Coverage for python/lsst/pipe/tasks/makeCoaddTempExp.py: 48%

1# 

2# LSST Data Management System 

3# Copyright 2008, 2009, 2010, 2011, 2012 LSST Corporation. 

4# 

5# This product includes software developed by the 

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

7# 

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

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

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

11# (at your option) any later version. 

12# 

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

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

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

16# GNU General Public License for more details. 

17# 

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

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

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

21# 

22import numpy 

23import logging 

24 

25import lsst.pex.config as pexConfig 

26import lsst.daf.persistence as dafPersist 

27import lsst.afw.image as afwImage 

28import lsst.coadd.utils as coaddUtils 

29import lsst.pipe.base as pipeBase 

30import lsst.pipe.base.connectionTypes as connectionTypes 

31import lsst.utils as utils 

32import lsst.geom 

33from lsst.meas.algorithms import CoaddPsf, CoaddPsfConfig 

34from lsst.skymap import BaseSkyMap 

35from lsst.utils.timer import timeMethod 

36from .coaddBase import CoaddBaseTask, makeSkyInfo, reorderAndPadList 

37from .selectImages import PsfWcsSelectImagesTask 

38from .warpAndPsfMatch import WarpAndPsfMatchTask 

39from .coaddHelpers import groupPatchExposures, getGroupDataRef 

40from collections.abc import Iterable 

41 

42__all__ = ["MakeCoaddTempExpTask", "MakeWarpTask", "MakeWarpConfig"] 

43 

44log = logging.getLogger(__name__) 

45 

46 

47class MissingExposureError(Exception): 

48 """Raised when data cannot be retrieved for an exposure. 

49 When processing patches, sometimes one exposure is missing; this lets us 

50 distinguish bewteen that case, and other errors. 

51 """ 

52 pass 

53 

54 

55class MakeCoaddTempExpConfig(CoaddBaseTask.ConfigClass): 

56 """Config for MakeCoaddTempExpTask 

57 """ 

58 warpAndPsfMatch = pexConfig.ConfigurableField( 

59 target=WarpAndPsfMatchTask, 

60 doc="Task to warp and PSF-match calexp", 

61 ) 

62 doWrite = pexConfig.Field( 

63 doc="persist <coaddName>Coadd_<warpType>Warp", 

64 dtype=bool, 

65 default=True, 

66 ) 

67 bgSubtracted = pexConfig.Field( 

68 doc="Work with a background subtracted calexp?", 

69 dtype=bool, 

70 default=True, 

71 ) 

72 coaddPsf = pexConfig.ConfigField( 

73 doc="Configuration for CoaddPsf", 

74 dtype=CoaddPsfConfig, 

75 ) 

76 makeDirect = pexConfig.Field( 

77 doc="Make direct Warp/Coadds", 

78 dtype=bool, 

79 default=True, 

80 ) 

81 makePsfMatched = pexConfig.Field( 

82 doc="Make Psf-Matched Warp/Coadd?", 

83 dtype=bool, 

84 default=False, 

85 ) 

86 

87 doWriteEmptyWarps = pexConfig.Field( 

88 dtype=bool, 

89 default=False, 

90 doc="Write out warps even if they are empty" 

91 ) 

92 

93 hasFakes = pexConfig.Field( 

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

95 dtype=bool, 

96 default=False, 

97 ) 

98 doApplySkyCorr = pexConfig.Field(dtype=bool, default=False, doc="Apply sky correction?") 

99 

100 def validate(self): 

101 CoaddBaseTask.ConfigClass.validate(self) 

102 if not self.makePsfMatched and not self.makeDirect: 

103 raise RuntimeError("At least one of config.makePsfMatched and config.makeDirect must be True") 

104 if self.doPsfMatch: 

105 # Backwards compatibility. 

106 log.warning("Config doPsfMatch deprecated. Setting makePsfMatched=True and makeDirect=False") 

107 self.makePsfMatched = True 

108 self.makeDirect = False 

109 

110 def setDefaults(self): 

111 CoaddBaseTask.ConfigClass.setDefaults(self) 

112 self.warpAndPsfMatch.psfMatch.kernel.active.kernelSize = self.matchingKernelSize 

113 self.select.retarget(PsfWcsSelectImagesTask) 

114 

115## \addtogroup LSST_task_documentation 

116## \{ 

117## \page MakeCoaddTempExpTask 

118## \ref MakeCoaddTempExpTask_ "MakeCoaddTempExpTask" 

119## \copybrief MakeCoaddTempExpTask 

120## \} 

121 

122 

123class MakeCoaddTempExpTask(CoaddBaseTask): 

124 r"""!Warp and optionally PSF-Match calexps onto an a common projection. 

125 

126 @anchor MakeCoaddTempExpTask_ 

127 

128 @section pipe_tasks_makeCoaddTempExp_Contents Contents 

129 

130 - @ref pipe_tasks_makeCoaddTempExp_Purpose 

131 - @ref pipe_tasks_makeCoaddTempExp_Initialize 

132 - @ref pipe_tasks_makeCoaddTempExp_IO 

133 - @ref pipe_tasks_makeCoaddTempExp_Config 

134 - @ref pipe_tasks_makeCoaddTempExp_Debug 

135 - @ref pipe_tasks_makeCoaddTempExp_Example 

136 

137 @section pipe_tasks_makeCoaddTempExp_Purpose Description 

138 

139 Warp and optionally PSF-Match calexps onto a common projection, by 

140 performing the following operations: 

141 - Group calexps by visit/run 

142 - For each visit, generate a Warp by calling method @ref makeTempExp. 

143 makeTempExp loops over the visit's calexps calling @ref WarpAndPsfMatch 

144 on each visit 

145 

146 The result is a `directWarp` (and/or optionally a `psfMatchedWarp`). 

147 

148 @section pipe_tasks_makeCoaddTempExp_Initialize Task Initialization 

149 

150 @copydoc \_\_init\_\_ 

151 

152 This task has one special keyword argument: passing reuse=True will cause 

153 the task to skip the creation of warps that are already present in the 

154 output repositories. 

155 

156 @section pipe_tasks_makeCoaddTempExp_IO Invoking the Task 

157 

158 This task is primarily designed to be run from the command line. 

159 

160 The main method is `runDataRef`, which takes a single butler data reference for the patch(es) 

161 to process. 

162 

163 @copydoc run 

164 

165 WarpType identifies the types of convolutions applied to Warps (previously CoaddTempExps). 

166 Only two types are available: direct (for regular Warps/Coadds) and psfMatched 

167 (for Warps/Coadds with homogenized PSFs). We expect to add a third type, likelihood, 

168 for generating likelihood Coadds with Warps that have been correlated with their own PSF. 

169 

170 @section pipe_tasks_makeCoaddTempExp_Config Configuration parameters 

171 

172 See @ref MakeCoaddTempExpConfig and parameters inherited from 

173 @link lsst.pipe.tasks.coaddBase.CoaddBaseConfig CoaddBaseConfig @endlink 

174 

175 @subsection pipe_tasks_MakeCoaddTempExp_psfMatching Guide to PSF-Matching Configs 

176 

177 To make `psfMatchedWarps`, select `config.makePsfMatched=True`. The subtask 

178 @link lsst.ip.diffim.modelPsfMatch.ModelPsfMatchTask ModelPsfMatchTask @endlink 

179 is responsible for the PSF-Matching, and its config is accessed via `config.warpAndPsfMatch.psfMatch`. 

180 The optimal configuration depends on aspects of dataset: the pixel scale, average PSF FWHM and 

181 dimensions of the PSF kernel. These configs include the requested model PSF, the matching kernel size, 

182 padding of the science PSF thumbnail and spatial sampling frequency of the PSF. 

183 

184 *Config Guidelines*: The user must specify the size of the model PSF to which to match by setting 

185 `config.modelPsf.defaultFwhm` in units of pixels. The appropriate values depends on science case. 

186 In general, for a set of input images, this config should equal the FWHM of the visit 

187 with the worst seeing. The smallest it should be set to is the median FWHM. The defaults 

188 of the other config options offer a reasonable starting point. 

189 The following list presents the most common problems that arise from a misconfigured 

190 @link lsst.ip.diffim.modelPsfMatch.ModelPsfMatchTask ModelPsfMatchTask @endlink 

191 and corresponding solutions. All assume the default Alard-Lupton kernel, with configs accessed via 

192 ```config.warpAndPsfMatch.psfMatch.kernel['AL']```. Each item in the list is formatted as: 

193 Problem: Explanation. *Solution* 

194 

195 *Troublshooting PSF-Matching Configuration:* 

196 - Matched PSFs look boxy: The matching kernel is too small. _Increase the matching kernel size. 

197 For example:_ 

198 

199 config.warpAndPsfMatch.psfMatch.kernel['AL'].kernelSize=27 # default 21 

200 

201 Note that increasing the kernel size also increases runtime. 

202 - Matched PSFs look ugly (dipoles, quadropoles, donuts): unable to find good solution 

203 for matching kernel. _Provide the matcher with more data by either increasing 

204 the spatial sampling by decreasing the spatial cell size,_ 

205 

206 config.warpAndPsfMatch.psfMatch.kernel['AL'].sizeCellX = 64 # default 128 

207 config.warpAndPsfMatch.psfMatch.kernel['AL'].sizeCellY = 64 # default 128 

208 

209 _or increasing the padding around the Science PSF, for example:_ 

210 

211 config.warpAndPsfMatch.psfMatch.autoPadPsfTo=1.6 # default 1.4 

212 

213 Increasing `autoPadPsfTo` increases the minimum ratio of input PSF dimensions to the 

214 matching kernel dimensions, thus increasing the number of pixels available to fit 

215 after convolving the PSF with the matching kernel. 

216 Optionally, for debugging the effects of padding, the level of padding may be manually 

217 controlled by setting turning off the automatic padding and setting the number 

218 of pixels by which to pad the PSF: 

219 

220 config.warpAndPsfMatch.psfMatch.doAutoPadPsf = False # default True 

221 config.warpAndPsfMatch.psfMatch.padPsfBy = 6 # pixels. default 0 

222 

223 - Deconvolution: Matching a large PSF to a smaller PSF produces 

224 a telltale noise pattern which looks like ripples or a brain. 

225 _Increase the size of the requested model PSF. For example:_ 

226 

227 config.modelPsf.defaultFwhm = 11 # Gaussian sigma in units of pixels. 

228 

229 - High frequency (sometimes checkered) noise: The matching basis functions are too small. 

230 _Increase the width of the Gaussian basis functions. For example:_ 

231 

232 config.warpAndPsfMatch.psfMatch.kernel['AL'].alardSigGauss=[1.5, 3.0, 6.0] 

233 # from default [0.7, 1.5, 3.0] 

234 

235 

236 @section pipe_tasks_makeCoaddTempExp_Debug Debug variables 

237 

238 MakeCoaddTempExpTask has no debug output, but its subtasks do. 

239 

240 @section pipe_tasks_makeCoaddTempExp_Example A complete example of using MakeCoaddTempExpTask 

241 

242 This example uses the package ci_hsc to show how MakeCoaddTempExp fits 

243 into the larger Data Release Processing. 

244 Set up by running: 

245 

246 setup ci_hsc 

247 cd $CI_HSC_DIR 

248 # if not built already: 

249 python $(which scons) # this will take a while 

250 

251 The following assumes that `processCcd.py` and `makeSkyMap.py` have previously been run 

252 (e.g. by building `ci_hsc` above) to generate a repository of calexps and an 

253 output respository with the desired SkyMap. The command, 

254 

255 makeCoaddTempExp.py $CI_HSC_DIR/DATA --rerun ci_hsc \ 

256 --id patch=5,4 tract=0 filter=HSC-I \ 

257 --selectId visit=903988 ccd=16 --selectId visit=903988 ccd=17 \ 

258 --selectId visit=903988 ccd=23 --selectId visit=903988 ccd=24 \ 

259 --config doApplyExternalPhotoCalib=False doApplyExternalSkyWcs=False \ 

260 makePsfMatched=True modelPsf.defaultFwhm=11 

261 

262 writes a direct and PSF-Matched Warp to 

263 - `$CI_HSC_DIR/DATA/rerun/ci_hsc/deepCoadd/HSC-I/0/5,4/warp-HSC-I-0-5,4-903988.fits` and 

264 - `$CI_HSC_DIR/DATA/rerun/ci_hsc/deepCoadd/HSC-I/0/5,4/psfMatchedWarp-HSC-I-0-5,4-903988.fits` 

265 respectively. 

266 

267 @note PSF-Matching in this particular dataset would benefit from adding 

268 `--configfile ./matchingConfig.py` to 

269 the command line arguments where `matchingConfig.py` is defined by: 

270 

271 echo " 

272 config.warpAndPsfMatch.psfMatch.kernel['AL'].kernelSize=27 

273 config.warpAndPsfMatch.psfMatch.kernel['AL'].alardSigGauss=[1.5, 3.0, 6.0]" > matchingConfig.py 

274 

275 

276 Add the option `--help` to see more options. 

277 """ 

278 ConfigClass = MakeCoaddTempExpConfig 

279 _DefaultName = "makeCoaddTempExp" 

280 

281 def __init__(self, reuse=False, **kwargs): 

282 CoaddBaseTask.__init__(self, **kwargs) 

283 self.reuse = reuse 

284 self.makeSubtask("warpAndPsfMatch") 

285 if self.config.hasFakes: 285 ↛ 286line 285 didn't jump to line 286, because the condition on line 285 was never true

286 self.calexpType = "fakes_calexp" 

287 else: 

288 self.calexpType = "calexp" 

289 

290 @timeMethod 

291 def runDataRef(self, patchRef, selectDataList=[]): 

292 """!Produce <coaddName>Coadd_<warpType>Warp images by warping and optionally PSF-matching. 

293 

294 @param[in] patchRef: data reference for sky map patch. Must include keys "tract", "patch", 

295 plus the camera-specific filter key (e.g. "filter" or "band") 

296 @return: dataRefList: a list of data references for the new <coaddName>Coadd_directWarps 

297 if direct or both warp types are requested and <coaddName>Coadd_psfMatchedWarps if only psfMatched 

298 warps are requested. 

299 

300 @warning: this task assumes that all exposures in a warp (coaddTempExp) have the same filter. 

301 

302 @warning: this task sets the PhotoCalib of the coaddTempExp to the PhotoCalib of the first calexp 

303 with any good pixels in the patch. For a mosaic camera the resulting PhotoCalib should be ignored 

304 (assembleCoadd should determine zeropoint scaling without referring to it). 

305 """ 

306 skyInfo = self.getSkyInfo(patchRef) 

307 

308 # DataRefs to return are of type *_directWarp unless only *_psfMatchedWarp requested 

309 if self.config.makePsfMatched and not self.config.makeDirect: 309 ↛ 310line 309 didn't jump to line 310, because the condition on line 309 was never true

310 primaryWarpDataset = self.getTempExpDatasetName("psfMatched") 

311 else: 

312 primaryWarpDataset = self.getTempExpDatasetName("direct") 

313 

314 calExpRefList = self.selectExposures(patchRef, skyInfo, selectDataList=selectDataList) 

315 

316 if len(calExpRefList) == 0: 316 ↛ 317line 316 didn't jump to line 317, because the condition on line 316 was never true

317 self.log.warning("No exposures to coadd for patch %s", patchRef.dataId) 

318 return None 

319 self.log.info("Selected %d calexps for patch %s", len(calExpRefList), patchRef.dataId) 

320 calExpRefList = [calExpRef for calExpRef in calExpRefList if calExpRef.datasetExists(self.calexpType)] 

321 self.log.info("Processing %d existing calexps for patch %s", len(calExpRefList), patchRef.dataId) 

322 

323 groupData = groupPatchExposures(patchRef, calExpRefList, self.getCoaddDatasetName(), 

324 primaryWarpDataset) 

325 self.log.info("Processing %d warp exposures for patch %s", len(groupData.groups), patchRef.dataId) 

326 

327 dataRefList = [] 

328 for i, (tempExpTuple, calexpRefList) in enumerate(groupData.groups.items()): 

329 tempExpRef = getGroupDataRef(patchRef.getButler(), primaryWarpDataset, 

330 tempExpTuple, groupData.keys) 

331 if self.reuse and tempExpRef.datasetExists(datasetType=primaryWarpDataset, write=True): 331 ↛ 332line 331 didn't jump to line 332, because the condition on line 331 was never true

332 self.log.info("Skipping makeCoaddTempExp for %s; output already exists.", tempExpRef.dataId) 

333 dataRefList.append(tempExpRef) 

334 continue 

335 self.log.info("Processing Warp %d/%d: id=%s", i, len(groupData.groups), tempExpRef.dataId) 

336 

337 # TODO: mappers should define a way to go from the "grouping keys" to a numeric ID (#2776). 

338 # For now, we try to get a long integer "visit" key, and if we can't, we just use the index 

339 # of the visit in the list. 

340 try: 

341 visitId = int(tempExpRef.dataId["visit"]) 

342 except (KeyError, ValueError): 

343 visitId = i 

344 

345 calExpList = [] 

346 ccdIdList = [] 

347 dataIdList = [] 

348 

349 for calExpInd, calExpRef in enumerate(calexpRefList): 

350 self.log.info("Reading calexp %s of %s for Warp id=%s", calExpInd+1, len(calexpRefList), 

351 calExpRef.dataId) 

352 try: 

353 ccdId = calExpRef.get("ccdExposureId", immediate=True) 

354 except Exception: 

355 ccdId = calExpInd 

356 try: 

357 # We augment the dataRef here with the tract, which is harmless for loading things 

358 # like calexps that don't need the tract, and necessary for meas_mosaic outputs, 

359 # which do. 

360 calExpRef = calExpRef.butlerSubset.butler.dataRef(self.calexpType, 

361 dataId=calExpRef.dataId, 

362 tract=skyInfo.tractInfo.getId()) 

363 calExp = self.getCalibratedExposure(calExpRef, bgSubtracted=self.config.bgSubtracted) 

364 except Exception as e: 

365 self.log.warning("Calexp %s not found; skipping it: %s", calExpRef.dataId, e) 

366 continue 

367 

368 if self.config.doApplySkyCorr: 368 ↛ 369line 368 didn't jump to line 369, because the condition on line 368 was never true

369 self.applySkyCorr(calExpRef, calExp) 

370 

371 calExpList.append(calExp) 

372 ccdIdList.append(ccdId) 

373 dataIdList.append(calExpRef.dataId) 

374 

375 exps = self.run(calExpList, ccdIdList, skyInfo, visitId, dataIdList).exposures 

376 

377 if any(exps.values()): 

378 dataRefList.append(tempExpRef) 

379 else: 

380 self.log.warning("Warp %s could not be created", tempExpRef.dataId) 

381 

382 if self.config.doWrite: 382 ↛ 328line 382 didn't jump to line 328, because the condition on line 382 was never false

383 for (warpType, exposure) in exps.items(): # compatible w/ Py3 

384 if exposure is not None: 

385 self.log.info("Persisting %s", self.getTempExpDatasetName(warpType)) 

386 tempExpRef.put(exposure, self.getTempExpDatasetName(warpType)) 

387 

388 return dataRefList 

389 

390 @timeMethod 

391 def run(self, calExpList, ccdIdList, skyInfo, visitId=0, dataIdList=None, **kwargs): 

392 """Create a Warp from inputs 

393 

394 We iterate over the multiple calexps in a single exposure to construct 

395 the warp (previously called a coaddTempExp) of that exposure to the 

396 supplied tract/patch. 

397 

398 Pixels that receive no pixels are set to NAN; this is not correct 

399 (violates LSST algorithms group policy), but will be fixed up by 

400 interpolating after the coaddition. 

401 

402 @param calexpRefList: List of data references for calexps that (may) 

403 overlap the patch of interest 

404 @param skyInfo: Struct from CoaddBaseTask.getSkyInfo() with geometric 

405 information about the patch 

406 @param visitId: integer identifier for visit, for the table that will 

407 produce the CoaddPsf 

408 @return a pipeBase Struct containing: 

409 - exposures: a dictionary containing the warps requested: 

410 "direct": direct warp if config.makeDirect 

411 "psfMatched": PSF-matched warp if config.makePsfMatched 

412 """ 

413 warpTypeList = self.getWarpTypeList() 

414 

415 totGoodPix = {warpType: 0 for warpType in warpTypeList} 

416 didSetMetadata = {warpType: False for warpType in warpTypeList} 

417 coaddTempExps = {warpType: self._prepareEmptyExposure(skyInfo) for warpType in warpTypeList} 

418 inputRecorder = {warpType: self.inputRecorder.makeCoaddTempExpRecorder(visitId, len(calExpList)) 

419 for warpType in warpTypeList} 

420 

421 modelPsf = self.config.modelPsf.apply() if self.config.makePsfMatched else None 

422 if dataIdList is None: 422 ↛ 423line 422 didn't jump to line 423, because the condition on line 422 was never true

423 dataIdList = ccdIdList 

424 

425 for calExpInd, (calExp, ccdId, dataId) in enumerate(zip(calExpList, ccdIdList, dataIdList)): 

426 self.log.info("Processing calexp %d of %d for this Warp: id=%s", 

427 calExpInd+1, len(calExpList), dataId) 

428 

429 try: 

430 warpedAndMatched = self.warpAndPsfMatch.run(calExp, modelPsf=modelPsf, 

431 wcs=skyInfo.wcs, maxBBox=skyInfo.bbox, 

432 makeDirect=self.config.makeDirect, 

433 makePsfMatched=self.config.makePsfMatched) 

434 except Exception as e: 

435 self.log.warning("WarpAndPsfMatch failed for calexp %s; skipping it: %s", dataId, e) 

436 continue 

437 try: 

438 numGoodPix = {warpType: 0 for warpType in warpTypeList} 

439 for warpType in warpTypeList: 

440 exposure = warpedAndMatched.getDict()[warpType] 

441 if exposure is None: 

442 continue 

443 coaddTempExp = coaddTempExps[warpType] 

444 if didSetMetadata[warpType]: 

445 mimg = exposure.getMaskedImage() 

446 mimg *= (coaddTempExp.getPhotoCalib().getInstFluxAtZeroMagnitude() 

447 / exposure.getPhotoCalib().getInstFluxAtZeroMagnitude()) 

448 del mimg 

449 numGoodPix[warpType] = coaddUtils.copyGoodPixels( 

450 coaddTempExp.getMaskedImage(), exposure.getMaskedImage(), self.getBadPixelMask()) 

451 totGoodPix[warpType] += numGoodPix[warpType] 

452 self.log.debug("Calexp %s has %d good pixels in this patch (%.1f%%) for %s", 

453 dataId, numGoodPix[warpType], 

454 100.0*numGoodPix[warpType]/skyInfo.bbox.getArea(), warpType) 

455 if numGoodPix[warpType] > 0 and not didSetMetadata[warpType]: 

456 coaddTempExp.info.id = exposure.info.id 

457 coaddTempExp.setPhotoCalib(exposure.getPhotoCalib()) 

458 coaddTempExp.setFilterLabel(exposure.getFilterLabel()) 

459 coaddTempExp.getInfo().setVisitInfo(exposure.getInfo().getVisitInfo()) 

460 # PSF replaced with CoaddPsf after loop if and only if creating direct warp 

461 coaddTempExp.setPsf(exposure.getPsf()) 

462 didSetMetadata[warpType] = True 

463 

464 # Need inputRecorder for CoaddApCorrMap for both direct and PSF-matched 

465 inputRecorder[warpType].addCalExp(calExp, ccdId, numGoodPix[warpType]) 

466 

467 except Exception as e: 

468 self.log.warning("Error processing calexp %s; skipping it: %s", dataId, e) 

469 continue 

470 

471 for warpType in warpTypeList: 

472 self.log.info("%sWarp has %d good pixels (%.1f%%)", 

473 warpType, totGoodPix[warpType], 100.0*totGoodPix[warpType]/skyInfo.bbox.getArea()) 

474 

475 if totGoodPix[warpType] > 0 and didSetMetadata[warpType]: 

476 inputRecorder[warpType].finish(coaddTempExps[warpType], totGoodPix[warpType]) 

477 if warpType == "direct": 

478 coaddTempExps[warpType].setPsf( 

479 CoaddPsf(inputRecorder[warpType].coaddInputs.ccds, skyInfo.wcs, 

480 self.config.coaddPsf.makeControl())) 

481 else: 

482 if not self.config.doWriteEmptyWarps: 482 ↛ 471line 482 didn't jump to line 471, because the condition on line 482 was never false

483 # No good pixels. Exposure still empty 

484 coaddTempExps[warpType] = None 

485 # NoWorkFound is unnecessary as the downstream tasks will 

486 # adjust the quantum accordingly, and it prevents gen2 

487 # MakeCoaddTempExp from continuing to loop over visits. 

488 

489 result = pipeBase.Struct(exposures=coaddTempExps) 

490 return result 

491 

492 def getCalibratedExposure(self, dataRef, bgSubtracted): 

493 """Return one calibrated Exposure, possibly with an updated SkyWcs. 

494 

495 @param[in] dataRef a sensor-level data reference 

496 @param[in] bgSubtracted return calexp with background subtracted? If False get the 

497 calexp's background background model and add it to the calexp. 

498 @return calibrated exposure 

499 

500 @raises MissingExposureError If data for the exposure is not available. 

501 

502 If config.doApplyExternalPhotoCalib is `True`, the photometric calibration 

503 (`photoCalib`) is taken from `config.externalPhotoCalibName` via the 

504 `name_photoCalib` dataset. Otherwise, the photometric calibration is 

505 retrieved from the processed exposure. When 

506 `config.doApplyExternalSkyWcs` is `True`, the astrometric calibration 

507 is taken from `config.externalSkyWcsName` with the `name_wcs` dataset. 

508 Otherwise, the astrometric calibration is taken from the processed 

509 exposure. 

510 """ 

511 try: 

512 exposure = dataRef.get(self.calexpType, immediate=True) 

513 except dafPersist.NoResults as e: 

514 raise MissingExposureError('Exposure not found: %s ' % str(e)) from e 

515 

516 if not bgSubtracted: 516 ↛ 517line 516 didn't jump to line 517, because the condition on line 516 was never true

517 background = dataRef.get("calexpBackground", immediate=True) 

518 mi = exposure.getMaskedImage() 

519 mi += background.getImage() 

520 del mi 

521 

522 if self.config.doApplyExternalPhotoCalib: 522 ↛ 523line 522 didn't jump to line 523, because the condition on line 522 was never true

523 source = f"{self.config.externalPhotoCalibName}_photoCalib" 

524 self.log.debug("Applying external photoCalib to %s from %s", dataRef.dataId, source) 

525 photoCalib = dataRef.get(source) 

526 exposure.setPhotoCalib(photoCalib) 

527 else: 

528 photoCalib = exposure.getPhotoCalib() 

529 

530 if self.config.doApplyExternalSkyWcs: 530 ↛ 531line 530 didn't jump to line 531, because the condition on line 530 was never true

531 source = f"{self.config.externalSkyWcsName}_wcs" 

532 self.log.debug("Applying external skyWcs to %s from %s", dataRef.dataId, source) 

533 skyWcs = dataRef.get(source) 

534 exposure.setWcs(skyWcs) 

535 

536 exposure.maskedImage = photoCalib.calibrateImage(exposure.maskedImage, 

537 includeScaleUncertainty=self.config.includeCalibVar) 

538 exposure.maskedImage /= photoCalib.getCalibrationMean() 

539 # TODO: The images will have a calibration of 1.0 everywhere once RFC-545 is implemented. 

540 # exposure.setCalib(afwImage.Calib(1.0)) 

541 return exposure 

542 

543 @staticmethod 

544 def _prepareEmptyExposure(skyInfo): 

545 """Produce an empty exposure for a given patch""" 

546 exp = afwImage.ExposureF(skyInfo.bbox, skyInfo.wcs) 

547 exp.getMaskedImage().set(numpy.nan, afwImage.Mask 

548 .getPlaneBitMask("NO_DATA"), numpy.inf) 

549 return exp 

550 

551 def getWarpTypeList(self): 

552 """Return list of requested warp types per the config. 

553 """ 

554 warpTypeList = [] 

555 if self.config.makeDirect: 555 ↛ 557line 555 didn't jump to line 557, because the condition on line 555 was never false

556 warpTypeList.append("direct") 

557 if self.config.makePsfMatched: 557 ↛ 559line 557 didn't jump to line 559, because the condition on line 557 was never false

558 warpTypeList.append("psfMatched") 

559 return warpTypeList 

560 

561 def applySkyCorr(self, dataRef, calexp): 

562 """Apply correction to the sky background level 

563 

564 Sky corrections can be generated with the 'skyCorrection.py' 

565 executable in pipe_drivers. Because the sky model used by that 

566 code extends over the entire focal plane, this can produce 

567 better sky subtraction. 

568 

569 The calexp is updated in-place. 

570 

571 Parameters 

572 ---------- 

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

574 Data reference for calexp. 

575 calexp : `lsst.afw.image.Exposure` or `lsst.afw.image.MaskedImage` 

576 Calibrated exposure. 

577 """ 

578 bg = dataRef.get("skyCorr") 

579 self.log.debug("Applying sky correction to %s", dataRef.dataId) 

580 if isinstance(calexp, afwImage.Exposure): 

581 calexp = calexp.getMaskedImage() 

582 calexp -= bg.getImage() 

583 

584 

585class MakeWarpConnections(pipeBase.PipelineTaskConnections, 

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

587 defaultTemplates={"coaddName": "deep", 

588 "skyWcsName": "jointcal", 

589 "photoCalibName": "fgcm", 

590 "calexpType": ""}): 

591 calExpList = connectionTypes.Input( 

592 doc="Input exposures to be resampled and optionally PSF-matched onto a SkyMap projection/patch", 

593 name="{calexpType}calexp", 

594 storageClass="ExposureF", 

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

596 multiple=True, 

597 deferLoad=True, 

598 ) 

599 backgroundList = connectionTypes.Input( 

600 doc="Input backgrounds to be added back into the calexp if bgSubtracted=False", 

601 name="calexpBackground", 

602 storageClass="Background", 

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

604 multiple=True, 

605 ) 

606 skyCorrList = connectionTypes.Input( 

607 doc="Input Sky Correction to be subtracted from the calexp if doApplySkyCorr=True", 

608 name="skyCorr", 

609 storageClass="Background", 

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

611 multiple=True, 

612 ) 

613 skyMap = connectionTypes.Input( 

614 doc="Input definition of geometry/bbox and projection/wcs for warped exposures", 

615 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME, 

616 storageClass="SkyMap", 

617 dimensions=("skymap",), 

618 ) 

619 externalSkyWcsTractCatalog = connectionTypes.Input( 

620 doc=("Per-tract, per-visit wcs calibrations. These catalogs use the detector " 

621 "id for the catalog id, sorted on id for fast lookup."), 

622 name="{skyWcsName}SkyWcsCatalog", 

623 storageClass="ExposureCatalog", 

624 dimensions=("instrument", "visit", "tract"), 

625 ) 

626 externalSkyWcsGlobalCatalog = connectionTypes.Input( 

627 doc=("Per-visit wcs calibrations computed globally (with no tract information). " 

628 "These catalogs use the detector id for the catalog id, sorted on id for " 

629 "fast lookup."), 

630 name="{skyWcsName}SkyWcsCatalog", 

631 storageClass="ExposureCatalog", 

632 dimensions=("instrument", "visit"), 

633 ) 

634 externalPhotoCalibTractCatalog = connectionTypes.Input( 

635 doc=("Per-tract, per-visit photometric calibrations. These catalogs use the " 

636 "detector id for the catalog id, sorted on id for fast lookup."), 

637 name="{photoCalibName}PhotoCalibCatalog", 

638 storageClass="ExposureCatalog", 

639 dimensions=("instrument", "visit", "tract"), 

640 ) 

641 externalPhotoCalibGlobalCatalog = connectionTypes.Input( 

642 doc=("Per-visit photometric calibrations computed globally (with no tract " 

643 "information). These catalogs use the detector id for the catalog id, " 

644 "sorted on id for fast lookup."), 

645 name="{photoCalibName}PhotoCalibCatalog", 

646 storageClass="ExposureCatalog", 

647 dimensions=("instrument", "visit"), 

648 ) 

649 direct = connectionTypes.Output( 

650 doc=("Output direct warped exposure (previously called CoaddTempExp), produced by resampling ", 

651 "calexps onto the skyMap patch geometry."), 

652 name="{coaddName}Coadd_directWarp", 

653 storageClass="ExposureF", 

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

655 ) 

656 psfMatched = connectionTypes.Output( 

657 doc=("Output PSF-Matched warped exposure (previously called CoaddTempExp), produced by resampling ", 

658 "calexps onto the skyMap patch geometry and PSF-matching to a model PSF."), 

659 name="{coaddName}Coadd_psfMatchedWarp", 

660 storageClass="ExposureF", 

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

662 ) 

663 # TODO DM-28769, have selectImages subtask indicate which connections they need: 

664 wcsList = connectionTypes.Input( 

665 doc="WCSs of calexps used by SelectImages subtask to determine if the calexp overlaps the patch", 

666 name="{calexpType}calexp.wcs", 

667 storageClass="Wcs", 

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

669 multiple=True, 

670 ) 

671 bboxList = connectionTypes.Input( 

672 doc="BBoxes of calexps used by SelectImages subtask to determine if the calexp overlaps the patch", 

673 name="{calexpType}calexp.bbox", 

674 storageClass="Box2I", 

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

676 multiple=True, 

677 ) 

678 visitSummary = connectionTypes.Input( 

679 doc="Consolidated exposure metadata from ConsolidateVisitSummaryTask", 

680 name="{calexpType}visitSummary", 

681 storageClass="ExposureCatalog", 

682 dimensions=("instrument", "visit",), 

683 ) 

684 srcList = connectionTypes.Input( 

685 doc="Source catalogs used by PsfWcsSelectImages subtask to further select on PSF stability", 

686 name="src", 

687 storageClass="SourceCatalog", 

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

689 multiple=True, 

690 ) 

691 

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

693 super().__init__(config=config) 

694 if config.bgSubtracted: 

695 self.inputs.remove("backgroundList") 

696 if not config.doApplySkyCorr: 

697 self.inputs.remove("skyCorrList") 

698 if config.doApplyExternalSkyWcs: 

699 if config.useGlobalExternalSkyWcs: 

700 self.inputs.remove("externalSkyWcsTractCatalog") 

701 else: 

702 self.inputs.remove("externalSkyWcsGlobalCatalog") 

703 else: 

704 self.inputs.remove("externalSkyWcsTractCatalog") 

705 self.inputs.remove("externalSkyWcsGlobalCatalog") 

706 if config.doApplyExternalPhotoCalib: 

707 if config.useGlobalExternalPhotoCalib: 

708 self.inputs.remove("externalPhotoCalibTractCatalog") 

709 else: 

710 self.inputs.remove("externalPhotoCalibGlobalCatalog") 

711 else: 

712 self.inputs.remove("externalPhotoCalibTractCatalog") 

713 self.inputs.remove("externalPhotoCalibGlobalCatalog") 

714 if not config.makeDirect: 

715 self.outputs.remove("direct") 

716 if not config.makePsfMatched: 

717 self.outputs.remove("psfMatched") 

718 # TODO DM-28769: add connection per selectImages connections 

719 if config.select.target != lsst.pipe.tasks.selectImages.PsfWcsSelectImagesTask: 

720 self.inputs.remove("visitSummary") 

721 self.inputs.remove("srcList") 

722 elif not config.select.doLegacyStarSelectionComputation: 

723 # Remove backwards-compatibility connections. 

724 self.inputs.remove("srcList") 

725 

726 

727class MakeWarpConfig(pipeBase.PipelineTaskConfig, MakeCoaddTempExpConfig, 

728 pipelineConnections=MakeWarpConnections): 

729 

730 def validate(self): 

731 super().validate() 

732 

733 

734class MakeWarpTask(MakeCoaddTempExpTask): 

735 """Warp and optionally PSF-Match calexps onto an a common projection 

736 """ 

737 ConfigClass = MakeWarpConfig 

738 _DefaultName = "makeWarp" 

739 

740 @utils.inheritDoc(pipeBase.PipelineTask) 

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

742 """ 

743 Notes 

744 ---- 

745 Construct warps for requested warp type for single epoch 

746 

747 PipelineTask (Gen3) entry point to warp and optionally PSF-match 

748 calexps. This method is analogous to `runDataRef`. 

749 """ 

750 # Obtain the list of input detectors from calExpList. Sort them by 

751 # detector order (to ensure reproducibility). Then ensure all input 

752 # lists are in the same sorted detector order. 

753 detectorOrder = [ref.datasetRef.dataId['detector'] for ref in inputRefs.calExpList] 

754 detectorOrder.sort() 

755 inputRefs = reorderRefs(inputRefs, detectorOrder, dataIdKey='detector') 

756 

757 # Read in all inputs. 

758 inputs = butlerQC.get(inputRefs) 

759 

760 # Construct skyInfo expected by `run`. We remove the SkyMap itself 

761 # from the dictionary so we can pass it as kwargs later. 

762 skyMap = inputs.pop("skyMap") 

763 quantumDataId = butlerQC.quantum.dataId 

764 skyInfo = makeSkyInfo(skyMap, tractId=quantumDataId['tract'], patchId=quantumDataId['patch']) 

765 

766 # Construct list of input DataIds expected by `run` 

767 dataIdList = [ref.datasetRef.dataId for ref in inputRefs.calExpList] 

768 # Construct list of packed integer IDs expected by `run` 

769 ccdIdList = [dataId.pack("visit_detector") for dataId in dataIdList] 

770 

771 # Run the selector and filter out calexps that were not selected 

772 # primarily because they do not overlap the patch 

773 cornerPosList = lsst.geom.Box2D(skyInfo.bbox).getCorners() 

774 coordList = [skyInfo.wcs.pixelToSky(pos) for pos in cornerPosList] 

775 goodIndices = self.select.run(**inputs, coordList=coordList, dataIds=dataIdList) 

776 inputs = self.filterInputs(indices=goodIndices, inputs=inputs) 

777 

778 # Read from disk only the selected calexps 

779 inputs['calExpList'] = [ref.get() for ref in inputs['calExpList']] 

780 

781 # Extract integer visitId requested by `run` 

782 visits = [dataId['visit'] for dataId in dataIdList] 

783 visitId = visits[0] 

784 

785 if self.config.doApplyExternalSkyWcs: 

786 if self.config.useGlobalExternalSkyWcs: 

787 externalSkyWcsCatalog = inputs.pop("externalSkyWcsGlobalCatalog") 

788 else: 

789 externalSkyWcsCatalog = inputs.pop("externalSkyWcsTractCatalog") 

790 else: 

791 externalSkyWcsCatalog = None 

792 

793 if self.config.doApplyExternalPhotoCalib: 

794 if self.config.useGlobalExternalPhotoCalib: 

795 externalPhotoCalibCatalog = inputs.pop("externalPhotoCalibGlobalCatalog") 

796 else: 

797 externalPhotoCalibCatalog = inputs.pop("externalPhotoCalibTractCatalog") 

798 else: 

799 externalPhotoCalibCatalog = None 

800 

801 completeIndices = self.prepareCalibratedExposures(**inputs, 

802 externalSkyWcsCatalog=externalSkyWcsCatalog, 

803 externalPhotoCalibCatalog=externalPhotoCalibCatalog) 

804 # Redo the input selection with inputs with complete wcs/photocalib info. 

805 inputs = self.filterInputs(indices=completeIndices, inputs=inputs) 

806 

807 results = self.run(**inputs, visitId=visitId, 

808 ccdIdList=[ccdIdList[i] for i in goodIndices], 

809 dataIdList=[dataIdList[i] for i in goodIndices], 

810 skyInfo=skyInfo) 

811 if self.config.makeDirect and results.exposures["direct"] is not None: 

812 butlerQC.put(results.exposures["direct"], outputRefs.direct) 

813 if self.config.makePsfMatched and results.exposures["psfMatched"] is not None: 

814 butlerQC.put(results.exposures["psfMatched"], outputRefs.psfMatched) 

815 

816 def filterInputs(self, indices, inputs): 

817 """Return task inputs with their lists filtered by indices 

818 

819 Parameters 

820 ---------- 

821 indices : `list` of integers 

822 inputs : `dict` of `list` of input connections to be passed to run 

823 """ 

824 for key in inputs.keys(): 

825 # Only down-select on list inputs 

826 if isinstance(inputs[key], list): 

827 inputs[key] = [inputs[key][ind] for ind in indices] 

828 return inputs 

829 

830 def prepareCalibratedExposures(self, calExpList, backgroundList=None, skyCorrList=None, 

831 externalSkyWcsCatalog=None, externalPhotoCalibCatalog=None, 

832 **kwargs): 

833 """Calibrate and add backgrounds to input calExpList in place 

834 

835 Parameters 

836 ---------- 

837 calExpList : `list` of `lsst.afw.image.Exposure` 

838 Sequence of calexps to be modified in place 

839 backgroundList : `list` of `lsst.afw.math.backgroundList`, optional 

840 Sequence of backgrounds to be added back in if bgSubtracted=False 

841 skyCorrList : `list` of `lsst.afw.math.backgroundList`, optional 

842 Sequence of background corrections to be subtracted if doApplySkyCorr=True 

843 externalSkyWcsCatalog : `lsst.afw.table.ExposureCatalog`, optional 

844 Exposure catalog with external skyWcs to be applied 

845 if config.doApplyExternalSkyWcs=True. Catalog uses the detector id 

846 for the catalog id, sorted on id for fast lookup. 

847 externalPhotoCalibCatalog : `lsst.afw.table.ExposureCatalog`, optional 

848 Exposure catalog with external photoCalib to be applied 

849 if config.doApplyExternalPhotoCalib=True. Catalog uses the detector 

850 id for the catalog id, sorted on id for fast lookup. 

851 

852 Returns 

853 ------- 

854 indices : `list` [`int`] 

855 Indices of calExpList and friends that have valid photoCalib/skyWcs 

856 """ 

857 backgroundList = len(calExpList)*[None] if backgroundList is None else backgroundList 

858 skyCorrList = len(calExpList)*[None] if skyCorrList is None else skyCorrList 

859 

860 includeCalibVar = self.config.includeCalibVar 

861 

862 indices = [] 

863 for index, (calexp, background, skyCorr) in enumerate(zip(calExpList, 

864 backgroundList, 

865 skyCorrList)): 

866 if not self.config.bgSubtracted: 

867 calexp.maskedImage += background.getImage() 

868 

869 if externalSkyWcsCatalog is not None or externalPhotoCalibCatalog is not None: