssembleCoaddConfig", 

52 "SafeClipAssembleCoaddTask", "SafeClipAssembleCoaddConfig", 

53 "CompareWarpAssembleCoaddTask", "CompareWarpAssembleCoaddConfig"] 

54 

55log = logging.getLogger(__name__.partition(".")[2]) 

56 

57 

58class AssembleCoaddConnections(pipeBase.PipelineTaskConnections, 

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

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

61 "outputCoaddName": "deep", 

62 "warpType": "direct", 

63 "warpTypeSuffix": ""}): 

64 

65 inputWarps = pipeBase.connectionTypes.Input( 

66 doc=("Input list of warps to be assemebled i.e. stacked." 

67 "WarpType (e.g. direct, psfMatched) is controlled by the warpType config parameter"), 

68 name="{inputCoaddName}Coadd_{warpType}Warp", 

69 storageClass="ExposureF", 

70 dimensions=("tract", "patch", "skymap", "visit", "instrument"), 

71 deferLoad=True, 

72 multiple=True 

73 ) 

74 skyMap = pipeBase.connectionTypes.Input( 

75 doc="Input definition of geometry/bbox and projection/wcs for coadded exposures", 

76 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME, 

77 storageClass="SkyMap", 

78 dimensions=("skymap", ), 

79 ) 

80 selectedVisits = pipeBase.connectionTypes.Input( 

81 doc="Selected visits to be coadded.", 

82 name="{outputCoaddName}Visits", 

83 storageClass="StructuredDataDict", 

84 dimensions=("instrument", "tract", "patch", "skymap", "band") 

85 ) 

86 brightObjectMask = pipeBase.connectionTypes.PrerequisiteInput( 

87 doc=("Input Bright Object Mask mask produced with external catalogs to be applied to the mask plane" 

88 " BRIGHT_OBJECT."), 

89 name="brightObjectMask", 

90 storageClass="ObjectMaskCatalog", 

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

92 ) 

93 coaddExposure = pipeBase.connectionTypes.Output( 

94 doc="Output coadded exposure, produced by stacking input warps", 

95 name="{outputCoaddName}Coadd{warpTypeSuffix}", 

96 storageClass="ExposureF", 

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

98 ) 

99 nImage = pipeBase.connectionTypes.Output( 

100 doc="Output image of number of input images per pixel", 

101 name="{outputCoaddName}Coadd_nImage", 

102 storageClass="ImageU", 

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

104 ) 

105 inputMap = pipeBase.connectionTypes.Output( 

106 doc="Output healsparse map of input images", 

107 name="{outputCoaddName}Coadd_inputMap", 

108 storageClass="HealSparseMap", 

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

110 ) 

111 

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

113 super().__init__(config=config) 

114 

115 # Override the connection's name template with config to replicate Gen2 behavior 

116 # This duplicates some of the logic in the base class, due to wanting Gen2 and 

117 # Gen3 configs to stay in sync. This should be removed when gen2 is deprecated 

118 templateValues = {name: getattr(config.connections, name) for name in self.defaultTemplates} 

119 templateValues['warpType'] = config.warpType 

120 templateValues['warpTypeSuffix'] = makeCoaddSuffix(config.warpType) 

121 self._nameOverrides = {name: getattr(config.connections, name).format(**templateValues) 

122 for name in self.allConnections} 

123 self._typeNameToVarName = {v: k for k, v in self._nameOverrides.items()} 

124 # End code to remove after deprecation 

125 

126 if not config.doMaskBrightObjects: 

127 self.prerequisiteInputs.remove("brightObjectMask") 

128 

129 if not config.doSelectVisits: 

130 self.inputs.remove("selectedVisits") 

131 

132 if not config.doNImage: 

133 self.outputs.remove("nImage") 

134 

135 if not self.config.doInputMap: 

136 self.outputs.remove("inputMap") 

137 

138 

139class AssembleCoaddConfig(CoaddBaseTask.ConfigClass, pipeBase.PipelineTaskConfig, 

140 pipelineConnections=AssembleCoaddConnections): 

141 """Configuration parameters for the `AssembleCoaddTask`. 

142 

143 Notes 

144 ----- 

145 The `doMaskBrightObjects` and `brightObjectMaskName` configuration options 

146 only set the bitplane config.brightObjectMaskName. To make this useful you 

147 *must* also configure the flags.pixel algorithm, for example by adding 

148 

149 .. code-block:: none 

150 

151 config.measurement.plugins["base_PixelFlags"].masksFpCenter.append("BRIGHT_OBJECT") 

152 config.measurement.plugins["base_PixelFlags"].masksFpAnywhere.append("BRIGHT_OBJECT") 

153 

154 to your measureCoaddSources.py and forcedPhotCoadd.py config overrides. 

155 """ 

156 warpType = pexConfig.Field( 

157 doc="Warp name: one of 'direct' or 'psfMatched'", 

158 dtype=str, 

159 default="direct", 

160 ) 

161 subregionSize = pexConfig.ListField( 

162 dtype=int, 

163 doc="Width, height of stack subregion size; " 

164 "make small enough that a full stack of images will fit into memory at once.", 

165 length=2, 

166 default=(2000, 2000), 

167 ) 

168 statistic = pexConfig.Field( 

169 dtype=str, 

170 doc="Main stacking statistic for aggregating over the epochs.", 

171 default="MEANCLIP", 

172 ) 

173 doOnlineForMean = pexConfig.Field( 

174 dtype=bool, 

175 doc="Perform online coaddition when statistic=\"MEAN\" to save memory?", 

176 default=False, 

177 ) 

178 doSigmaClip = pexConfig.Field( 

179 dtype=bool, 

180 doc="Perform sigma clipped outlier rejection with MEANCLIP statistic? (DEPRECATED)", 

181 default=False, 

182 ) 

183 sigmaClip = pexConfig.Field( 

184 dtype=float, 

185 doc="Sigma for outlier rejection; ignored if non-clipping statistic selected.", 

186 default=3.0, 

187 ) 

188 clipIter = pexConfig.Field( 

189 dtype=int, 

190 doc="Number of iterations of outlier rejection; ignored if non-clipping statistic selected.", 

191 default=2, 

192 ) 

193 calcErrorFromInputVariance = pexConfig.Field( 

194 dtype=bool, 

195 doc="Calculate coadd variance from input variance by stacking statistic." 

196 "Passed to StatisticsControl.setCalcErrorFromInputVariance()", 

197 default=True, 

198 ) 

199 scaleZeroPoint = pexConfig.ConfigurableField( 

200 target=ScaleZeroPointTask, 

201 doc="Task to adjust the photometric zero point of the coadd temp exposures", 

202 ) 

203 doInterp = pexConfig.Field( 

204 doc="Interpolate over NaN pixels? Also extrapolate, if necessary, but the results are ugly.", 

205 dtype=bool, 

206 default=True, 

207 ) 

208 interpImage = pexConfig.ConfigurableField( 

209 target=InterpImageTask, 

210 doc="Task to interpolate (and extrapolate) over NaN pixels", 

211 ) 

212 doWrite = pexConfig.Field( 

213 doc="Persist coadd?", 

214 dtype=bool, 

215 default=True, 

216 ) 

217 doNImage = pexConfig.Field( 

218 doc="Create image of number of contributing exposures for each pixel", 

219 dtype=bool, 

220 default=False, 

221 ) 

222 doUsePsfMatchedPolygons = pexConfig.Field( 

223 doc="Use ValidPolygons from shrunk Psf-Matched Calexps? Should be set to True by CompareWarp only.", 

224 dtype=bool, 

225 default=False, 

226 ) 

227 maskPropagationThresholds = pexConfig.DictField( 

228 keytype=str, 

229 itemtype=float, 

230 doc=("Threshold (in fractional weight) of rejection at which we propagate a mask plane to " 

231 "the coadd; that is, we set the mask bit on the coadd if the fraction the rejected frames " 

232 "would have contributed exceeds this value."), 

233 default={"SAT": 0.1}, 

234 ) 

235 removeMaskPlanes = pexConfig.ListField(dtype=str, default=["NOT_DEBLENDED"], 

236 doc="Mask planes to remove before coadding") 

237 doMaskBrightObjects = pexConfig.Field(dtype=bool, default=False, 

238 doc="Set mask and flag bits for bright objects?") 

239 brightObjectMaskName = pexConfig.Field(dtype=str, default="BRIGHT_OBJECT", 

240 doc="Name of mask bit used for bright objects") 

241 coaddPsf = pexConfig.ConfigField( 

242 doc="Configuration for CoaddPsf", 

243 dtype=measAlg.CoaddPsfConfig, 

244 ) 

245 doAttachTransmissionCurve = pexConfig.Field( 

246 dtype=bool, default=False, optional=False, 

247 doc=("Attach a piecewise TransmissionCurve for the coadd? " 

248 "(requires all input Exposures to have TransmissionCurves).") 

249 ) 

250 hasFakes = pexConfig.Field( 

251 dtype=bool, 

252 default=False, 

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

254 ) 

255 doSelectVisits = pexConfig.Field( 

256 doc="Coadd only visits selected by a SelectVisitsTask", 

257 dtype=bool, 

258 default=False, 

259 ) 

260 doInputMap = pexConfig.Field( 

261 doc="Create a bitwise map of coadd inputs", 

262 dtype=bool, 

263 default=False, 

264 ) 

265 inputMapper = pexConfig.ConfigurableField( 

266 doc="Input map creation subtask.", 

267 target=HealSparseInputMapTask, 

268 ) 

269 

270 def setDefaults(self): 

271 super().setDefaults() 

272 self.badMaskPlanes = ["NO_DATA", "BAD", "SAT", "EDGE"] 

273 

274 def validate(self): 

275 super().validate() 

276 if self.doPsfMatch: 

277 # Backwards compatibility. 

278 # Configs do not have loggers 

279 log.warning("Config doPsfMatch deprecated. Setting warpType='psfMatched'") 

280 self.warpType = 'psfMatched' 

281 if self.doSigmaClip and self.statistic != "MEANCLIP": 

282 log.warning('doSigmaClip deprecated. To replicate behavior, setting statistic to "MEANCLIP"') 

283 self.statistic = "MEANCLIP" 

284 if self.doInterp and self.statistic not in ['MEAN', 'MEDIAN', 'MEANCLIP', 'VARIANCE', 'VARIANCECLIP']: 

285 raise ValueError("Must set doInterp=False for statistic=%s, which does not " 

286 "compute and set a non-zero coadd variance estimate." % (self.statistic)) 

287 

288 unstackableStats = ['NOTHING', 'ERROR', 'ORMASK'] 

289 if not hasattr(afwMath.Property, self.statistic) or self.statistic in unstackableStats: 

290 stackableStats = [str(k) for k in afwMath.Property.__members__.keys() 

291 if str(k) not in unstackableStats] 

292 raise ValueError("statistic %s is not allowed. Please choose one of %s." 

293 % (self.statistic, stackableStats)) 

294 

295 

296class AssembleCoaddTask(CoaddBaseTask, pipeBase.PipelineTask): 

297 """Assemble a coadded image from a set of warps (coadded temporary exposures). 

298 

299 We want to assemble a coadded image from a set of Warps (also called 

300 coadded temporary exposures or ``coaddTempExps``). 

301 Each input Warp covers a patch on the sky and corresponds to a single 

302 run/visit/exposure of the covered patch. We provide the task with a list 

303 of Warps (``selectDataList``) from which it selects Warps that cover the 

304 specified patch (pointed at by ``dataRef``). 

305 Each Warp that goes into a coadd will typically have an independent 

306 photometric zero-point. Therefore, we must scale each Warp to set it to 

307 a common photometric zeropoint. WarpType may be one of 'direct' or 

308 'psfMatched', and the boolean configs `config.makeDirect` and 

309 `config.makePsfMatched` set which of the warp types will be coadded. 

310 The coadd is computed as a mean with optional outlier rejection. 

311 Criteria for outlier rejection are set in `AssembleCoaddConfig`. 

312 Finally, Warps can have bad 'NaN' pixels which received no input from the 

313 source calExps. We interpolate over these bad (NaN) pixels. 

314 

315 `AssembleCoaddTask` uses several sub-tasks. These are 

316 

317 - `ScaleZeroPointTask` 

318 - create and use an ``imageScaler`` object to scale the photometric zeropoint for each Warp 

319 - `InterpImageTask` 

320 - interpolate across bad pixels (NaN) in the final coadd 

321 

322 You can retarget these subtasks if you wish. 

323 

324 Notes 

325 ----- 

326 The `lsst.pipe.base.cmdLineTask.CmdLineTask` interface supports a 

327 flag ``-d`` to import ``debug.py`` from your ``PYTHONPATH``; see 

328 `baseDebug` for more about ``debug.py`` files. `AssembleCoaddTask` has 

329 no debug variables of its own. Some of the subtasks may support debug 

330 variables. See the documentation for the subtasks for further information. 

331 

332 Examples 

333 -------- 

334 `AssembleCoaddTask` assembles a set of warped images into a coadded image. 

335 The `AssembleCoaddTask` can be invoked by running ``assembleCoadd.py`` 

336 with the flag '--legacyCoadd'. Usage of assembleCoadd.py expects two 

337 inputs: a data reference to the tract patch and filter to be coadded, and 

338 a list of Warps to attempt to coadd. These are specified using ``--id`` and 

339 ``--selectId``, respectively: 

340 

341 .. code-block:: none 

342 

343 --id = [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]] 

344 --selectId [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]] 

345 

346 Only the Warps that cover the specified tract and patch will be coadded. 

347 A list of the available optional arguments can be obtained by calling 

348 ``assembleCoadd.py`` with the ``--help`` command line argument: 

349 

350 .. code-block:: none 

351 

352 assembleCoadd.py --help 

353 

354 To demonstrate usage of the `AssembleCoaddTask` in the larger context of 

355 multi-band processing, we will generate the HSC-I & -R band coadds from 

356 HSC engineering test data provided in the ``ci_hsc`` package. To begin, 

357 assuming that the lsst stack has been already set up, we must set up the 

358 obs_subaru and ``ci_hsc`` packages. This defines the environment variable 

359 ``$CI_HSC_DIR`` and points at the location of the package. The raw HSC 

360 data live in the ``$CI_HSC_DIR/raw directory``. To begin assembling the 

361 coadds, we must first 

362 

363 - processCcd 

364 - process the individual ccds in $CI_HSC_RAW to produce calibrated exposures 

365 - makeSkyMap 

366 - create a skymap that covers the area of the sky present in the raw exposures 

367 - makeCoaddTempExp 

368 - warp the individual calibrated exposures to the tangent plane of the coadd 

369 

370 We can perform all of these steps by running 

371 

372 .. code-block:: none 

373 

374 $CI_HSC_DIR scons warp-903986 warp-904014 warp-903990 warp-904010 warp-903988 

375 

376 This will produce warped exposures for each visit. To coadd the warped 

377 data, we call assembleCoadd.py as follows: 

378 

379 .. code-block:: none 

380 

381 assembleCoadd.py --legacyCoadd $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I \ 

382 --selectId visit=903986 ccd=16 --selectId visit=903986 ccd=22 --selectId visit=903986 ccd=23 \ 

383 --selectId visit=903986 ccd=100 --selectId visit=904014 ccd=1 --selectId visit=904014 ccd=6 \ 

384 --selectId visit=904014 ccd=12 --selectId visit=903990 ccd=18 --selectId visit=903990 ccd=25 \ 

385 --selectId visit=904010 ccd=4 --selectId visit=904010 ccd=10 --selectId visit=904010 ccd=100 \ 

386 --selectId visit=903988 ccd=16 --selectId visit=903988 ccd=17 --selectId visit=903988 ccd=23 \ 

387 --selectId visit=903988 ccd=24 

388 

389 that will process the HSC-I band data. The results are written in 

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

391 

392 You may also choose to run: 

393 

394 .. code-block:: none 

395 

396 scons warp-903334 warp-903336 warp-903338 warp-903342 warp-903344 warp-903346 

397 assembleCoadd.py --legacyCoadd $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R \ 

398 --selectId visit=903334 ccd=16 --selectId visit=903334 ccd=22 --selectId visit=903334 ccd=23 \ 

399 --selectId visit=903334 ccd=100 --selectId visit=903336 ccd=17 --selectId visit=903336 ccd=24 \ 

400 --selectId visit=903338 ccd=18 --selectId visit=903338 ccd=25 --selectId visit=903342 ccd=4 \ 

401 --selectId visit=903342 ccd=10 --selectId visit=903342 ccd=100 --selectId visit=903344 ccd=0 \ 

402 --selectId visit=903344 ccd=5 --selectId visit=903344 ccd=11 --selectId visit=903346 ccd=1 \ 

403 --selectId visit=903346 ccd=6 --selectId visit=903346 ccd=12 

404 

405 to generate the coadd for the HSC-R band if you are interested in 

406 following multiBand Coadd processing as discussed in `pipeTasks_multiBand` 

407 (but note that normally, one would use the `SafeClipAssembleCoaddTask` 

408 rather than `AssembleCoaddTask` to make the coadd. 

409 """ 

410 ConfigClass = AssembleCoaddConfig 

411 _DefaultName = "assembleCoadd" 

412 

413 def __init__(self, *args, **kwargs): 

414 # TODO: DM-17415 better way to handle previously allowed passed args e.g.`AssembleCoaddTask(config)` 

415 if args: 415 ↛ 416line 415 didn't jump to line 416, because the condition on line 415 was never true

416 argNames = ["config", "name", "parentTask", "log"] 

417 kwargs.update({k: v for k, v in zip(argNames, args)}) 

418 warnings.warn("AssembleCoadd received positional args, and casting them as kwargs: %s. " 

419 "PipelineTask will not take positional args" % argNames, FutureWarning) 

420 

421 super().__init__(**kwargs) 

422 self.makeSubtask("interpImage") 

423 self.makeSubtask("scaleZeroPoint") 

424 

425 if self.config.doMaskBrightObjects: 425 ↛ 426line 425 didn't jump to line 426, because the condition on line 425 was never true

426 mask = afwImage.Mask() 

427 try: 

428 self.brightObjectBitmask = 1 << mask.addMaskPlane(self.config.brightObjectMaskName) 

429 except pexExceptions.LsstCppException: 

430 raise RuntimeError("Unable to define mask plane for bright objects; planes used are %s" % 

431 mask.getMaskPlaneDict().keys()) 

432 del mask 

433 

434 if self.config.doInputMap: 434 ↛ 435line 434 didn't jump to line 435, because the condition on line 434 was never true

435 self.makeSubtask("inputMapper") 

436 

437 self.warpType = self.config.warpType 

438 

439 @utils.inheritDoc(pipeBase.PipelineTask) 

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

441 # Docstring to be formatted with info from PipelineTask.runQuantum 

442 """ 

443 Notes 

444 ----- 

445 Assemble a coadd from a set of Warps. 

446 

447 PipelineTask (Gen3) entry point to Coadd a set of Warps. 

448 Analogous to `runDataRef`, it prepares all the data products to be 

449 passed to `run`, and processes the results before returning a struct 

450 of results to be written out. AssembleCoadd cannot fit all Warps in memory. 

451 Therefore, its inputs are accessed subregion by subregion 

452 by the Gen3 `DeferredDatasetHandle` that is analagous to the Gen2 

453 `lsst.daf.persistence.ButlerDataRef`. Any updates to this method should 

454 correspond to an update in `runDataRef` while both entry points 

455 are used. 

456 """ 

457 inputData = butlerQC.get(inputRefs) 

458 

459 # Construct skyInfo expected by run 

460 # Do not remove skyMap from inputData in case makeSupplementaryDataGen3 needs it 

461 skyMap = inputData["skyMap"] 

462 outputDataId = butlerQC.quantum.dataId 

463 

464 inputData['skyInfo'] = makeSkyInfo(skyMap, 

465 tractId=outputDataId['tract'], 

466 patchId=outputDataId['patch']) 

467 

468 if self.config.doSelectVisits: 

469 warpRefList = self.filterWarps(inputData['inputWarps'], inputData['selectedVisits']) 

470 else: 

471 warpRefList = inputData['inputWarps'] 

472 

473 # Perform same middle steps as `runDataRef` does 

474 inputs = self.prepareInputs(warpRefList) 

475 self.log.info("Found %d %s", len(inputs.tempExpRefList), 

476 self.getTempExpDatasetName(self.warpType)) 

477 if len(inputs.tempExpRefList) == 0: 

478 raise pipeBase.NoWorkFound("No coadd temporary exposures found") 

479 

480 supplementaryData = self.makeSupplementaryDataGen3(butlerQC, inputRefs, outputRefs) 

481 retStruct = self.run(inputData['skyInfo'], inputs.tempExpRefList, inputs.imageScalerList, 

482 inputs.weightList, supplementaryData=supplementaryData) 

483 

484 inputData.setdefault('brightObjectMask', None) 

485 self.processResults(retStruct.coaddExposure, inputData['brightObjectMask'], outputDataId) 

486 

487 if self.config.doWrite: 

488 butlerQC.put(retStruct, outputRefs) 

489 return retStruct 

490 

491 @pipeBase.timeMethod 

492 def runDataRef(self, dataRef, selectDataList=None, warpRefList=None): 

493 """Assemble a coadd from a set of Warps. 

494 

495 Pipebase.CmdlineTask entry point to Coadd a set of Warps. 

496 Compute weights to be applied to each Warp and 

497 find scalings to match the photometric zeropoint to a reference Warp. 

498 Assemble the Warps using `run`. Interpolate over NaNs and 

499 optionally write the coadd to disk. Return the coadded exposure. 

500 

501 Parameters 

502 ---------- 

503 dataRef : `lsst.daf.persistence.butlerSubset.ButlerDataRef` 

504 Data reference defining the patch for coaddition and the 

505 reference Warp (if ``config.autoReference=False``). 

506 Used to access the following data products: 

507 - ``self.config.coaddName + "Coadd_skyMap"`` 

508 - ``self.config.coaddName + "Coadd_ + <warpType> + "Warp"`` (optionally) 

509 - ``self.config.coaddName + "Coadd"`` 

510 selectDataList : `list` 

511 List of data references to Calexps. Data to be coadded will be 

512 selected from this list based on overlap with the patch defined 

513 by dataRef, grouped by visit, and converted to a list of data 

514 references to warps. 

515 warpRefList : `list` 

516 List of data references to Warps to be coadded. 

517 Note: `warpRefList` is just the new name for `tempExpRefList`. 

518 

519 Returns 

520 ------- 

521 retStruct : `lsst.pipe.base.Struct` 

522 Result struct with components: 

523 

524 - ``coaddExposure``: coadded exposure (``Exposure``). 

525 - ``nImage``: exposure count image (``Image``). 

526 """ 

527 if selectDataList and warpRefList: 527 ↛ 528line 527 didn't jump to line 528, because the condition on line 527 was never true

528 raise RuntimeError("runDataRef received both a selectDataList and warpRefList, " 

529 "and which to use is ambiguous. Please pass only one.") 

530 

531 skyInfo = self.getSkyInfo(dataRef) 

532 if warpRefList is None: 

533 calExpRefList = self.selectExposures(dataRef, skyInfo, selectDataList=selectDataList) 

534 if len(calExpRefList) == 0: 534 ↛ 535line 534 didn't jump to line 535, because the condition on line 534 was never true

535 self.log.warning("No exposures to coadd") 

536 return 

537 self.log.info("Coadding %d exposures", len(calExpRefList)) 

538 

539 warpRefList = self.getTempExpRefList(dataRef, calExpRefList) 

540 

541 inputData = self.prepareInputs(warpRefList) 

542 self.log.info("Found %d %s", len(inputData.tempExpRefList), 

543 self.getTempExpDatasetName(self.warpType)) 

544 if len(inputData.tempExpRefList) == 0: 544 ↛ 545line 544 didn't jump to line 545, because the condition on line 544 was never true

545 self.log.warning("No coadd temporary exposures found") 

546 return 

547 

548 supplementaryData = self.makeSupplementaryData(dataRef, warpRefList=inputData.tempExpRefList) 

549 

550 retStruct = self.run(skyInfo, inputData.tempExpRefList, inputData.imageScalerList, 

551 inputData.weightList, supplementaryData=supplementaryData) 

552 

553 brightObjects = self.readBrightObjectMasks(dataRef) if self.config.doMaskBrightObjects else None 

554 self.processResults(retStruct.coaddExposure, brightObjectMasks=brightObjects, dataId=dataRef.dataId) 

555 

556 if self.config.doWrite: 

557 if self.getCoaddDatasetName(self.warpType) == "deepCoadd" and self.config.hasFakes: 557 ↛ 558line 557 didn't jump to line 558, because the condition on line 557 was never true

558 coaddDatasetName = "fakes_" + self.getCoaddDatasetName(self.warpType) 

559 else: 

560 coaddDatasetName = self.getCoaddDatasetName(self.warpType) 

561 self.log.info("Persisting %s", coaddDatasetName) 

562 dataRef.put(retStruct.coaddExposure, coaddDatasetName) 

563 if self.config.doNImage and retStruct.nImage is not None: 563 ↛ 564line 563 didn't jump to line 564, because the condition on line 563 was never true

564 dataRef.put(retStruct.nImage, self.getCoaddDatasetName(self.warpType) + '_nImage') 

565 

566 return retStruct 

567 

568 def processResults(self, coaddExposure, brightObjectMasks=None, dataId=None): 

569 """Interpolate over missing data and mask bright stars. 

570 

571 Parameters 

572 ---------- 

573 coaddExposure : `lsst.afw.image.Exposure` 

574 The coadded exposure to process. 

575 dataRef : `lsst.daf.persistence.ButlerDataRef` 

576 Butler data reference for supplementary data. 

577 """ 

578 if self.config.doInterp: 578 ↛ 585line 578 didn't jump to line 585, because the condition on line 578 was never false

579 self.interpImage.run(coaddExposure.getMaskedImage(), planeName="NO_DATA") 

580 # The variance must be positive; work around for DM-3201. 

581 varArray = coaddExposure.variance.array 

582 with numpy.errstate(invalid="ignore"): 

583 varArray[:] = numpy.where(varArray > 0, varArray, numpy.inf) 

584 

585 if self.config.doMaskBrightObjects: 585 ↛ 586line 585 didn't jump to line 586, because the condition on line 585 was never true

586 self.setBrightObjectMasks(coaddExposure, brightObjectMasks, dataId) 

587 

588 def makeSupplementaryData(self, dataRef, selectDataList=None, warpRefList=None): 

589 """Make additional inputs to run() specific to subclasses (Gen2) 

590 

591 Duplicates interface of `runDataRef` method 

592 Available to be implemented by subclasses only if they need the 

593 coadd dataRef for performing preliminary processing before 

594 assembling the coadd. 

595 

596 Parameters 

597 ---------- 

598 dataRef : `lsst.daf.persistence.ButlerDataRef` 

599 Butler data reference for supplementary data. 

600 selectDataList : `list` (optional) 

601 Optional List of data references to Calexps. 

602 warpRefList : `list` (optional) 

603 Optional List of data references to Warps. 

604 """ 

605 return pipeBase.Struct() 

606 

607 def makeSupplementaryDataGen3(self, butlerQC, inputRefs, outputRefs): 

608 """Make additional inputs to run() specific to subclasses (Gen3) 

609 

610 Duplicates interface of `runQuantum` method. 

611 Available to be implemented by subclasses only if they need the 

612 coadd dataRef for performing preliminary processing before 

613 assembling the coadd. 

614 

615 Parameters 

616 ---------- 

617 butlerQC : `lsst.pipe.base.ButlerQuantumContext` 

618 Gen3 Butler object for fetching additional data products before 

619 running the Task specialized for quantum being processed 

620 inputRefs : `lsst.pipe.base.InputQuantizedConnection` 

621 Attributes are the names of the connections describing input dataset types. 

622 Values are DatasetRefs that task consumes for corresponding dataset type. 

623 DataIds are guaranteed to match data objects in ``inputData``. 

624 outputRefs : `lsst.pipe.base.OutputQuantizedConnection` 

625 Attributes are the names of the connections describing output dataset types. 

626 Values are DatasetRefs that task is to produce 

627 for corresponding dataset type. 

628 """ 

629 return pipeBase.Struct() 

630 

631 def getTempExpRefList(self, patchRef, calExpRefList): 

632 """Generate list data references corresponding to warped exposures 

633 that lie within the patch to be coadded. 

634 

635 Parameters 

636 ---------- 

637 patchRef : `dataRef` 

638 Data reference for patch. 

639 calExpRefList : `list` 

640 List of data references for input calexps. 

641 

642 Returns 

643 ------- 

644 tempExpRefList : `list` 

645 List of Warp/CoaddTempExp data references. 

646 """ 

647 butler = patchRef.getButler() 

648 groupData = groupPatchExposures(patchRef, calExpRefList, self.getCoaddDatasetName(self.warpType), 

649 self.getTempExpDatasetName(self.warpType)) 

650 tempExpRefList = [getGroupDataRef(butler, self.getTempExpDatasetName(self.warpType), 

651 g, groupData.keys) for 

652 g in groupData.groups.keys()] 

653 return tempExpRefList 

654 

655 def prepareInputs(self, refList): 

656 """Prepare the input warps for coaddition by measuring the weight for 

657 each warp and the scaling for the photometric zero point. 

658 

659 Each Warp has its own photometric zeropoint and background variance. 

660 Before coadding these Warps together, compute a scale factor to 

661 normalize the photometric zeropoint and compute the weight for each Warp. 

662 

663 Parameters 

664 ---------- 

665 refList : `list` 

666 List of data references to tempExp 

667 

668 Returns 

669 ------- 

670 result : `lsst.pipe.base.Struct` 

671 Result struct with components: 

672 

673 - ``tempExprefList``: `list` of data references to tempExp. 

674 - ``weightList``: `list` of weightings. 

675 - ``imageScalerList``: `list` of image scalers. 

676 """ 

677 statsCtrl = afwMath.StatisticsControl() 

678 statsCtrl.setNumSigmaClip(self.config.sigmaClip) 

679 statsCtrl.setNumIter(self.config.clipIter) 

680 statsCtrl.setAndMask(self.getBadPixelMask()) 

681 statsCtrl.setNanSafe(True) 

682 # compute tempExpRefList: a list of tempExpRef that actually exist 

683 # and weightList: a list of the weight of the associated coadd tempExp 

684 # and imageScalerList: a list of scale factors for the associated coadd tempExp 

685 tempExpRefList = [] 

686 weightList = [] 

687 imageScalerList = [] 

688 tempExpName = self.getTempExpDatasetName(self.warpType) 

689 for tempExpRef in refList: 

690 # Gen3's DeferredDatasetHandles are guaranteed to exist and 

691 # therefore have no datasetExists() method 

692 if not isinstance(tempExpRef, DeferredDatasetHandle): 692 ↛ 697line 692 didn't jump to line 697, because the condition on line 692 was never false

693 if not tempExpRef.datasetExists(tempExpName): 

694 self.log.warning("Could not find %s %s; skipping it", tempExpName, tempExpRef.dataId) 

695 continue 

696 

697 tempExp = tempExpRef.get(datasetType=tempExpName, immediate=True) 

698 # Ignore any input warp that is empty of data 

699 if numpy.isnan(tempExp.image.array).all(): 699 ↛ 700line 699 didn't jump to line 700, because the condition on line 699 was never true

700 continue 

701 maskedImage = tempExp.getMaskedImage() 

702 imageScaler = self.scaleZeroPoint.computeImageScaler( 

703 exposure=tempExp, 

704 dataRef=tempExpRef, 

705 ) 

706 try: 

707 imageScaler.scaleMaskedImage(maskedImage) 

708 except Exception as e: 

709 self.log.warning("Scaling failed for %s (skipping it): %s", tempExpRef.dataId, e) 

710 continue 

711 statObj = afwMath.makeStatistics(maskedImage.getVariance(), maskedImage.getMask(), 

712 afwMath.MEANCLIP, statsCtrl) 

713 meanVar, meanVarErr = statObj.getResult(afwMath.MEANCLIP) 

714 weight = 1.0 / float(meanVar) 

715 if not numpy.isfinite(weight): 715 ↛ 716line 715 didn't jump to line 716, because the condition on line 715 was never true

716 self.log.warning("Non-finite weight for %s: skipping", tempExpRef.dataId) 

717 continue 

718 self.log.info("Weight of %s %s = %0.3f", tempExpName, tempExpRef.dataId, weight) 

719 

720 del maskedImage 

721 del tempExp 

722 

723 tempExpRefList.append(tempExpRef) 

724 weightList.append(weight) 

725 imageScalerList.append(imageScaler) 

726 

727 return pipeBase.Struct(tempExpRefList=tempExpRefList, weightList=weightList, 

728 imageScalerList=imageScalerList) 

729 

730 def prepareStats(self, mask=None): 

731 """Prepare the statistics for coadding images. 

732 

733 Parameters 

734 ---------- 

735 mask : `int`, optional 

736 Bit mask value to exclude from coaddition. 

737 

738 Returns 

739 ------- 

740 stats : `lsst.pipe.base.Struct` 

741 Statistics structure with the following fields: 

742 

743 - ``statsCtrl``: Statistics control object for coadd 

744 (`lsst.afw.math.StatisticsControl`) 

745 - ``statsFlags``: Statistic for coadd (`lsst.afw.math.Property`) 

746 """ 

747 if mask is None: 

748 mask = self.getBadPixelMask() 

749 statsCtrl = afwMath.StatisticsControl() 

750 statsCtrl.setNumSigmaClip(self.config.sigmaClip) 

751 statsCtrl.setNumIter(self.config.clipIter) 

752 statsCtrl.setAndMask(mask) 

753 statsCtrl.setNanSafe(True) 

754 statsCtrl.setWeighted(True) 

755 statsCtrl.setCalcErrorFromInputVariance(self.config.calcErrorFromInputVariance) 

756 for plane, threshold in self.config.maskPropagationThresholds.items(): 

757 bit = afwImage.Mask.getMaskPlane(plane) 

758 statsCtrl.setMaskPropagationThreshold(bit, threshold) 

759 statsFlags = afwMath.stringToStatisticsProperty(self.config.statistic) 

760 return pipeBase.Struct(ctrl=statsCtrl, flags=statsFlags) 

761 

762 @pipeBase.timeMethod 

763 def run(self, skyInfo, tempExpRefList, imageScalerList, weightList, 

764 altMaskList=None, mask=None, supplementaryData=None): 

765 """Assemble a coadd from input warps 

766 

767 Assemble the coadd using the provided list of coaddTempExps. Since 

768 the full coadd covers a patch (a large area), the assembly is 

769 performed over small areas on the image at a time in order to 

770 conserve memory usage. Iterate over subregions within the outer 

771 bbox of the patch using `assembleSubregion` to stack the corresponding 

772 subregions from the coaddTempExps with the statistic specified. 

773 Set the edge bits the coadd mask based on the weight map. 

774 

775 Parameters 

776 ---------- 

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

778 Struct with geometric information about the patch. 

779 tempExpRefList : `list` 

780 List of data references to Warps (previously called CoaddTempExps). 

781 imageScalerList : `list` 

782 List of image scalers. 

783 weightList : `list` 

784 List of weights 

785 altMaskList : `list`, optional 

786 List of alternate masks to use rather than those stored with 

787 tempExp. 

788 mask : `int`, optional 

789 Bit mask value to exclude from coaddition. 

790 supplementaryData : lsst.pipe.base.Struct, optional 

791 Struct with additional data products needed to assemble coadd. 

792 Only used by subclasses that implement `makeSupplementaryData` 

793 and override `run`. 

794 

795 Returns 

796 ------- 

797 result : `lsst.pipe.base.Struct` 

798 Result struct with components: 

799 

800 - ``coaddExposure``: coadded exposure (``lsst.afw.image.Exposure``). 

801 - ``nImage``: exposure count image (``lsst.afw.image.Image``), if requested. 

802 - ``inputMap``: bit-wise map of inputs, if requested. 

803 - ``warpRefList``: input list of refs to the warps ( 

804 ``lsst.daf.butler.DeferredDatasetHandle`` or 

805 ``lsst.daf.persistence.ButlerDataRef``) 

806 (unmodified) 

807 - ``imageScalerList``: input list of image scalers (unmodified) 

808 - ``weightList``: input list of weights (unmodified) 

809 """ 

810 tempExpName = self.getTempExpDatasetName(self.warpType) 

811 self.log.info("Assembling %s %s", len(tempExpRefList), tempExpName) 

812 stats = self.prepareStats(mask=mask) 

813 

814 if altMaskList is None: 

815 altMaskList = [None]*len(tempExpRefList) 

816 

817 coaddExposure = afwImage.ExposureF(skyInfo.bbox, skyInfo.wcs) 

818 coaddExposure.setPhotoCalib(self.scaleZeroPoint.getPhotoCalib()) 

819 coaddExposure.getInfo().setCoaddInputs(self.inputRecorder.makeCoaddInputs()) 

820 self.assembleMetadata(coaddExposure, tempExpRefList, weightList) 

821 coaddMaskedImage = coaddExposure.getMaskedImage() 

822 subregionSizeArr = self.config.subregionSize 

823 subregionSize = geom.Extent2I(subregionSizeArr[0], subregionSizeArr[1]) 

824 # if nImage is requested, create a zero one which can be passed to assembleSubregion 

825 if self.config.doNImage: 825 ↛ 826line 825 didn't jump to line 826, because the condition on line 825 was never true

826 nImage = afwImage.ImageU(skyInfo.bbox) 

827 else: 

828 nImage = None 

829 # If inputMap is requested, create the initial version that can be masked in 

830 # assembleSubregion. 

831 if self.config.doInputMap: 831 ↛ 832line 831 didn't jump to line 832, because the condition on line 831 was never true

832 self.inputMapper.build_ccd_input_map(skyInfo.bbox, 

833 skyInfo.wcs, 

834 coaddExposure.getInfo().getCoaddInputs().ccds) 

835 

836 if self.config.doOnlineForMean and self.config.statistic == "MEAN": 836 ↛ 837line 836 didn't jump to line 837, because the condition on line 836 was never true

837 try: 

838 self.assembleOnlineMeanCoadd(coaddExposure, tempExpRefList, imageScalerList, 

839 weightList, altMaskList, stats.ctrl, 

840 nImage=nImage) 

841 except Exception as e: 

842 self.log.fatal("Cannot compute online coadd %s", e) 

843 else: 

844 for subBBox in self._subBBoxIter(skyInfo.bbox, subregionSize): 

845 try: 

846 self.assembleSubregion(coaddExposure, subBBox, tempExpRefList, imageScalerList, 

847 weightList, altMaskList, stats.flags, stats.ctrl, 

848 nImage=nImage) 

849 except Exception as e: 

850 self.log.fatal("Cannot compute coadd %s: %s", subBBox, e) 

851 

852 # If inputMap is requested, we must finalize the map after the accumulation. 

853 if self.config.doInputMap: 853 ↛ 854line 853 didn't jump to line 854, because the condition on line 853 was never true

854 self.inputMapper.finalize_ccd_input_map_mask() 

855 inputMap = self.inputMapper.ccd_input_map 

856 else: 

857 inputMap = None 

858 

859 self.setInexactPsf(coaddMaskedImage.getMask()) 

860 # Despite the name, the following doesn't really deal with "EDGE" pixels: it identifies 

861 # pixels that didn't receive any unmasked inputs (as occurs around the edge of the field). 

862 coaddUtils.setCoaddEdgeBits(coaddMaskedImage.getMask(), coaddMaskedImage.getVariance()) 

863 return pipeBase.Struct(coaddExposure=coaddExposure, nImage=nImage, 

864 warpRefList=tempExpRefList, imageScalerList=imageScalerList, 

865 weightList=weightList, inputMap=inputMap) 

866 

867 def assembleMetadata(self, coaddExposure, tempExpRefList, weightList): 

868 """Set the metadata for the coadd. 

869 

870 This basic implementation sets the filter from the first input. 

871 

872 Parameters 

873 ---------- 

874 coaddExposure : `lsst.afw.image.Exposure` 

875 The target exposure for the coadd. 

876 tempExpRefList : `list` 

877 List of data references to tempExp. 

878 weightList : `list` 

879 List of weights. 

880 """ 

881 assert len(tempExpRefList) == len(weightList), "Length mismatch" 

882 tempExpName = self.getTempExpDatasetName(self.warpType) 

883 # We load a single pixel of each coaddTempExp, because we just want to get at the metadata 

884 # (and we need more than just the PropertySet that contains the header), which is not possible 

885 # with the current butler (see #2777). 

886 bbox = geom.Box2I(coaddExposure.getBBox().getMin(), geom.Extent2I(1, 1)) 

887 

888 if isinstance(tempExpRefList[0], DeferredDatasetHandle): 888 ↛ 890line 888 didn't jump to line 890, because the condition on line 888 was never true

889 # Gen 3 API 

890 tempExpList = [tempExpRef.get(parameters={'bbox': bbox}) for tempExpRef in tempExpRefList] 

891 else: 

892 # Gen 2 API. Delete this when Gen 2 retired 

893 tempExpList = [tempExpRef.get(tempExpName + "_sub", bbox=bbox, immediate=True) 

894 for tempExpRef in tempExpRefList] 

895 numCcds = sum(len(tempExp.getInfo().getCoaddInputs().ccds) for tempExp in tempExpList) 

896 

897 # Set the coadd FilterLabel to the band of the first input exposure: 

898 # Coadds are calibrated, so the physical label is now meaningless. 

899 coaddExposure.setFilterLabel(afwImage.FilterLabel(tempExpList[0].getFilterLabel().bandLabel)) 

900 coaddInputs = coaddExposure.getInfo().getCoaddInputs() 

901 coaddInputs.ccds.reserve(numCcds) 

902 coaddInputs.visits.reserve(len(tempExpList)) 

903 

904 for tempExp, weight in zip(tempExpList, weightList): 

905 self.inputRecorder.addVisitToCoadd(coaddInputs, tempExp, weight) 

906 

907 if self.config.doUsePsfMatchedPolygons: 

908 self.shrinkValidPolygons(coaddInputs) 

909 

910 coaddInputs.visits.sort() 

911 if self.warpType == "psfMatched": 

912 # The modelPsf BBox for a psfMatchedWarp/coaddTempExp was dynamically defined by 

913 # ModelPsfMatchTask as the square box bounding its spatially-variable, pre-matched WarpedPsf. 

914 # Likewise, set the PSF of a PSF-Matched Coadd to the modelPsf 

915 # having the maximum width (sufficient because square) 

916 modelPsfList = [tempExp.getPsf() for tempExp in tempExpList] 

917 modelPsfWidthList = [modelPsf.computeBBox().getWidth() for modelPsf in modelPsfList] 

918 psf = modelPsfList[modelPsfWidthList.index(max(modelPsfWidthList))] 

919 else: 

920 psf = measAlg.CoaddPsf(coaddInputs.ccds, coaddExposure.getWcs(), 

921 self.config.coaddPsf.makeControl()) 

922 coaddExposure.setPsf(psf) 

923 apCorrMap = measAlg.makeCoaddApCorrMap(coaddInputs.ccds, coaddExposure.getBBox(afwImage.PARENT), 

924 coaddExposure.getWcs()) 

925 coaddExposure.getInfo().setApCorrMap(apCorrMap) 

926 if self.config.doAttachTransmissionCurve: 

927 transmissionCurve = measAlg.makeCoaddTransmissionCurve(coaddExposure.getWcs(), coaddInputs.ccds) 

928 coaddExposure.getInfo().setTransmissionCurve(transmissionCurve) 

929 

930 def assembleSubregion(self, coaddExposure, bbox, tempExpRefList, imageScalerList, weightList, 

931 altMaskList, statsFlags, statsCtrl, nImage=None): 

932 """Assemble the coadd for a sub-region. 

933 

934 For each coaddTempExp, check for (and swap in) an alternative mask 

935 if one is passed. Remove mask planes listed in 

936 `config.removeMaskPlanes`. Finally, stack the actual exposures using 

937 `lsst.afw.math.statisticsStack` with the statistic specified by 

938 statsFlags. Typically, the statsFlag will be one of lsst.afw.math.MEAN for 

939 a mean-stack or `lsst.afw.math.MEANCLIP` for outlier rejection using 

940 an N-sigma clipped mean where N and iterations are specified by 

941 statsCtrl. Assign the stacked subregion back to the coadd. 

942 

943 Parameters 

944 ---------- 

945 coaddExposure : `lsst.afw.image.Exposure` 

946 The target exposure for the coadd. 

947 bbox : `lsst.geom.Box` 

948 Sub-region to coadd. 

949 tempExpRefList : `list` 

950 List of data reference to tempExp. 

951 imageScalerList : `list` 

952 List of image scalers. 

953 weightList : `list` 

954 List of weights. 

955 altMaskList : `list` 

956 List of alternate masks to use rather than those stored with 

957 tempExp, or None. Each element is dict with keys = mask plane 

958 name to which to add the spans. 

959 statsFlags : `lsst.afw.math.Property` 

960 Property object for statistic for coadd. 

961 statsCtrl : `lsst.afw.math.StatisticsControl` 

962 Statistics control object for coadd. 

963 nImage : `lsst.afw.image.ImageU`, optional 

964 Keeps track of exposure count for each pixel. 

965 """ 

966 self.log.debug("Computing coadd over %s", bbox) 

967 tempExpName = self.getTempExpDatasetName(self.warpType) 

968 coaddExposure.mask.addMaskPlane("REJECTED") 

969 coaddExposure.mask.addMaskPlane("CLIPPED") 

970 coaddExposure.mask.addMaskPlane("SENSOR_EDGE") 

971 maskMap = self.setRejectedMaskMapping(statsCtrl) 

972 clipped = afwImage.Mask.getPlaneBitMask("CLIPPED") 

973 maskedImageList = [] 

974 if nImage is not None: 974 ↛ 975line 974 didn't jump to line 975, because the condition on line 974 was never true

975 subNImage = afwImage.ImageU(bbox.getWidth(), bbox.getHeight()) 

976 for tempExpRef, imageScaler, altMask in zip(tempExpRefList, imageScalerList, altMaskList): 

977 

978 if isinstance(tempExpRef, DeferredDatasetHandle): 978 ↛ 980line 978 didn't jump to line 980, because the condition on line 978 was never true

979 # Gen 3 API 

980 exposure = tempExpRef.get(parameters={'bbox': bbox}) 

981 else: 

982 # Gen 2 API. Delete this when Gen 2 retired 

983 exposure = tempExpRef.get(tempExpName + "_sub", bbox=bbox) 

984 

985 maskedImage = exposure.getMaskedImage() 

986 mask = maskedImage.getMask() 

987 if altMask is not None: 

988 self.applyAltMaskPlanes(mask, altMask) 

989 imageScaler.scaleMaskedImage(maskedImage) 

990 

991 # Add 1 for each pixel which is not excluded by the exclude mask. 

992 # In legacyCoadd, pixels may also be excluded by afwMath.statisticsStack. 

993 if nImage is not None: 993 ↛ 994line 993 didn't jump to line 994, because the condition on line 993 was never true

994 subNImage.getArray()[maskedImage.getMask().getArray() & statsCtrl.getAndMask() == 0] += 1 

995 if self.config.removeMaskPlanes: 995 ↛ 997line 995 didn't jump to line 997, because the condition on line 995 was never false

996 self.removeMaskPlanes(maskedImage) 

997 maskedImageList.append(maskedImage) 

998 

999 if self.config.doInputMap: 999 ↛ 1000line 999 didn't jump to line 1000, because the condition on line 999 was never true

1000 visit = exposure.getInfo().getCoaddInputs().visits[0].getId() 

1001 self.inputMapper.mask_warp_bbox(bbox, visit, mask, statsCtrl.getAndMask()) 

1002 

1003 with self.timer("stack"): 

1004 coaddSubregion = afwMath.statisticsStack(maskedImageList, statsFlags, statsCtrl, weightList, 

1005 clipped, # also set output to CLIPPED if sigma-clipped 

1006 maskMap) 

1007 coaddExposure.maskedImage.assign(coaddSubregion, bbox) 

1008 if nImage is not None: 1008 ↛ 1009line 1008 didn't jump to line 1009, because the condition on line 1008 was never true

1009 nImage.assign(subNImage, bbox) 

1010 

1011 def assembleOnlineMeanCoadd(self, coaddExposure, tempExpRefList, imageScalerList, weightList, 

1012 altMaskList, statsCtrl, nImage=None): 

1013 """Assemble the coadd using the "online" method. 

1014 

1015 This method takes a running sum of images and weights to save memory. 

1016 It only works for MEAN statistics. 

1017 

1018 Parameters 

1019 ---------- 

1020 coaddExposure : `lsst.afw.image.Exposure` 

1021 The target exposure for the coadd. 

1022 tempExpRefList : `list` 

1023 List of data reference to tempExp. 

1024 imageScalerList : `list` 

1025 List of image scalers. 

1026 weightList : `list` 

1027 List of weights. 

1028 altMaskList : `list` 

1029 List of alternate masks to use rather than those stored with 

1030 tempExp, or None. Each element is dict with keys = mask plane 

1031 name to which to add the spans. 

1032 statsCtrl : `lsst.afw.math.StatisticsControl` 

1033 Statistics control object for coadd 

1034 nImage : `lsst.afw.image.ImageU`, optional 

1035 Keeps track of exposure count for each pixel. 

1036 """ 

1037 self.log.debug("Computing online coadd.") 

1038 tempExpName = self.getTempExpDatasetName(self.warpType) 

1039 coaddExposure.mask.addMaskPlane("REJECTED") 

1040 coaddExposure.mask.addMaskPlane("CLIPPED") 

1041 coaddExposure.mask.addMaskPlane("SENSOR_EDGE") 

1042 maskMap = self.setRejectedMaskMapping(statsCtrl) 

1043 thresholdDict = AccumulatorMeanStack.stats_ctrl_to_threshold_dict(statsCtrl) 

1044 

1045 bbox = coaddExposure.maskedImage.getBBox() 

1046 

1047 stacker = AccumulatorMeanStack( 

1048 coaddExposure.image.array.shape, 

1049 statsCtrl.getAndMask(), 

1050 mask_threshold_dict=thresholdDict, 

1051 mask_map=maskMap, 

1052 no_good_pixels_mask=statsCtrl.getNoGoodPixelsMask(), 

1053 calc_error_from_input_variance=self.config.calcErrorFromInputVariance, 

1054 compute_n_image=(nImage is not None) 

1055 ) 

1056 

1057 for tempExpRef, imageScaler, altMask, weight in zip(tempExpRefList, 

1058 imageScalerList, 

1059 altMaskList, 

1060 weightList): 

1061 if isinstance(tempExpRef, DeferredDatasetHandle): 

1062 # Gen 3 API 

1063 exposure = tempExpRef.get() 

1064 else: 

1065 # Gen 2 API. Delete this when Gen 2 retired 

1066 exposure = tempExpRef.get(tempExpName) 

1067 

1068 maskedImage = exposure.getMaskedImage() 

1069 mask = maskedImage.getMask() 

1070 if altMask is not None: 

1071 self.applyAltMaskPlanes(mask, altMask) 

1072 imageScaler.scaleMaskedImage(maskedImage) 

1073 if self.config.removeMaskPlanes: 

1074 self.removeMaskPlanes(maskedImage) 

1075 

1076 stacker.add_masked_image(maskedImage, weight=weight) 

1077 

1078 if self.config.doInputMap: 

1079 visit = exposure.getInfo().getCoaddInputs().visits[0].getId() 

1080 self.inputMapper.mask_warp_bbox(bbox, visit, mask, statsCtrl.getAndMask()) 

1081 

1082 stacker.fill_stacked_masked_image(coaddExposure.maskedImage) 

1083 

1084 if nImage is not None: 

1085 nImage.array[:, :] = stacker.n_image 

1086 

1087 def removeMaskPlanes(self, maskedImage): 

1088 """Unset the mask of an image for mask planes specified in the config. 

1089 

1090 Parameters 

1091 ---------- 

1092 maskedImage : `lsst.afw.image.MaskedImage` 

1093 The masked image to be modified. 

1094 """ 

1095 mask = maskedImage.getMask() 

1096 for maskPlane in self.config.removeMaskPlanes: 

1097 try: 

1098 mask &= ~mask.getPlaneBitMask(maskPlane) 

1099 except pexExceptions.InvalidParameterError: 

1100 self.log.debug("Unable to remove mask plane %s: no mask plane with that name was found.", 

1101 maskPlane) 

1102 

1103 @staticmethod 

1104 def setRejectedMaskMapping(statsCtrl): 

1105 """Map certain mask planes of the warps to new planes for the coadd. 

1106 

1107 If a pixel is rejected due to a mask value other than EDGE, NO_DATA, 

1108 or CLIPPED, set it to REJECTED on the coadd. 

1109 If a pixel is rejected due to EDGE, set the coadd pixel to SENSOR_EDGE. 

1110 If a pixel is rejected due to CLIPPED, set the coadd pixel to CLIPPED. 

1111 

1112 Parameters 

1113 ---------- 

1114 statsCtrl : `lsst.afw.math.StatisticsControl` 

1115 Statistics control object for coadd 

1116 

1117 Returns 

1118 ------- 

1119 maskMap : `list` of `tuple` of `int` 

1120 A list of mappings of mask planes of the warped exposures to 

1121 mask planes of the coadd. 

1122 """ 

1123 edge = afwImage.Mask.getPlaneBitMask("EDGE") 

1124 noData = afwImage.Mask.getPlaneBitMask("NO_DATA") 

1125 clipped = afwImage.Mask.getPlaneBitMask("CLIPPED") 

1126 toReject = statsCtrl.getAndMask() & (~noData) & (~edge) & (~clipped) 

1127 maskMap = [(toReject, afwImage.Mask.getPlaneBitMask("REJECTED")), 

1128 (edge, afwImage.Mask.getPlaneBitMask("SENSOR_EDGE")), 

1129 (clipped, clipped)] 

1130 return maskMap 

1131 

1132 def applyAltMaskPlanes(self, mask, altMaskSpans): 

1133 """Apply in place alt mask formatted as SpanSets to a mask. 

1134 

1135 Parameters 

1136 ---------- 

1137 mask : `lsst.afw.image.Mask` 

1138 Original mask. 

1139 altMaskSpans : `dict` 

1140 SpanSet lists to apply. Each element contains the new mask 

1141 plane name (e.g. "CLIPPED and/or "NO_DATA") as the key, 

1142 and list of SpanSets to apply to the mask. 

1143 

1144 Returns 

1145 ------- 

1146 mask : `lsst.afw.image.Mask` 

1147 Updated mask. 

1148 """ 

1149 if self.config.doUsePsfMatchedPolygons: 

1150 if ("NO_DATA" in altMaskSpans) and ("NO_DATA" in self.config.badMaskPlanes): 1150 ↛ 1158line 1150 didn't jump to line 1158, because the condition on line 1150 was never false

1151 # Clear away any other masks outside the validPolygons. These pixels are no longer 

1152 # contributing to inexact PSFs, and will still be rejected because of NO_DATA 

1153 # self.config.doUsePsfMatchedPolygons should be True only in CompareWarpAssemble 

1154 # This mask-clearing step must only occur *before* applying the new masks below 

1155 for spanSet in altMaskSpans['NO_DATA']: 

1156 spanSet.clippedTo(mask.getBBox()).clearMask(mask, self.getBadPixelMask()) 

1157 

1158 for plane, spanSetList in altMaskSpans.items(): 

1159 maskClipValue = mask.addMaskPlane(plane) 

1160 for spanSet in spanSetList: 

1161 spanSet.clippedTo(mask.getBBox()).setMask(mask, 2**maskClipValue) 

1162 return mask 

1163 

1164 def shrinkValidPolygons(self, coaddInputs): 

1165 """Shrink coaddInputs' ccds' ValidPolygons in place. 

1166 

1167 Either modify each ccd's validPolygon in place, or if CoaddInputs 

1168 does not have a validPolygon, create one from its bbox. 

1169 

1170 Parameters 

1171 ---------- 

1172 coaddInputs : `lsst.afw.image.coaddInputs` 

1173 Original mask. 

1174 

1175 """ 

1176 for ccd in coaddInputs.ccds: 

1177 polyOrig = ccd.getValidPolygon() 

1178 validPolyBBox = polyOrig.getBBox() if polyOrig else ccd.getBBox() 

1179 validPolyBBox.grow(-self.config.matchingKernelSize//2) 

1180 if polyOrig: 1180 ↛ 1181line 1180 didn't jump to line 1181, because the condition on line 1180 was never true

1181 validPolygon = polyOrig.intersectionSingle(validPolyBBox) 

1182 else: 

1183 validPolygon = afwGeom.polygon.Polygon(geom.Box2D(validPolyBBox)) 

1184 ccd.setValidPolygon(validPolygon) 

1185 

1186 def readBrightObjectMasks(self, dataRef): 

1187 """Retrieve the bright object masks. 

1188 

1189 Returns None on failure. 

1190 

1191 Parameters 

1192 ---------- 

1193 dataRef : `lsst.daf.persistence.butlerSubset.ButlerDataRef` 

1194 A Butler dataRef. 

1195 

1196 Returns 

1197 ------- 

1198 result : `lsst.daf.persistence.butlerSubset.ButlerDataRef` 

1199 Bright object mask from the Butler object, or None if it cannot 

1200 be retrieved. 

1201 """ 

1202 try: 

1203 return dataRef.get(datasetType="brightObjectMask", immediate=True) 

1204 except Exception as e: 

1205 self.log.warning("Unable to read brightObjectMask for %s: %s", dataRef.dataId, e) 

1206 return None 

1207 

1208 def setBrightObjectMasks(self, exposure, brightObjectMasks, dataId=None): 

1209 """Set the bright object masks. 

1210 

1211 Parameters 

1212 ---------- 

1213 exposure : `lsst.afw.image.Exposure` 

1214 Exposure under consideration. 

1215 dataId : `lsst.daf.persistence.dataId` 

1216 Data identifier dict for patch. 

1217 brightObjectMasks : `lsst.afw.table` 

1218 Table of bright objects to mask. 

1219 """ 

1220 

1221 if brightObjectMasks is None: 

1222 self.log.warning("Unable to apply bright object mask: none supplied") 

1223 return 

1224 self.log.info("Applying %d bright object masks to %s", len(brightObjectMasks), dataId) 

1225 mask = exposure.getMaskedImage().getMask() 

1226 wcs = exposure.getWcs() 

1227 plateScale = wcs.getPixelScale().asArcseconds() 

1228 

1229 for rec in brightObjectMasks: 

1230 center = geom.PointI(wcs.skyToPixel(rec.getCoord())) 

1231 if rec["type"] == "box": 

1232 assert rec["angle"] == 0.0, ("Angle != 0 for mask object %s" % rec["id"]) 

1233 width = rec["width"].asArcseconds()/plateScale # convert to pixels 

1234 height = rec["height"].asArcseconds()/plateScale # convert to pixels 

1235 

1236 halfSize = geom.ExtentI(0.5*width, 0.5*height) 

1237 bbox = geom.Box2I(center - halfSize, center + halfSize) 

1238 

1239 bbox = geom.BoxI(geom.PointI(int(center[0] - 0.5*width), int(center[1] - 0.5*height)), 

1240 geom.PointI(int(center[0] + 0.5*width), int(center[1] + 0.5*height))) 

1241 spans = afwGeom.SpanSet(bbox) 

1242 elif rec["type"] == "circle": 

1243 radius = int(rec["radius"].asArcseconds()/plateScale) # convert to pixels 

1244 spans = afwGeom.SpanSet.fromShape(radius, offset=center) 

1245 else: 

1246 self.log.warning("Unexpected region type %s at %s", rec["type"], center) 

1247 continue 

1248 spans.clippedTo(mask.getBBox()).setMask(mask, self.brightObjectBitmask) 

1249 

1250 def setInexactPsf(self, mask): 

1251 """Set INEXACT_PSF mask plane. 

1252 

1253 If any of the input images isn't represented in the coadd (due to 

1254 clipped pixels or chip gaps), the `CoaddPsf` will be inexact. Flag 

1255 these pixels. 

1256 

1257 Parameters 

1258 ---------- 

1259 mask : `lsst.afw.image.Mask` 

1260 Coadded exposure's mask, modified in-place. 

1261 """ 

1262 mask.addMaskPlane("INEXACT_PSF") 

1263 inexactPsf = mask.getPlaneBitMask("INEXACT_PSF") 

1264 sensorEdge = mask.getPlaneBitMask("SENSOR_EDGE") # chip edges (so PSF is discontinuous) 

1265 clipped = mask.getPlaneBitMask("CLIPPED") # pixels clipped from coadd 

1266 rejected = mask.getPlaneBitMask("REJECTED") # pixels rejected from coadd due to masks 

1267 array = mask.getArray() 

1268 selected = array & (sensorEdge | clipped | rejected) > 0 

1269 array[selected] |= inexactPsf 

1270 

1271 @classmethod 

1272 def _makeArgumentParser(cls): 

1273 """Create an argument parser. 

1274 """ 

1275 parser = pipeBase.ArgumentParser(name=cls._DefaultName) 

1276 parser.add_id_argument("--id", cls.ConfigClass().coaddName + "Coadd_" 

1277 + cls.ConfigClass().warpType + "Warp", 

1278 help="data ID, e.g. --id tract=12345 patch=1,2", 

1279 ContainerClass=AssembleCoaddDataIdContainer) 

1280 parser.add_id_argument("--selectId", "calexp", help="data ID, e.g. --selectId visit=6789 ccd=0..9", 

1281 ContainerClass=SelectDataIdContainer) 

1282 return parser 

1283 

1284 @staticmethod 

1285 def _subBBoxIter(bbox, subregionSize): 

1286 """Iterate over subregions of a bbox. 

1287 

1288 Parameters 

1289 ---------- 

1290 bbox : `lsst.geom.Box2I` 

1291 Bounding box over which to iterate. 

1292 subregionSize: `lsst.geom.Extent2I` 

1293 Size of sub-bboxes. 

1294 

1295 Yields 

1296 ------ 

1297 subBBox : `lsst.geom.Box2I` 

1298 Next sub-bounding box of size ``subregionSize`` or smaller; each ``subBBox`` 

1299 is contained within ``bbox``, so it may be smaller than ``subregionSize`` at 

1300 the edges of ``bbox``, but it will never be empty. 

1301 """ 

1302 if bbox.isEmpty(): 1302 ↛ 1303line 1302 didn't jump to line 1303, because the condition on line 1302 was never true

1303 raise RuntimeError("bbox %s is empty" % (bbox,)) 

1304 if subregionSize[0] < 1 or subregionSize[1] < 1: 1304 ↛ 1305line 1304 didn't jump to line 1305, because the condition on line 1304 was never true

1305 raise RuntimeError("subregionSize %s must be nonzero" % (subregionSize,)) 

1306 

1307 for rowShift in range(0, bbox.getHeight(), subregionSize[1]): 

1308 for colShift in range(0, bbox.getWidth(), subregionSize[0]): 

1309 subBBox = geom.Box2I(bbox.getMin() + geom.Extent2I(colShift, rowShift), subregionSize) 

1310 subBBox.clip(bbox) 

1311 if subBBox.isEmpty(): 1311 ↛ 1312line 1311 didn't jump to line 1312, because the condition on line 1311 was never true

1312 raise RuntimeError("Bug: empty bbox! bbox=%s, subregionSize=%s, " 

1313 "colShift=%s, rowShift=%s" % 

1314 (bbox, subregionSize, colShift, rowShift)) 

1315 yield subBBox 

1316 

1317 def filterWarps(self, inputs, goodVisits): 

1318 """Return list of only inputRefs with visitId in goodVisits ordered by goodVisit 

1319 

1320 Parameters 

1321 ---------- 

1322 inputs : list 

1323 List of `lsst.pipe.base.connections.DeferredDatasetRef` with dataId containing visit 

1324 goodVisit : `dict` 

1325 Dictionary with good visitIds as the keys. Value ignored. 

1326 

1327 Returns: 

1328 -------- 

1329 filteredInputs : `list` 

1330 Filtered and sorted list of `lsst.pipe.base.connections.DeferredDatasetRef` 

1331 """ 

1332 inputWarpDict = {inputRef.ref.dataId['visit']: inputRef for inputRef in inputs} 

1333 filteredInputs = [] 

1334 for visit in goodVisits.keys(): 

1335 filteredInputs.append(inputWarpDict[visit]) 

1336 return filteredInputs 

1337 

1338 

1339class AssembleCoaddDataIdContainer(pipeBase.DataIdContainer): 

1340 """A version of `lsst.pipe.base.DataIdContainer` specialized for assembleCoadd. 

1341 """ 

1342 

1343 def makeDataRefList(self, namespace): 

1344 """Make self.refList from self.idList. 

1345 

1346 Parameters 

1347 ---------- 

1348 namespace 

1349 Results of parsing command-line (with ``butler`` and ``log`` elements). 

1350 """ 

1351 datasetType = namespace.config.coaddName + "Coadd" 

1352 keysCoadd = namespace.butler.getKeys(datasetType=datasetType, level=self.level) 

1353 

1354 for dataId in self.idList: 

1355 # tract and patch are required 

1356 for key in keysCoadd: 

1357 if key not in dataId: 

1358 raise RuntimeError("--id must include " + key) 

1359 

1360 dataRef = namespace.butler.dataRef( 

1361 datasetType=datasetType, 

1362 dataId=dataId, 

1363 ) 

1364 self.refList.append(dataRef) 

1365 

1366 

1367def countMaskFromFootprint(mask, footprint, bitmask, ignoreMask): 

1368 """Function to count the number of pixels with a specific mask in a 

1369 footprint. 

1370 

1371 Find the intersection of mask & footprint. Count all pixels in the mask 

1372 that are in the intersection that have bitmask set but do not have 

1373 ignoreMask set. Return the count. 

1374 

1375 Parameters 

1376 ---------- 

1377 mask : `lsst.afw.image.Mask` 

1378 Mask to define intersection region by. 

1379 footprint : `lsst.afw.detection.Footprint` 

1380 Footprint to define the intersection region by. 

1381 bitmask 

1382 Specific mask that we wish to count the number of occurances of. 

1383 ignoreMask 

1384 Pixels to not consider. 

1385 

1386 Returns 

1387 ------- 

1388 result : `int` 

1389 Count of number of pixels in footprint with specified mask. 

1390 """ 

1391 bbox = footprint.getBBox() 

1392 bbox.clip(mask.getBBox(afwImage.PARENT)) 

1393 fp = afwImage.Mask(bbox) 

1394 subMask = mask.Factory(mask, bbox, afwImage.PARENT) 

1395 footprint.spans.setMask(fp, bitmask) 

1396 return numpy.logical_and((subMask.getArray() & fp.getArray()) > 0, 

1397 (subMask.getArray() & ignoreMask) == 0).sum() 

1398 

1399 

1400class SafeClipAssembleCoaddConfig(AssembleCoaddConfig, pipelineConnections=AssembleCoaddConnections): 

1401 """Configuration parameters for the SafeClipAssembleCoaddTask. 

1402 """ 

1403 clipDetection = pexConfig.ConfigurableField( 

1404 target=SourceDetectionTask, 

1405 doc="Detect sources on difference between unclipped and clipped coadd") 

1406 minClipFootOverlap = pexConfig.Field( 

1407 doc="Minimum fractional overlap of clipped footprint with visit DETECTED to be clipped", 

1408 dtype=float, 

1409 default=0.6 

1410 ) 

1411 minClipFootOverlapSingle = pexConfig.Field( 

1412 doc="Minimum fractional overlap of clipped footprint with visit DETECTED to be " 

1413 "clipped when only one visit overlaps", 

1414 dtype=float, 

1415 default=0.5 

1416 ) 

1417 minClipFootOverlapDouble = pexConfig.Field( 

1418 doc="Minimum fractional overlap of clipped footprints with visit DETECTED to be " 

1419 "clipped when two visits overlap", 

1420 dtype=float, 

1421 default=0.45 

1422 ) 

1423 maxClipFootOverlapDouble = pexConfig.Field( 

1424 doc="Maximum fractional overlap of clipped footprints with visit DETECTED when " 

1425 "considering two visits", 

1426 dtype=float, 

1427 default=0.15 

1428 ) 

1429 minBigOverlap = pexConfig.Field( 

1430 doc="Minimum number of pixels in footprint to use DETECTED mask from the single visits " 

1431 "when labeling clipped footprints", 

1432 dtype=int, 

1433 default=100 

1434 ) 

1435 

1436 def setDefaults(self): 

1437 """Set default values for clipDetection. 

1438 

1439 Notes 

1440 ----- 

1441 The numeric values for these configuration parameters were 

1442 empirically determined, future work may further refine them. 

1443 """ 

1444 AssembleCoaddConfig.setDefaults(self) 

1445 self.clipDetection.doTempLocalBackground = False 

1446 self.clipDetection.reEstimateBackground = False 

1447 self.clipDetection.returnOriginalFootprints = False 

1448 self.clipDetection.thresholdPolarity = "both" 

1449 self.clipDetection.thresholdValue = 2 

1450 self.clipDetection.nSigmaToGrow = 2 

1451 self.clipDetection.minPixels = 4 

1452 self.clipDetection.isotropicGrow = True 

1453 self.clipDetection.thresholdType = "pixel_stdev" 

1454 self.sigmaClip = 1.5 

1455 self.clipIter = 3 

1456 self.statistic = "MEAN" 

1457 

1458 def validate(self): 

1459 if self.doSigmaClip: 

1460 log.warning("Additional Sigma-clipping not allowed in Safe-clipped Coadds. " 

1461 "Ignoring doSigmaClip.") 

1462 self.doSigmaClip = False 

1463 if self.statistic != "MEAN": 

1464 raise ValueError("Only MEAN statistic allowed for final stacking in SafeClipAssembleCoadd " 

1465 "(%s chosen). Please set statistic to MEAN." 

1466 % (self.statistic)) 

1467 AssembleCoaddTask.ConfigClass.validate(self) 

1468 

1469 

1470class SafeClipAssembleCoaddTask(AssembleCoaddTask): 

1471 """Assemble a coadded image from a set of coadded temporary exposures, 

1472 being careful to clip & flag areas with potential artifacts. 

1473 

1474 In ``AssembleCoaddTask``, we compute the coadd as an clipped mean (i.e., 

1475 we clip outliers). The problem with doing this is that when computing the 

1476 coadd PSF at a given location, individual visit PSFs from visits with 

1477 outlier pixels contribute to the coadd PSF and cannot be treated correctly. 

1478 In this task, we correct for this behavior by creating a new 

1479 ``badMaskPlane`` 'CLIPPED'. We populate this plane on the input 

1480 coaddTempExps and the final coadd where 

1481 

1482 i. difference imaging suggests that there is an outlier and 

1483 ii. this outlier appears on only one or two images. 

1484 

1485 Such regions will not contribute to the final coadd. Furthermore, any 

1486 routine to determine the coadd PSF can now be cognizant of clipped regions. 

1487 Note that the algorithm implemented by this task is preliminary and works 

1488 correctly for HSC data. Parameter modifications and or considerable 

1489 redesigning of the algorithm is likley required for other surveys. 

1490 

1491 ``SafeClipAssembleCoaddTask`` uses a ``SourceDetectionTask`` 

1492 "clipDetection" subtask and also sub-classes ``AssembleCoaddTask``. 

1493 You can retarget the ``SourceDetectionTask`` "clipDetection" subtask 

1494 if you wish. 

1495 

1496 Notes 

1497 ----- 

1498 The `lsst.pipe.base.cmdLineTask.CmdLineTask` interface supports a 

1499 flag ``-d`` to import ``debug.py`` from your ``PYTHONPATH``; 

1500 see `baseDebug` for more about ``debug.py`` files. 

1501 `SafeClipAssembleCoaddTask` has no debug variables of its own. 

1502 The ``SourceDetectionTask`` "clipDetection" subtasks may support debug 

1503 variables. See the documetation for `SourceDetectionTask` "clipDetection" 

1504 for further information. 

1505 

1506 Examples 

1507 -------- 

1508 `SafeClipAssembleCoaddTask` assembles a set of warped ``coaddTempExp`` 

1509 images into a coadded image. The `SafeClipAssembleCoaddTask` is invoked by 

1510 running assembleCoadd.py *without* the flag '--legacyCoadd'. 

1511 

1512 Usage of ``assembleCoadd.py`` expects a data reference to the tract patch 

1513 and filter to be coadded (specified using 

1514 '--id = [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]') 

1515 along with a list of coaddTempExps to attempt to coadd (specified using 

1516 '--selectId [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]'). 

1517 Only the coaddTempExps that cover the specified tract and patch will be 

1518 coadded. A list of the available optional arguments can be obtained by 

1519 calling assembleCoadd.py with the --help command line argument: 

1520 

1521 .. code-block:: none 

1522 

1523 assembleCoadd.py --help 

1524 

1525 To demonstrate usage of the `SafeClipAssembleCoaddTask` in the larger 

1526 context of multi-band processing, we will generate the HSC-I & -R band 

1527 coadds from HSC engineering test data provided in the ci_hsc package. 

1528 To begin, assuming that the lsst stack has been already set up, we must 

1529 set up the obs_subaru and ci_hsc packages. This defines the environment 

1530 variable $CI_HSC_DIR and points at the location of the package. The raw 

1531 HSC data live in the ``$CI_HSC_DIR/raw`` directory. To begin assembling 

1532 the coadds, we must first 

1533 

1534 - ``processCcd`` 

1535 process the individual ccds in $CI_HSC_RAW to produce calibrated exposures 

1536 - ``makeSkyMap`` 

1537 create a skymap that covers the area of the sky present in the raw exposures 

1538 - ``makeCoaddTempExp`` 

1539 warp the individual calibrated exposures to the tangent plane of the coadd</DD> 

1540 

1541 We can perform all of these steps by running 

1542 

1543 .. code-block:: none 

1544 

1545 $CI_HSC_DIR scons warp-903986 warp-904014 warp-903990 warp-904010 warp-903988 

1546 

1547 This will produce warped coaddTempExps for each visit. To coadd the 

1548 warped data, we call ``assembleCoadd.py`` as follows: 

1549 

1550 .. code-block:: none 

1551 

1552 assembleCoadd.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I \ 

1553 --selectId visit=903986 ccd=16 --selectId visit=903986 ccd=22 --selectId visit=903986 ccd=23 \ 

1554 --selectId visit=903986 ccd=100--selectId visit=904014 ccd=1 --selectId visit=904014 ccd=6 \ 

1555 --selectId visit=904014 ccd=12 --selectId visit=903990 ccd=18 --selectId visit=903990 ccd=25 \ 

1556 --selectId visit=904010 ccd=4 --selectId visit=904010 ccd=10 --selectId visit=904010 ccd=100 \ 

1557 --selectId visit=903988 ccd=16 --selectId visit=903988 ccd=17 --selectId visit=903988 ccd=23 \ 

1558 --selectId visit=903988 ccd=24 

1559 

1560 This will process the HSC-I band data. The results are written in 

1561 ``$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I``. 

1562 

1563 You may also choose to run: 

1564 

1565 .. code-block:: none 

1566 

1567 scons warp-903334 warp-903336 warp-903338 warp-903342 warp-903344 warp-903346 nnn 

1568 assembleCoadd.py $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-R --selectId visit=903334 ccd=16 \ 

1569 --selectId visit=903334 ccd=22 --selectId visit=903334 ccd=23 --selectId visit=903334 ccd=100 \ 

1570 --selectId visit=903336 ccd=17 --selectId visit=903336 ccd=24 --selectId visit=903338 ccd=18 \ 

1571 --selectId visit=903338 ccd=25 --selectId visit=903342 ccd=4 --selectId visit=903342 ccd=10 \ 

1572 --selectId visit=903342 ccd=100 --selectId visit=903344 ccd=0 --selectId visit=903344 ccd=5 \ 

1573 --selectId visit=903344 ccd=11 --selectId visit=903346 ccd=1 --selectId visit=903346 ccd=6 \ 

1574 --selectId visit=903346 ccd=12 

1575 

1576 to generate the coadd for the HSC-R band if you are interested in following 

1577 multiBand Coadd processing as discussed in ``pipeTasks_multiBand``. 

1578 """ 

1579 ConfigClass = SafeClipAssembleCoaddConfig 

1580 _DefaultName = "safeClipAssembleCoadd" 

1581 

1582 def __init__(self, *args, **kwargs): 

1583 AssembleCoaddTask.__init__(self, *args, **kwargs) 

1584 schema = afwTable.SourceTable.makeMinimalSchema() 

1585 self.makeSubtask("clipDetection", schema=schema) 

1586 

1587 @utils.inheritDoc(AssembleCoaddTask) 

1588 @pipeBase.timeMethod 

1589 def run(self, skyInfo, tempExpRefList, imageScalerList, weightList, *args, **kwargs): 

1590 """Assemble the coadd for a region. 

1591 

1592 Compute the difference of coadds created with and without outlier 

1593 rejection to identify coadd pixels that have outlier values in some 

1594 individual visits. 

1595 Detect clipped regions on the difference image and mark these regions 

1596 on the one or two individual coaddTempExps where they occur if there 

1597 is significant overlap between the clipped region and a source. This 

1598 leaves us with a set of footprints from the difference image that have 

1599 been identified as having occured on just one or two individual visits. 

1600 However, these footprints were generated from a difference image. It 

1601 is conceivable for a large diffuse source to have become broken up 

1602 into multiple footprints acrosss the coadd difference in this process. 

1603 Determine the clipped region from all overlapping footprints from the 

1604 detected sources in each visit - these are big footprints. 

1605 Combine the small and big clipped footprints and mark them on a new 

1606 bad mask plane. 

1607 Generate the coadd using `AssembleCoaddTask.run` without outlier 

1608 removal. Clipped footprints will no longer make it into the coadd 

1609 because they are marked in the new bad mask plane. 

1610 

1611 Notes 

1612 ----- 

1613 args and kwargs are passed but ignored in order to match the call 

1614 signature expected by the parent task. 

1615 """ 

1616 exp = self.buildDifferenceImage(skyInfo, tempExpRefList, imageScalerList, weightList) 

1617 mask = exp.getMaskedImage().getMask() 

1618 mask.addMaskPlane("CLIPPED") 

1619 

1620 result = self.detectClip(exp, tempExpRefList) 

1621 

1622 self.log.info('Found %d clipped objects', len(result.clipFootprints)) 

1623 

1624 maskClipValue = mask.getPlaneBitMask("CLIPPED") 

1625 maskDetValue = mask.getPlaneBitMask("DETECTED") | mask.getPlaneBitMask("DETECTED_NEGATIVE") 

1626 # Append big footprints from individual Warps to result.clipSpans 

1627 bigFootprints = self.detectClipBig(result.clipSpans, result.clipFootprints, result.clipIndices, 

1628 result.detectionFootprints, maskClipValue, maskDetValue, 

1629 exp.getBBox()) 

1630 # Create mask of the current clipped footprints 

1631 maskClip = mask.Factory(mask.getBBox(afwImage.PARENT)) 

1632 afwDet.setMaskFromFootprintList(maskClip, result.clipFootprints, maskClipValue) 

1633 

1634 maskClipBig = maskClip.Factory(mask.getBBox(afwImage.PARENT)) 

1635 afwDet.setMaskFromFootprintList(maskClipBig, bigFootprints, maskClipValue) 

1636 maskClip |= maskClipBig 

1637 

1638 # Assemble coadd from base class, but ignoring CLIPPED pixels 

1639 badMaskPlanes = self.config.badMaskPlanes[:] 

1640 badMaskPlanes.append("CLIPPED") 

1641 badPixelMask = afwImage.Mask.getPlaneBitMask(badMaskPlanes) 

1642 return AssembleCoaddTask.run(self, skyInfo, tempExpRefList, imageScalerList, weightList, 

1643 result.clipSpans, mask=badPixelMask) 

1644 

1645 def buildDifferenceImage(self, skyInfo, tempExpRefList, imageScalerList, weightList): 

1646 """Return an exposure that contains the difference between unclipped 

1647 and clipped coadds. 

1648 

1649 Generate a difference image between clipped and unclipped coadds. 

1650 Compute the difference image by subtracting an outlier-clipped coadd 

1651 from an outlier-unclipped coadd. Return the difference image. 

1652 

1653 Parameters 

1654 ---------- 

1655 skyInfo : `lsst.pipe.base.Struct` 

1656 Patch geometry information, from getSkyInfo 

1657 tempExpRefList : `list` 

1658 List of data reference to tempExp 

1659 imageScalerList : `list` 

1660 List of image scalers 

1661 weightList : `list` 

1662 List of weights 

1663 

1664 Returns 

1665 ------- 

1666 exp : `lsst.afw.image.Exposure` 

1667 Difference image of unclipped and clipped coadd wrapped in an Exposure 

1668 """ 

1669 config = AssembleCoaddConfig() 

1670 # getattr necessary because subtasks do not survive Config.toDict() 

1671 # exclude connections because the class of self.config.connections is not 

1672 # the same as AssembleCoaddConfig.connections, and the connections are not 

1673 # needed to run this task anyway. 

1674 configIntersection = {k: getattr(self.config, k) 

1675 for k, v in self.config.toDict().items() 

1676 if (k in config.keys() and k != "connections")} 

1677 configIntersection['doInputMap'] = False 

1678 configIntersection['doNImage'] = False 

1679 config.update(**configIntersection) 

1680 

1681 # statistic MEAN copied from self.config.statistic, but for clarity explicitly assign 

1682 config.statistic = 'MEAN' 

1683 task = AssembleCoaddTask(config=config) 

1684 coaddMean = task.run(skyInfo, tempExpRefList, imageScalerList, weightList).coaddExposure 

1685 

1686 config.statistic = 'MEANCLIP' 

1687 task = AssembleCoaddTask(config=config) 

1688 coaddClip = task.run(skyInfo, tempExpRefList, imageScalerList, weightList).coaddExposure 

1689 

1690 coaddDiff = coaddMean.getMaskedImage().Factory(coaddMean.getMaskedImage()) 

1691 coaddDiff -= coaddClip.getMaskedImage() 

1692 exp = afwImage.ExposureF(coaddDiff) 

1693 exp.setPsf(coaddMean.getPsf()) 

1694 return exp 

1695 

1696 def detectClip(self, exp, tempExpRefList): 

1697 """Detect clipped regions on an exposure and set the mask on the 

1698 individual tempExp masks. 

1699 

1700 Detect footprints in the difference image after smoothing the 

1701 difference image with a Gaussian kernal. Identify footprints that 

1702 overlap with one or two input ``coaddTempExps`` by comparing the 

1703 computed overlap fraction to thresholds set in the config. A different 

1704 threshold is applied depending on the number of overlapping visits 

1705 (restricted to one or two). If the overlap exceeds the thresholds, 

1706 the footprint is considered "CLIPPED" and is marked as such on the 

1707 coaddTempExp. Return a struct with the clipped footprints, the indices 

1708 of the ``coaddTempExps`` that end up overlapping with the clipped 

1709 footprints, and a list of new masks for the ``coaddTempExps``. 

1710 

1711 Parameters 

1712 ---------- 

1713 exp : `lsst.afw.image.Exposure` 

1714 Exposure to run detection on. 

1715 tempExpRefList : `list` 

1716 List of data reference to tempExp. 

1717 

1718 Returns 

1719 ------- 

1720 result : `lsst.pipe.base.Struct` 

1721 Result struct with components: 

1722 

1723 - ``clipFootprints``: list of clipped footprints. 

1724 - ``clipIndices``: indices for each ``clippedFootprint`` in 

1725 ``tempExpRefList``. 

1726 - ``clipSpans``: List of dictionaries containing spanSet lists 

1727 to clip. Each element contains the new maskplane name 

1728 ("CLIPPED") as the key and list of ``SpanSets`` as the value. 

1729 - ``detectionFootprints``: List of DETECTED/DETECTED_NEGATIVE plane 

1730 compressed into footprints. 

1731 """ 

1732 mask = exp.getMaskedImage().getMask() 

1733 maskDetValue = mask.getPlaneBitMask("DETECTED") | mask.getPlaneBitMask("DETECTED_NEGATIVE") 

1734 fpSet = self.clipDetection.detectFootprints(exp, doSmooth=True, clearMask=True) 

1735 # Merge positive and negative together footprints together 

1736 fpSet.positive.merge(fpSet.negative) 

1737 footprints = fpSet.positive 

1738 self.log.info('Found %d potential clipped objects', len(footprints.getFootprints())) 

1739 ignoreMask = self.getBadPixelMask() 

1740 

1741 clipFootprints = [] 

1742 clipIndices = [] 

1743 artifactSpanSets = [{'CLIPPED': list()} for _ in tempExpRefList] 

1744 

1745 # for use by detectClipBig 

1746 visitDetectionFootprints = [] 

1747 

1748 dims = [len(tempExpRefList), len(footprints.getFootprints())] 

1749 overlapDetArr = numpy.zeros(dims, dtype=numpy.uint16) 

1750 ignoreArr = numpy.zeros(dims, dtype=numpy.uint16) 

1751 

1752 # Loop over masks once and extract/store only relevant overlap metrics and detection footprints 

1753 for i, warpRef in enumerate(tempExpRefList): 

1754 tmpExpMask = warpRef.get(datasetType=self.getTempExpDatasetName(self.warpType), 

1755 immediate=True).getMaskedImage().getMask() 

1756 maskVisitDet = tmpExpMask.Factory(tmpExpMask, tmpExpMask.getBBox(afwImage.PARENT), 

1757 afwImage.PARENT, True) 

1758 maskVisitDet &= maskDetValue 

1759 visitFootprints = afwDet.FootprintSet(maskVisitDet, afwDet.Threshold(1)) 

1760 visitDetectionFootprints.append(visitFootprints) 

1761 

1762 for j, footprint in enumerate(footprints.getFootprints()): 

1763 ignoreArr[i, j] = countMaskFromFootprint(tmpExpMask, footprint, ignoreMask, 0x0) 

1764 overlapDetArr[i, j] = countMaskFromFootprint(tmpExpMask, footprint, maskDetValue, ignoreMask) 

1765 

1766 # build a list of clipped spans for each visit 

1767 for j, footprint in enumerate(footprints.getFootprints()): 

1768 nPixel = footprint.getArea() 

1769 overlap = [] # hold the overlap with each visit 

1770 indexList = [] # index of visit in global list 

1771 for i in range(len(tempExpRefList)): 

1772 ignore = ignoreArr[i, j] 

1773 overlapDet = overlapDetArr[i, j] 

1774 totPixel = nPixel - ignore 

1775 

1776 # If we have more bad pixels than detection skip 

1777 if ignore > overlapDet or totPixel <= 0.5*nPixel or overlapDet == 0: 1777 ↛ 1779line 1777 didn't jump to line 1779, because the condition on line 1777 was never false

1778 continue 

1779 overlap.append(overlapDet/float(totPixel)) 

1780 indexList.append(i) 

1781 

1782 overlap = numpy.array(overlap) 

1783 if not len(overlap): 1783 ↛ 1786line 1783 didn't jump to line 1786, because the condition on line 1783 was never false

1784 continue 

1785 

1786 keep = False # Should this footprint be marked as clipped? 

1787 keepIndex = [] # Which tempExps does the clipped footprint belong to 

1788 

1789 # If footprint only has one overlap use a lower threshold 

1790 if len(overlap) == 1: 

1791 if overlap[0] > self.config.minClipFootOverlapSingle: 

1792 keep = True 

1793 keepIndex = [0] 

1794 else: 

1795 # This is the general case where only visit should be clipped 

1796 clipIndex = numpy.where(overlap > self.config.minClipFootOverlap)[0] 

1797 if len(clipIndex) == 1: 

1798 keep = True 

1799 keepIndex = [clipIndex[0]] 

1800 

1801 # Test if there are clipped objects that overlap two different visits 

1802 clipIndex = numpy.where(overlap > self.config.minClipFootOverlapDouble)[0] 

1803 if len(clipIndex) == 2 and len(overlap) > 3: 

1804 clipIndexComp = numpy.where(overlap <= self.config.minClipFootOverlapDouble)[0] 

1805 if numpy.max(overlap[clipIndexComp]) <= self.config.maxClipFootOverlapDouble: 

1806 keep = True 

1807 keepIndex = clipIndex 

1808 

1809 if not keep: 

1810 continue 

1811 

1812 for index in keepIndex: 

1813 globalIndex = indexList[index] 

1814 artifactSpanSets[globalIndex]['CLIPPED'].append(footprint.spans) 

1815 

1816 clipIndices.append(numpy.array(indexList)[keepIndex]) 

1817 clipFootprints.append(footprint) 

1818 

1819 return pipeBase.Struct(clipFootprints=clipFootprints, clipIndices=clipIndices, 

1820 clipSpans=artifactSpanSets, detectionFootprints=visitDetectionFootprints) 

1821 

1822 def detectClipBig(self, clipList, clipFootprints, clipIndices, detectionFootprints, 

1823 maskClipValue, maskDetValue, coaddBBox): 

1824 """Return individual warp footprints for large artifacts and append 

1825 them to ``clipList`` in place. 

1826 

1827 Identify big footprints composed of many sources in the coadd 

1828 difference that may have originated in a large diffuse source in the 

1829 coadd. We do this by indentifying all clipped footprints that overlap 

1830 significantly with each source in all the coaddTempExps. 

1831 

1832 Parameters 

1833 ---------- 

1834 clipList : `list` 

1835 List of alt mask SpanSets with clipping information. Modified. 

1836 clipFootprints : `list` 

1837 List of clipped footprints. 

1838 clipIndices : `list` 

1839 List of which entries in tempExpClipList each footprint belongs to. 

1840 maskClipValue 

1841 Mask value of clipped pixels. 

1842 maskDetValue 

1843 Mask value of detected pixels. 

1844 coaddBBox : `lsst.geom.Box` 

1845 BBox of the coadd and warps. 

1846 

1847 Returns 

1848 ------- 

1849 bigFootprintsCoadd : `list` 

1850 List of big footprints 

1851 """ 

1852 bigFootprintsCoadd = [] 

1853 ignoreMask = self.getBadPixelMask() 

1854 for index, (clippedSpans, visitFootprints) in enumerate(zip(clipList, detectionFootprints)): 

1855 maskVisitDet = afwImage.MaskX(coaddBBox, 0x0) 

1856 for footprint in visitFootprints.getFootprints(): 1856 ↛ 1857line 1856 didn't jump to line 1857, because the loop on line 1856 never started

1857 footprint.spans.setMask(maskVisitDet, maskDetValue) 

1858 

1859 # build a mask of clipped footprints that are in this visit 

1860 clippedFootprintsVisit = [] 

1861 for foot, clipIndex in zip(clipFootprints, clipIndices): 1861 ↛ 1862line 1861 didn't jump to line 1862, because the loop on line 1861 never started

1862 if index not in clipIndex: 

1863 continue 

1864 clippedFootprintsVisit.append(foot) 

1865 maskVisitClip = maskVisitDet.Factory(maskVisitDet.getBBox(afwImage.PARENT)) 

1866 afwDet.setMaskFromFootprintList(maskVisitClip, clippedFootprintsVisit, maskClipValue) 

1867 

1868 bigFootprintsVisit = [] 

1869 for foot in visitFootprints.getFootprints(): 1869 ↛ 1870line 1869 didn't jump to line 1870, because the loop on line 1869 never started

1870 if foot.getArea() < self.config.minBigOverlap: 

1871 continue 

1872 nCount = countMaskFromFootprint(maskVisitClip, foot, maskClipValue, ignoreMask) 

1873 if nCount > self.config.minBigOverlap: 

1874 bigFootprintsVisit.append(foot) 

1875 bigFootprintsCoadd.append(foot) 

1876 

1877 for footprint in bigFootprintsVisit: 1877 ↛ 1878line 1877 didn't jump to line 1878, because the loop on line 1877 never started

1878 clippedSpans["CLIPPED"].append(footprint.spans) 

1879 

1880 return bigFootprintsCoadd 

1881 

1882 

1883class CompareWarpAssembleCoaddConnections(AssembleCoaddConnections): 

1884 psfMatchedWarps = pipeBase.connectionTypes.Input( 

1885 doc=("PSF-Matched Warps are required by CompareWarp regardless of the coadd type requested. " 

1886 "Only PSF-Matched Warps make sense for image subtraction. " 

1887 "Therefore, they must be an additional declared input."), 

1888 name="{inputCoaddName}Coadd_psfMatchedWarp", 

1889 storageClass="ExposureF", 

1890 dimensions=("tract", "patch", "skymap", "visit"), 

1891 deferLoad=True, 

1892 multiple=True 

1893 ) 

1894 templateCoadd = pipeBase.connectionTypes.Output( 

1895 doc=("Model of the static sky, used to find temporal artifacts. Typically a PSF-Matched, " 

1896 "sigma-clipped coadd. Written if and only if assembleStaticSkyModel.doWrite=True"), 

1897 name="{outputCoaddName}CoaddPsfMatched", 

1898 storageClass="ExposureF", 

1899 dimensions=("tract", "patch", "skymap", "band"), 

1900 ) 

1901 

1902 def __init__(self, *, config=None): 

1903 super().__init__(config=config) 

1904 if not config.assembleStaticSkyModel.doWrite: 

1905 self.outputs.remove("templateCoadd") 

1906 config.validate() 

1907 

1908 

1909class CompareWarpAssembleCoaddConfig(AssembleCoaddConfig, 

1910 pipelineConnections=CompareWarpAssembleCoaddConnections): 

1911 assembleStaticSkyModel = pexConfig.ConfigurableField( 

1912 target=AssembleCoaddTask, 

1913 doc="Task to assemble an artifact-free, PSF-matched Coadd to serve as a" 

1914 " naive/first-iteration model of the static sky.", 

1915 ) 

1916 detect = pexConfig.ConfigurableField( 

1917 target=SourceDetectionTask, 

1918 doc="Detect outlier sources on difference between each psfMatched warp and static sky model" 

1919 ) 

1920 detectTemplate = pexConfig.ConfigurableField( 

1921 target=SourceDetectionTask, 

1922 doc="Detect sources on static sky model. Only used if doPreserveContainedBySource is True" 

1923 ) 

1924 maskStreaks = pexConfig.ConfigurableField( 

1925 target=MaskStreaksTask, 

1926 doc="Detect streaks on difference between each psfMatched warp and static sky model. Only used if " 

1927 "doFilterMorphological is True. Adds a mask plane to an exposure, with the mask plane name set by" 

1928 "streakMaskName" 

1929 ) 

1930 streakMaskName = pexConfig.Field( 

1931 dtype=str, 

1932 default="STREAK", 

1933 doc="Name of mask bit used for streaks" 

1934 ) 

1935 maxNumEpochs = pexConfig.Field( 

1936 doc="Charactistic maximum local number of epochs/visits in which an artifact candidate can appear " 

1937 "and still be masked. The effective maxNumEpochs is a broken linear function of local " 

1938 "number of epochs (N): min(maxFractionEpochsLow*N, maxNumEpochs + maxFractionEpochsHigh*N). " 

1939 "For each footprint detected on the image difference between the psfMatched warp and static sky " 

1940 "model, if a significant fraction of pixels (defined by spatialThreshold) are residuals in more " 

1941 "than the computed effective maxNumEpochs, the artifact candidate is deemed persistant rather " 

1942 "than transient and not masked.", 

1943 dtype=int, 

1944 default=2 

1945 ) 

1946 maxFractionEpochsLow = pexConfig.RangeField( 

1947 doc="Fraction of local number of epochs (N) to use as effective maxNumEpochs for low N. " 

1948 "Effective maxNumEpochs = " 

1949 "min(maxFractionEpochsLow * N, maxNumEpochs + maxFractionEpochsHigh * N)", 

1950 dtype=float, 

1951 default=0.4, 

1952 min=0., max=1., 

1953 ) 

1954 maxFractionEpochsHigh = pexConfig.RangeField( 

1955 doc="Fraction of local number of epochs (N) to use as effective maxNumEpochs for high N. " 

1956 "Effective maxNumEpochs = " 

1957 "min(maxFractionEpochsLow * N, maxNumEpochs + maxFractionEpochsHigh * N)", 

1958 dtype=float, 

1959 default=0.03, 

1960 min=0., max=1., 

1961 ) 

1962 spatialThreshold = pexConfig.RangeField( 

1963 doc="Unitless fraction of pixels defining how much of the outlier region has to meet the " 

1964 "temporal criteria. If 0, clip all. If 1, clip none.", 

1965 dtype=float, 

1966 default=0.5, 

1967 min=0., max=1., 

1968 inclusiveMin=True, inclusiveMax=True 

1969 ) 

1970 doScaleWarpVariance = pexConfig.Field( 

1971 doc="Rescale Warp variance plane using empirical noise?", 

1972 dtype=bool, 

1973 default=True, 

1974 ) 

1975 scaleWarpVariance = pexConfig.ConfigurableField( 

1976 target=ScaleVarianceTask, 

1977 doc="Rescale variance on warps", 

1978 ) 

1979 doPreserveContainedBySource = pexConfig.Field( 

1980 doc="Rescue artifacts from clipping that completely lie within a footprint detected" 

1981 "on the PsfMatched Template Coadd. Replicates a behavior of SafeClip.", 

1982 dtype=bool, 

1983 default=True, 

1984 ) 

1985 doPrefilterArtifacts = pexConfig.Field( 

1986 doc="Ignore artifact candidates that are mostly covered by the bad pixel mask, " 

1987 "because they will be excluded anyway. This prevents them from contributing " 

1988 "to the outlier epoch count image and potentially being labeled as persistant." 

1989 "'Mostly' is defined by the config 'prefilterArtifactsRatio'.", 

1990 dtype=bool, 

1991 default=True 

1992 ) 

1993 prefilterArtifactsMaskPlanes = pexConfig.ListField( 

1994 doc="Prefilter artifact candidates that are mostly covered by these bad mask planes.", 

1995 dtype=str, 

1996 default=('NO_DATA', 'BAD', 'SAT', 'SUSPECT'), 

1997 ) 

1998 prefilterArtifactsRatio = pexConfig.Field( 

1999 doc="Prefilter artifact candidates with less than this fraction overlapping good pixels", 

2000 dtype=float, 

2001 default=0.05 

2002 ) 

2003 doFilterMorphological = pexConfig.Field( 

2004 doc="Filter artifact candidates based on morphological criteria, i.g. those that appear to " 

2005 "be streaks.", 

2006 dtype=bool, 

2007 default=False 

2008 ) 

2009 

2010 def setDefaults(self): 

2011 AssembleCoaddConfig.setDefaults(self) 

2012 self.statistic = 'MEAN' 

2013 self.doUsePsfMatchedPolygons = True 

2014 

2015 # Real EDGE removed by psfMatched NO_DATA border half the width of the matching kernel 

2016 # CompareWarp applies psfMatched EDGE pixels to directWarps before assembling 

2017 if "EDGE" in self.badMaskPlanes: 2017 ↛ 2019line 2017 didn't jump to line 2019, because the condition on line 2017 was never false

2018 self.badMaskPlanes.remove('EDGE') 

2019 self.removeMaskPlanes.append('EDGE') 

2020 self.assembleStaticSkyModel.badMaskPlanes = ["NO_DATA", ] 

2021 self.assembleStaticSkyModel.warpType = 'psfMatched' 

2022 self.assembleStaticSkyModel.connections.warpType = 'psfMatched' 

2023 self.assembleStaticSkyModel.statistic = 'MEANCLIP' 

2024 self.assembleStaticSkyModel.sigmaClip = 2.5 

2025 self.assembleStaticSkyModel.clipIter = 3 

2026 self.assembleStaticSkyModel.calcErrorFromInputVariance = False 

2027 self.assembleStaticSkyModel.doWrite = False 

2028 self.detect.doTempLocalBackground = False 

2029 self.detect.reEstimateBackground = False 

2030 self.detect.returnOriginalFootprints = False 

2031 self.detect.thresholdPolarity = "both" 

2032 self.detect.thresholdValue = 5 

2033 self.detect.minPixels = 4 

2034 self.detect.isotropicGrow = True 

2035 self.detect.thresholdType = "pixel_stdev" 

2036 self.detect.nSigmaToGrow = 0.4 

2037 # The default nSigmaToGrow for SourceDetectionTask is already 2.4, 

2038 # Explicitly restating because ratio with detect.nSigmaToGrow matters 

2039 self.detectTemplate.nSigmaToGrow = 2.4 

2040 self.detectTemplate.doTempLocalBackground = False 

2041 self.detectTemplate.reEstimateBackground = False 

2042 self.detectTemplate.returnOriginalFootprints = False 

2043 

2044 def validate(self): 

2045 super().validate() 

2046 if self.assembleStaticSkyModel.doNImage: 

2047 raise ValueError("No dataset type exists for a PSF-Matched Template N Image." 

2048 "Please set assembleStaticSkyModel.doNImage=False") 

2049 

2050 if self.assembleStaticSkyModel.doWrite and (self.warpType == self.assembleStaticSkyModel.warpType): 

2051 raise ValueError("warpType (%s) == assembleStaticSkyModel.warpType (%s) and will compete for " 

2052 "the same dataset name. Please set assembleStaticSkyModel.doWrite to False " 

2053 "or warpType to 'direct'. assembleStaticSkyModel.warpType should ways be " 

2054 "'PsfMatched'" % (self.warpType, self.assembleStaticSkyModel.warpType)) 

2055 

2056 

2057class CompareWarpAssembleCoaddTask(AssembleCoaddTask): 

2058 """Assemble a compareWarp coadded image from a set of warps 

2059 by masking artifacts detected by comparing PSF-matched warps. 

2060 

2061 In ``AssembleCoaddTask``, we compute the coadd as an clipped mean (i.e., 

2062 we clip outliers). The problem with doing this is that when computing the 

2063 coadd PSF at a given location, individual visit PSFs from visits with 

2064 outlier pixels contribute to the coadd PSF and cannot be treated correctly. 

2065 In this task, we correct for this behavior by creating a new badMaskPlane 

2066 'CLIPPED' which marks pixels in the individual warps suspected to contain 

2067 an artifact. We populate this plane on the input warps by comparing 

2068 PSF-matched warps with a PSF-matched median coadd which serves as a 

2069 model of the static sky. Any group of pixels that deviates from the 

2070 PSF-matched template coadd by more than config.detect.threshold sigma, 

2071 is an artifact candidate. The candidates are then filtered to remove 

2072 variable sources and sources that are difficult to subtract such as 

2073 bright stars. This filter is configured using the config parameters 

2074 ``temporalThreshold`` and ``spatialThreshold``. The temporalThreshold is 

2075 the maximum fraction of epochs that the deviation can appear in and still 

2076 be considered an artifact. The spatialThreshold is the maximum fraction of 

2077 pixels in the footprint of the deviation that appear in other epochs 

2078 (where other epochs is defined by the temporalThreshold). If the deviant 

2079 region meets this criteria of having a significant percentage of pixels 

2080 that deviate in only a few epochs, these pixels have the 'CLIPPED' bit 

2081 set in the mask. These regions will not contribute to the final coadd. 

2082 Furthermore, any routine to determine the coadd PSF can now be cognizant 

2083 of clipped regions. Note that the algorithm implemented by this task is 

2084 preliminary and works correctly for HSC data. Parameter modifications and 

2085 or considerable redesigning of the algorithm is likley required for other 

2086 surveys. 

2087 

2088 ``CompareWarpAssembleCoaddTask`` sub-classes 

2089 ``AssembleCoaddTask`` and instantiates ``AssembleCoaddTask`` 

2090 as a subtask to generate the TemplateCoadd (the model of the static sky). 

2091 

2092 Notes 

2093 ----- 

2094 The `lsst.pipe.base.cmdLineTask.CmdLineTask` interface supports a 

2095 flag ``-d`` to import ``debug.py`` from your ``PYTHONPATH``; see 

2096 ``baseDebug`` for more about ``debug.py`` files. 

2097 

2098 This task supports the following debug variables: 

2099 

2100 - ``saveCountIm`` 

2101 If True then save the Epoch Count Image as a fits file in the `figPath` 

2102 - ``figPath`` 

2103 Path to save the debug fits images and figures 

2104 

2105 For example, put something like: 

2106 

2107 .. code-block:: python 

2108 

2109 import lsstDebug 

2110 def DebugInfo(name): 

2111 di = lsstDebug.getInfo(name) 

2112 if name == "lsst.pipe.tasks.assembleCoadd": 

2113 di.saveCountIm = True 

2114 di.figPath = "/desired/path/to/debugging/output/images" 

2115 return di 

2116 lsstDebug.Info = DebugInfo 

2117 

2118 into your ``debug.py`` file and run ``assemebleCoadd.py`` with the 

2119 ``--debug`` flag. Some subtasks may have their own debug variables; 

2120 see individual Task documentation. 

2121 

2122 Examples 

2123 -------- 

2124 ``CompareWarpAssembleCoaddTask`` assembles a set of warped images into a 

2125 coadded image. The ``CompareWarpAssembleCoaddTask`` is invoked by running 

2126 ``assembleCoadd.py`` with the flag ``--compareWarpCoadd``. 

2127 Usage of ``assembleCoadd.py`` expects a data reference to the tract patch 

2128 and filter to be coadded (specified using 

2129 '--id = [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]') 

2130 along with a list of coaddTempExps to attempt to coadd (specified using 

2131 '--selectId [KEY=VALUE1[^VALUE2[^VALUE3...] [KEY=VALUE1[^VALUE2[^VALUE3...] ...]]'). 

2132 Only the warps that cover the specified tract and patch will be coadded. 

2133 A list of the available optional arguments can be obtained by calling 

2134 ``assembleCoadd.py`` with the ``--help`` command line argument: 

2135 

2136 .. code-block:: none 

2137 

2138 assembleCoadd.py --help 

2139 

2140 To demonstrate usage of the ``CompareWarpAssembleCoaddTask`` in the larger 

2141 context of multi-band processing, we will generate the HSC-I & -R band 

2142 oadds from HSC engineering test data provided in the ``ci_hsc`` package. 

2143 To begin, assuming that the lsst stack has been already set up, we must 

2144 set up the ``obs_subaru`` and ``ci_hsc`` packages. 

2145 This defines the environment variable ``$CI_HSC_DIR`` and points at the 

2146 location of the package. The raw HSC data live in the ``$CI_HSC_DIR/raw`` 

2147 directory. To begin assembling the coadds, we must first 

2148 

2149 - processCcd 

2150 process the individual ccds in $CI_HSC_RAW to produce calibrated exposures 

2151 - makeSkyMap 

2152 create a skymap that covers the area of the sky present in the raw exposures 

2153 - makeCoaddTempExp 

2154 warp the individual calibrated exposures to the tangent plane of the coadd 

2155 

2156 We can perform all of these steps by running 

2157 

2158 .. code-block:: none 

2159 

2160 $CI_HSC_DIR scons warp-903986 warp-904014 warp-903990 warp-904010 warp-903988 

2161 

2162 This will produce warped ``coaddTempExps`` for each visit. To coadd the 

2163 warped data, we call ``assembleCoadd.py`` as follows: 

2164 

2165 .. code-block:: none 

2166 

2167 assembleCoadd.py --compareWarpCoadd $CI_HSC_DIR/DATA --id patch=5,4 tract=0 filter=HSC-I \ 

2168 --selectId visit=903986 ccd=16 --selectId visit=903986 ccd=22 --selectId visit=903986 ccd=23 \ 

2169 --selectId visit=903986 ccd=100 --selectId visit=904014 ccd=1 --selectId visit=904014 ccd=6 \ 

2170 --selectId visit=904014 ccd=12 --selectId visit=903990 ccd=18 --selectId visit=903990 ccd=25 \ 

2171 --selectId visit=904010 ccd=4 --selectId visit=904010 ccd=10 --selectId visit=904010 ccd=100 \ 

2172 --selectId visit=903988 ccd=16 --selectId visit=903988 ccd=17 --selectId visit=903988 ccd=23 \ 

2173 --selectId visit=903988 ccd=24 

2174 

2175 This will process the HSC-I band data. The results are written in 

2176 ``$CI_HSC_DIR/DATA/deepCoadd-results/HSC-I``. 

2177 """ 

2178 ConfigClass = CompareWarpAssembleCoaddConfig 

2179 _DefaultName = "compareWarpAssembleCoadd" 

2180 

2181 def __init__(self, *args, **kwargs): 

2182 AssembleCoaddTask.__init__(self, *args, **kwargs) 

2183 self.makeSubtask("assembleStaticSkyModel") 

2184 detectionSchema = afwTable.SourceTable.makeMinimalSchema() 

2185 self.makeSubtask("detect", schema=detectionSchema) 

2186 if self.config.doPreserveContainedBySource: 2186 ↛ 2188line 2186 didn't jump to line 2188, because the condition on line 2186 was never false

2187 self.makeSubtask("detectTemplate", schema=afwTable.SourceTable.makeMinimalSchema()) 

2188 if self.config.doScaleWarpVariance: 2188 ↛ 2190line 2188 didn't jump to line 2190, because the condition on line 2188 was never false

2189 self.makeSubtask("scaleWarpVariance") 

2190 if self.config.doFilterMorphological: 2190 ↛ 2191line 2190 didn't jump to line 2191, because the condition on line 2190 was never true

2191 self.makeSubtask("maskStreaks") 

2192 

2193 @utils.inheritDoc(AssembleCoaddTask) 

2194 def makeSupplementaryDataGen3(self, butlerQC, inputRefs, outputRefs): 

2195 """ 

2196 Generate a templateCoadd to use as a naive model of static sky to 

2197 subtract from PSF-Matched warps. 

2198 

2199 Returns 

2200 ------- 

2201 result : `lsst.pipe.base.Struct` 

2202 Result struct with components: 

2203 

2204 - ``templateCoadd`` : coadded exposure (``lsst.afw.image.Exposure``) 

2205 - ``nImage`` : N Image (``lsst.afw.image.Image``) 

2206 """ 

2207 # Ensure that psfMatchedWarps are used as input warps for template generation 

2208 staticSkyModelInputRefs = copy.deepcopy(inputRefs) 

2209 staticSkyModelInputRefs.inputWarps = inputRefs.psfMatchedWarps 

2210 

2211 # Because subtasks don't have connections we have to make one. 

2212 # The main task's `templateCoadd` is the subtask's `coaddExposure` 

2213 staticSkyModelOutputRefs = copy.deepcopy(outputRefs) 

2214 if self.config.assembleStaticSkyModel.doWrite: 

2215 staticSkyModelOutputRefs.coaddExposure = staticSkyModelOutputRefs.templateCoadd 

2216 # Remove template coadd from both subtask's and main tasks outputs, 

2217 # because it is handled by the subtask as `coaddExposure` 

2218 del outputRefs.templateCoadd 

2219 del staticSkyModelOutputRefs.templateCoadd 

2220 

2221 # A PSF-Matched nImage does not exist as a dataset type 

2222 if 'nImage' in staticSkyModelOutputRefs.keys(): 

2223 del staticSkyModelOutputRefs.nImage 

2224 

2225 templateCoadd = self.assembleStaticSkyModel.runQuantum(butlerQC, staticSkyModelInputRefs, 

2226 staticSkyModelOutputRefs) 

2227 if templateCoadd is None: 

2228 raise RuntimeError(self._noTemplateMessage(self.assembleStaticSkyModel.warpType)) 

2229 

2230 return pipeBase.Struct(templateCoadd=templateCoadd.coaddExposure, 

2231 nImage=templateCoadd.nImage, 

2232 warpRefList=templateCoadd.warpRefList, 

2233 imageScalerList=templateCoadd.imageScalerList, 

2234 weightList=templateCoadd.weightList) 

2235 

2236 @utils.inheritDoc(AssembleCoaddTask) 

2237 def makeSupplementaryData(self, dataRef, selectDataList=None, warpRefList=None): 

2238 """ 

2239 Generate a templateCoadd to use as a naive model of static sky to 

2240 subtract from PSF-Matched warps. 

2241 

2242 Returns 

2243 ------- 

2244 result : `lsst.pipe.base.Struct` 

2245 Result struct with components: 

2246 

2247 - ``templateCoadd``: coadded exposure (``lsst.afw.image.Exposure``) 

2248 - ``nImage``: N Image (``lsst.afw.image.Image``) 

2249 """ 

2250 templateCoadd = self.assembleStaticSkyModel.runDataRef(dataRef, selectDataList, warpRefList) 

2251 if templateCoadd is None: 2251 ↛ 2252line 2251 didn't jump to line 2252, because the condition on line 2251 was never true

2252 raise RuntimeError(self._noTemplateMessage(self.assembleStaticSkyModel.warpType)) 

2253 

2254 return pipeBase.Struct(templateCoadd=templateCoadd.coaddExposure, 

2255 nImage=templateCoadd.nImage, 

2256 warpRefList=templateCoadd.warpRefList, 

2257 imageScalerList=templateCoadd.imageScalerList, 

2258 weightList=templateCoadd.weightList) 

2259 

2260 def _noTemplateMessage(self, warpType): 

2261 warpName = (warpType[0].upper() + warpType[1:]) 

2262 message = """No %(warpName)s warps were found to build the template coadd which is 

2263 required to run CompareWarpAssembleCoaddTask. To continue assembling this type of coadd, 

2264 first either rerun makeCoaddTempExp with config.make%(warpName)s=True or 

2265 coaddDriver with config.makeCoadTempExp.make%(warpName)s=True, before assembleCoadd. 

2266 

2267 Alternatively, to use another algorithm with existing warps, retarget the CoaddDriverConfig to 

2268 another algorithm like: 

2269 

2270 from lsst.pipe.tasks.assembleCoadd import SafeClipAssembleCoaddTask 

2271 config.assemble.retarget(SafeClipAssembleCoaddTask) 

2272 """ % {"warpName": warpName} 

2273 return message 

2274 

2275 @utils.inheritDoc(AssembleCoaddTask) 

2276 @pipeBase.timeMethod 

2277 def run(self, skyInfo, tempExpRefList, imageScalerList, weightList, 

2278 supplementaryData, *args, **kwargs): 

2279 """Assemble the coadd. 

2280 

2281 Find artifacts and apply them to the warps' masks creating a list of 

2282 alternative masks with a new "CLIPPED" plane and updated "NO_DATA" 

2283 plane. Then pass these alternative masks to the base class's `run` 

2284 method. 

2285 

2286 The input parameters ``supplementaryData`` is a `lsst.pipe.base.Struct` 

2287 that must contain a ``templateCoadd`` that serves as the 

2288 model of the static sky. 

2289 """ 

2290 

2291 # Check and match the order of the supplementaryData 

2292 # (PSF-matched) inputs to the order of the direct inputs, 

2293 # so that the artifact mask is applied to the right warp 

2294 dataIds = [ref.dataId for ref in tempExpRefList] 

2295 psfMatchedDataIds = [ref.dataId for ref in supplementaryData.warpRefList] 

2296 

2297 if dataIds != psfMatchedDataIds: 

2298 self.log.info("Reordering and or/padding PSF-matched visit input list") 

2299 supplementaryData.warpRefList = reorderAndPadList(supplementaryData.warpRefList, 

2300 psfMatchedDataIds, dataIds) 

2301 supplementaryData.imageScalerList = reorderAndPadList(supplementaryData.imageScalerList, 

2302 psfMatchedDataIds, dataIds) 

2303 

2304 # Use PSF-Matched Warps (and corresponding scalers) and coadd to find artifacts 

2305 spanSetMaskList = self.findArtifacts(supplementaryData.templateCoadd, 

2306 supplementaryData.warpRefList, 

2307 supplementaryData.imageScalerList) 

2308 

2309 badMaskPlanes = self.config.badMaskPlanes[:] 

2310 badMaskPlanes.append("CLIPPED") 

2311 badPixelMask = afwImage.Mask.getPlaneBitMask(badMaskPlanes) 

2312 

2313 result = AssembleCoaddTask.run(self, skyInfo, tempExpRefList, imageScalerList, weightList, 

2314 spanSetMaskList, mask=badPixelMask) 

2315 

2316 # Propagate PSF-matched EDGE pixels to coadd SENSOR_EDGE and INEXACT_PSF 

2317 # Psf-Matching moves the real edge inwards 

2318 self.applyAltEdgeMask(result.coaddExposure.maskedImage.mask, spanSetMaskList) 

2319 return result 

2320 

2321 def applyAltEdgeMask(self, mask, altMaskList): 

2322 """Propagate alt EDGE mask to SENSOR_EDGE AND INEXACT_PSF planes. 

2323 

2324 Parameters 

2325 ---------- 

2326 mask : `lsst.afw.image.Mask` 

2327 Original mask. 

2328 altMaskList : `list` 

2329 List of Dicts containing ``spanSet`` lists. 

2330 Each element contains the new mask plane name (e.g. "CLIPPED 

2331 and/or "NO_DATA") as the key, and list of ``SpanSets`` to apply to 

2332 the mask. 

2333 """ 

2334 maskValue = mask.getPlaneBitMask(["SENSOR_EDGE", "INEXACT_PSF"]) 

2335 for visitMask in altMaskList: 

2336 if "EDGE" in visitMask: 2336 ↛ 2335line 2336 didn't jump to line 2335, because the condition on line 2336 was never false

2337 for spanSet in visitMask['EDGE']: 

2338 spanSet.clippedTo(mask.getBBox()).setMask(mask, maskValue) 

2339 

2340 def findArtifacts(self, templateCoadd, tempExpRefList, imageScalerList): 

2341 """Find artifacts. 

2342 

2343 Loop through warps twice. The first loop builds a map with the count 

2344 of how many epochs each pixel deviates from the templateCoadd by more 

2345 than ``config.chiThreshold`` sigma. The second loop takes each 

2346 difference image and filters the artifacts detected in each using 

2347 count map to filter out variable sources and sources that are 

2348 difficult to subtract cleanly. 

2349 

2350 Parameters 

2351 ---------- 

2352 templateCoadd : `lsst.afw.image.Exposure` 

2353 Exposure to serve as model of static sky. 

2354 tempExpRefList : `list` 

2355 List of data references to warps. 

2356 imageScalerList : `list` 

2357 List of image scalers. 

2358 

2359 Returns 

2360 ------- 

2361 altMasks : `list` 

2362 List of dicts containing information about CLIPPED 

2363 (i.e., artifacts), NO_DATA, and EDGE pixels. 

2364 """ 

2365 

2366 self.log.debug("Generating Count Image, and mask lists.") 

2367 coaddBBox = templateCoadd.getBBox() 

2368 slateIm = afwImage.ImageU(coaddBBox) 

2369 epochCountImage = afwImage.ImageU(coaddBBox) 

2370 nImage = afwImage.ImageU(coaddBBox) 

2371 spanSetArtifactList = [] 

2372 spanSetNoDataMaskList = [] 

2373 spanSetEdgeList = [] 

2374 spanSetBadMorphoList = [] 

2375 badPixelMask = self.getBadPixelMask() 

2376 

2377 # mask of the warp diffs should = that of only the warp 

2378 templateCoadd.mask.clearAllMaskPlanes() 

2379 

2380 if self.config.doPreserveContainedBySource: 2380 ↛ 2383line 2380 didn't jump to line 2383, because the condition on line 2380 was never false

2381 templateFootprints = self.detectTemplate.detectFootprints(templateCoadd) 

2382 else: 

2383 templateFootprints = None 

2384 

2385 for warpRef, imageScaler in zip(tempExpRefList, imageScalerList): 

2386 warpDiffExp = self._readAndComputeWarpDiff(warpRef, imageScaler, templateCoadd) 

2387 if warpDiffExp is not None: 

2388 # This nImage only approximates the final nImage because it uses the PSF-matched mask 

2389 nImage.array += (numpy.isfinite(warpDiffExp.image.array) 

2390 * ((warpDiffExp.mask.array & badPixelMask) == 0)).astype(numpy.uint16) 

2391 fpSet = self.detect.detectFootprints(warpDiffExp, doSmooth=False, clearMask=True) 

2392 fpSet.positive.merge(fpSet.negative) 

2393 footprints = fpSet.positive 

2394 slateIm.set(0) 

2395 spanSetList = [footprint.spans for footprint in footprints.getFootprints()] 

2396 

2397 # Remove artifacts due to defects before they contribute to the epochCountImage 

2398 if self.config.doPrefilterArtifacts: 2398 ↛ 2402line 2398 didn't jump to line 2402, because the condition on line 2398 was never false

2399 spanSetList = self.prefilterArtifacts(spanSetList, warpDiffExp) 

2400 

2401 # Clear mask before adding prefiltered spanSets 

2402 self.detect.clearMask(warpDiffExp.mask) 

2403 for spans in spanSetList: 

2404 spans.setImage(slateIm, 1, doClip=True) 

2405 spans.setMask(warpDiffExp.mask, warpDiffExp.mask.getPlaneBitMask("DETECTED")) 

2406 epochCountImage += slateIm 

2407 

2408 if self.config.doFilterMorphological: 2408 ↛ 2409line 2408 didn't jump to line 2409, because the condition on line 2408 was never true

2409 maskName = self.config.streakMaskName 

2410 _ = self.maskStreaks.run(warpDiffExp) 

2411 streakMask = warpDiffExp.mask 

2412 spanSetStreak = afwGeom.SpanSet.fromMask(streakMask, 

2413 streakMask.getPlaneBitMask(maskName)).split() 

2414 

2415 # PSF-Matched warps have less available area (~the matching kernel) because the calexps 

2416 # undergo a second convolution. Pixels with data in the direct warp 

2417 # but not in the PSF-matched warp will not have their artifacts detected. 

2418 # NaNs from the PSF-matched warp therefore must be masked in the direct warp 

2419 nans = numpy.where(numpy.isnan(warpDiffExp.maskedImage.image.array), 1, 0) 

2420 nansMask = afwImage.makeMaskFromArray(nans.astype(afwImage.MaskPixel)) 

2421 nansMask.setXY0(warpDiffExp.getXY0()) 

2422 edgeMask = warpDiffExp.mask 

2423 spanSetEdgeMask = afwGeom.SpanSet.fromMask(edgeMask, 

2424 edgeMask.getPlaneBitMask("EDGE")).split() 

2425 else: 

2426 # If the directWarp has <1% coverage, the psfMatchedWarp can have 0% and not exist 

2427 # In this case, mask the whole epoch 

2428 nansMask = afwImage.MaskX(coaddBBox, 1) 

2429 spanSetList = [] 

2430 spanSetEdgeMask = [] 

2431 spanSetStreak = [] 

2432 

2433 spanSetNoDataMask = afwGeom.SpanSet.fromMask(nansMask).split() 

2434 

2435 spanSetNoDataMaskList.append(spanSetNoDataMask) 

2436 spanSetArtifactList.append(spanSetList) 

2437 spanSetEdgeList.append(spanSetEdgeMask) 

2438 if self.config.doFilterMorphological: 2438 ↛ 2439line 2438 didn't jump to line 2439, because the condition on line 2438 was never true

2439 spanSetBadMorphoList.append(spanSetStreak) 

2440 

2441 if lsstDebug.Info(__name__).saveCountIm: 2441 ↛ 2442line 2441 didn't jump to line 2442, because the condition on line 2441 was never true

2442 path = self._dataRef2DebugPath("epochCountIm", tempExpRefList[0], coaddLevel=True) 

2443 epochCountImage.writeFits(path) 

2444 

2445 for i, spanSetList in enumerate(spanSetArtifactList): 

2446 if spanSetList: 

2447 filteredSpanSetList = self.filterArtifacts(spanSetList, epochCountImage, nImage, 

2448 templateFootprints) 

2449 spanSetArtifactList[i] = filteredSpanSetList 

2450 if self.config.doFilterMorphological: 2450 ↛ 2451line 2450 didn't jump to line 2451, because the condition on line 2450 was never true

2451 spanSetArtifactList[i] += spanSetBadMorphoList[i] 

2452 

2453 altMasks = [] 

2454 for artifacts, noData, edge in zip(spanSetArtifactList, spanSetNoDataMaskList, spanSetEdgeList): 

2455 altMasks.append({'CLIPPED': artifacts, 

2456 'NO_DATA': noData, 

2457 'EDGE': edge}) 

2458 return altMasks 

2459 

2460 def prefilterArtifacts(self, spanSetList, exp): 

2461 """Remove artifact candidates covered by bad mask plane. 

2462 

2463 Any future editing of the candidate list that does not depend on 

2464 temporal information should go in this method. 

2465 

2466 Parameters 

2467 ---------- 

2468 spanSetList : `list` 

2469 List of SpanSets representing artifact candidates. 

2470 exp : `lsst.afw.image.Exposure` 

2471 Exposure containing mask planes used to prefilter. 

2472 

2473 Returns 

2474 ------- 

2475 returnSpanSetList : `list` 

2476 List of SpanSets with artifacts. 

2477 """ 

2478 badPixelMask = exp.mask.getPlaneBitMask(self.config.prefilterArtifactsMaskPlanes) 

2479 goodArr = (exp.mask.array & badPixelMask) == 0 

2480 returnSpanSetList = [] 

2481 bbox = exp.getBBox() 

2482 x0, y0 = exp.getXY0() 

2483 for i, span in enumerate(spanSetList): 

2484 y, x = span.clippedTo(bbox).indices() 

2485 yIndexLocal = numpy.array(y) - y0 

2486 xIndexLocal = numpy.array(x) - x0 

2487 goodRatio = numpy.count_nonzero(goodArr[yIndexLocal, xIndexLocal])/span.getArea() 

2488 if goodRatio > self.config.prefilterArtifactsRatio: 2488 ↛ 2483line 2488 didn't jump to line 2483, because the condition on line 2488 was never false

2489 returnSpanSetList.append(span) 

2490 return returnSpanSetList 

2491 

2492 def filterArtifacts(self, spanSetList, epochCountImage, nImage, footprintsToExclude=None): 

2493 """Filter artifact candidates. 

2494 

2495 Parameters 

2496 ---------- 

2497 spanSetList : `list` 

2498 List of SpanSets representing artifact candidates. 

2499 epochCountImage : `lsst.afw.image.Image` 

2500 Image of accumulated number of warpDiff detections. 

2501 nImage : `lsst.afw.image.Image` 

2502 Image of the accumulated number of total epochs contributing. 

2503 

2504 Returns 

2505 ------- 

2506 maskSpanSetList : `list` 

2507 List of SpanSets with artifacts. 

2508 """ 

2509 

2510 maskSpanSetList = [] 

2511 x0, y0 = epochCountImage.getXY0() 

2512 for i, span in enumerate(spanSetList): 

2513 y, x = span.indices() 

2514 yIdxLocal = [y1 - y0 for y1 in y] 

2515 xIdxLocal = [x1 - x0 for x1 in x] 

2516 outlierN = epochCountImage.array[yIdxLocal, xIdxLocal] 

2517 totalN = nImage.array[yIdxLocal, xIdxLocal] 

2518 

2519 # effectiveMaxNumEpochs is broken line (fraction of N) with characteristic config.maxNumEpochs 

2520 effMaxNumEpochsHighN = (self.config.maxNumEpochs 

2521 + self.config.maxFractionEpochsHigh*numpy.mean(totalN)) 

2522 effMaxNumEpochsLowN = self.config.maxFractionEpochsLow * numpy.mean(totalN) 

2523 effectiveMaxNumEpochs = int(min(effMaxNumEpochsLowN, effMaxNumEpochsHighN)) 

2524 nPixelsBelowThreshold = numpy.count_nonzero((outlierN > 0) 

2525 & (outlierN <= effectiveMaxNumEpochs)) 

2526 percentBelowThreshold = nPixelsBelowThreshold / len(outlierN) 

2527 if percentBelowThreshold > self.config.spatialThreshold: 

2528 maskSpanSetList.append(span) 

2529 

2530 if self.config.doPreserveContainedBySource and footprintsToExclude is not None: 2530 ↛ 2543line 2530 didn't jump to line 2543, because the condition on line 2530 was never false

2531 # If a candidate is contained by a footprint on the template coadd, do not clip 

2532 filteredMaskSpanSetList = [] 

2533 for span in maskSpanSetList: 

2534 doKeep = True 

2535 for footprint in footprintsToExclude.positive.getFootprints(): 

2536 if footprint.spans.contains(span): 

2537 doKeep = False 

2538 break 

2539 if doKeep: 

2540 filteredMaskSpanSetList.append(span) 

2541 maskSpanSetList = filteredMaskSpanSetList 

2542 

2543 return maskSpanSetList 

2544 

2545 def _readAndComputeWarpDiff(self, warpRef, imageScaler, templateCoadd): 

2546 """Fetch a warp from the butler and return a warpDiff. 

2547 

2548 Parameters 

2549 ---------- 

2550 warpRef : `lsst.daf.persistence.butlerSubset.ButlerDataRef` 

2551 Butler dataRef for the warp. 

2552 imageScaler : `lsst.pipe.tasks.scaleZeroPoint.ImageScaler` 

2553 An image scaler object. 

2554 templateCoadd : `lsst.afw.image.Exposure` 

2555 Exposure to be substracted from the scaled warp. 

2556 

2557 Returns 

2558 ------- 

2559 warp : `lsst.afw.image.Exposure` 

2560 Exposure of the image difference between the warp and template. 

2561 """ 

2562 

2563 # If the PSF-Matched warp did not exist for this direct warp 

2564 # None is holding its place to maintain order in Gen 3 

2565 if warpRef is None: 

2566 return None 

2567 # Warp comparison must use PSF-Matched Warps regardless of requested coadd warp type 

2568 warpName = self.getTempExpDatasetName('psfMatched') 

2569 if not isinstance(warpRef, DeferredDatasetHandle): 2569 ↛ 2573line 2569 didn't jump to line 2573, because the condition on line 2569 was never false

2570 if not warpRef.datasetExists(warpName): 2570 ↛ 2571line 2570 didn't jump to line 2571, because the condition on line 2570 was never true

2571 self.log.warning("Could not find %s %s; skipping it", warpName, warpRef.dataId) 

2572 return None 

2573 warp = warpRef.get(datasetType=warpName, immediate=True) 

2574 # direct image scaler OK for PSF-matched Warp 

2575 imageScaler.scaleMaskedImage(warp.getMaskedImage()) 

2576 mi = warp.getMaskedImage() 

2577 if self.config.doScaleWarpVariance: 2577 ↛ 2582line 2577 didn't jump to line 2582, because the condition on line 2577 was never false

2578 try: 

2579 self.scaleWarpVariance.run(mi) 

2580 except Exception as exc: 

2581 self.log.warning("Unable to rescale variance of warp (%s); leaving it as-is", exc) 

2582 mi -= templateCoadd.getMaskedImage() 

2583 return warp 

2584 

2585 def _dataRef2DebugPath(self, prefix, warpRef, coaddLevel=False): 

2586 """Return a path to which to write debugging output. 

2587 

2588 Creates a hyphen-delimited string of dataId values for simple filenames. 

2589 

2590 Parameters 

2591 ---------- 

2592 prefix : `str` 

2593 Prefix for filename. 

2594 warpRef : `lsst.daf.persistence.butlerSubset.ButlerDataRef` 

2595 Butler dataRef to make the path from. 

2596 coaddLevel : `bool`, optional. 

2597 If True, include only coadd-level keys (e.g., 'tract', 'patch', 

2598 'filter', but no 'visit'). 

2599 

2600 Returns 

2601 ------- 

2602 result : `str` 

2603 Path for debugging output. 

2604 """ 

2605 if coaddLevel: 

2606 keys = warpRef.getButler().getKeys(self.getCoaddDatasetName(self.warpType)) 

2607 else: 

2608 keys = warpRef.dataId.keys() 

2609 keyList = sorted(keys, reverse=True) 

2610 directory = lsstDebug.Info(__name__).figPath if lsstDebug.Info(__name__).figPath else "." 

2611 filename = "%s-%s.fits" % (prefix, '-'.join([str(warpRef.dataId[k]) for k in keyList])) 

2612 return os.path.join(directory, filename)