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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 

23 

24import lsst.pex.config as pexConfig 

25import lsst.daf.persistence as dafPersist 

26import lsst.afw.image as afwImage 

27import lsst.coadd.utils as coaddUtils 

28import lsst.pipe.base as pipeBase 

29import lsst.pipe.base.connectionTypes as cT 

30import lsst.log as log 

31import lsst.utils as utils 

32from lsst.meas.algorithms import CoaddPsf, CoaddPsfConfig 

33from .coaddBase import CoaddBaseTask, makeSkyInfo 

34from .warpAndPsfMatch import WarpAndPsfMatchTask 

35from .coaddHelpers import groupPatchExposures, getGroupDataRef 

36 

37__all__ = ["MakeCoaddTempExpTask", "MakeWarpTask", "MakeWarpConfig"] 

38 

39 

40class MissingExposureError(Exception): 

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

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

43 distinguish bewteen that case, and other errors. 

44 """ 

45 pass 

46 

47 

48class MakeCoaddTempExpConfig(CoaddBaseTask.ConfigClass): 

49 """Config for MakeCoaddTempExpTask 

50 """ 

51 warpAndPsfMatch = pexConfig.ConfigurableField( 

52 target=WarpAndPsfMatchTask, 

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

54 ) 

55 doWrite = pexConfig.Field( 

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

57 dtype=bool, 

58 default=True, 

59 ) 

60 bgSubtracted = pexConfig.Field( 

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

62 dtype=bool, 

63 default=True, 

64 ) 

65 coaddPsf = pexConfig.ConfigField( 

66 doc="Configuration for CoaddPsf", 

67 dtype=CoaddPsfConfig, 

68 ) 

69 makeDirect = pexConfig.Field( 

70 doc="Make direct Warp/Coadds", 

71 dtype=bool, 

72 default=True, 

73 ) 

74 makePsfMatched = pexConfig.Field( 

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

76 dtype=bool, 

77 default=False, 

78 ) 

79 

80 doWriteEmptyWarps = pexConfig.Field( 

81 dtype=bool, 

82 default=False, 

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

84 ) 

85 

86 hasFakes = pexConfig.Field( 

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

88 dtype=bool, 

89 default=False, 

90 ) 

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

92 

93 def validate(self): 

94 CoaddBaseTask.ConfigClass.validate(self) 

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

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

97 if self.doPsfMatch: 

98 # Backwards compatibility. 

99 log.warn("Config doPsfMatch deprecated. Setting makePsfMatched=True and makeDirect=False") 

100 self.makePsfMatched = True 

101 self.makeDirect = False 

102 

103 def setDefaults(self): 

104 CoaddBaseTask.ConfigClass.setDefaults(self) 

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

106 

107## \addtogroup LSST_task_documentation 

108## \{ 

109## \page MakeCoaddTempExpTask 

110## \ref MakeCoaddTempExpTask_ "MakeCoaddTempExpTask" 

111## \copybrief MakeCoaddTempExpTask 

112## \} 

113 

114 

115class MakeCoaddTempExpTask(CoaddBaseTask): 

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

117 

118 @anchor MakeCoaddTempExpTask_ 

119 

120 @section pipe_tasks_makeCoaddTempExp_Contents Contents 

121 

122 - @ref pipe_tasks_makeCoaddTempExp_Purpose 

123 - @ref pipe_tasks_makeCoaddTempExp_Initialize 

124 - @ref pipe_tasks_makeCoaddTempExp_IO 

125 - @ref pipe_tasks_makeCoaddTempExp_Config 

126 - @ref pipe_tasks_makeCoaddTempExp_Debug 

127 - @ref pipe_tasks_makeCoaddTempExp_Example 

128 

129 @section pipe_tasks_makeCoaddTempExp_Purpose Description 

130 

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

132 performing the following operations: 

133 - Group calexps by visit/run 

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

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

136 on each visit 

137 

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

139 

140 @section pipe_tasks_makeCoaddTempExp_Initialize Task Initialization 

141 

142 @copydoc \_\_init\_\_ 

143 

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

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

146 output repositories. 

147 

148 @section pipe_tasks_makeCoaddTempExp_IO Invoking the Task 

149 

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

151 

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

153 to process. 

154 

155 @copydoc run 

156 

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

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

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

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

161 

162 @section pipe_tasks_makeCoaddTempExp_Config Configuration parameters 

163 

164 See @ref MakeCoaddTempExpConfig and parameters inherited from 

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

166 

167 @subsection pipe_tasks_MakeCoaddTempExp_psfMatching Guide to PSF-Matching Configs 

168 

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

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

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

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

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

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

175 

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

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

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

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

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

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

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

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

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

185 Problem: Explanation. *Solution* 

186 

187 *Troublshooting PSF-Matching Configuration:* 

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

189 For example:_ 

190 

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

192 

193 Note that increasing the kernel size also increases runtime. 

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

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

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

197 

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

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

200 

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

202 

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

204 

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

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

207 after convolving the PSF with the matching kernel. 

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

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

210 of pixels by which to pad the PSF: 

211 

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

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

214 

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

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

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

218 

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

220 

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

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

223 

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

225 # from default [0.7, 1.5, 3.0] 

226 

227 

228 @section pipe_tasks_makeCoaddTempExp_Debug Debug variables 

229 

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

231 

232 @section pipe_tasks_makeCoaddTempExp_Example A complete example of using MakeCoaddTempExpTask 

233 

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

235 into the larger Data Release Processing. 

236 Set up by running: 

237 

238 setup ci_hsc 

239 cd $CI_HSC_DIR 

240 # if not built already: 

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

242 

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

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

245 output respository with the desired SkyMap. The command, 

246 

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

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

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

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

251 --config doApplyExternalPhotoCalib=False doApplyExternalSkyWcs=False \ 

252 makePsfMatched=True modelPsf.defaultFwhm=11 

253 

254 writes a direct and PSF-Matched Warp to 

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

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

257 respectively. 

258 

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

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

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

262 

263 echo " 

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

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

266 

267 

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

269 """ 

270 ConfigClass = MakeCoaddTempExpConfig 

271 _DefaultName = "makeCoaddTempExp" 

272 

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

274 CoaddBaseTask.__init__(self, **kwargs) 

275 self.reuse = reuse 

276 self.makeSubtask("warpAndPsfMatch") 

277 if self.config.hasFakes: 277 ↛ 278line 277 didn't jump to line 278, because the condition on line 277 was never true

278 self.calexpType = "fakes_calexp" 

279 else: 

280 self.calexpType = "calexp" 

281 

282 @pipeBase.timeMethod 

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

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

285 

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

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

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

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

290 warps are requested. 

291 

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

293 

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

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

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

297 """ 

298 skyInfo = self.getSkyInfo(patchRef) 

299 

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

301 if self.config.makePsfMatched and not self.config.makeDirect: 301 ↛ 302line 301 didn't jump to line 302, because the condition on line 301 was never true

302 primaryWarpDataset = self.getTempExpDatasetName("psfMatched") 

303 else: 

304 primaryWarpDataset = self.getTempExpDatasetName("direct") 

305 

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

307 

308 if len(calExpRefList) == 0: 308 ↛ 309line 308 didn't jump to line 309, because the condition on line 308 was never true

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

310 return None 

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

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

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

314 

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

316 primaryWarpDataset) 

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

318 

319 dataRefList = [] 

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

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

322 tempExpTuple, groupData.keys) 

323 if self.reuse and tempExpRef.datasetExists(datasetType=primaryWarpDataset, write=True): 323 ↛ 324line 323 didn't jump to line 324, because the condition on line 323 was never true

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

325 dataRefList.append(tempExpRef) 

326 continue 

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

328 

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

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

331 # of the visit in the list. 

332 try: 

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

334 except (KeyError, ValueError): 

335 visitId = i 

336 

337 calExpList = [] 

338 ccdIdList = [] 

339 dataIdList = [] 

340 

341 for calExpInd, calExpRef in enumerate(calexpRefList): 

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

343 calExpRef.dataId) 

344 try: 

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

346 except Exception: 

347 ccdId = calExpInd 

348 try: 

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

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

351 # which do. 

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

353 dataId=calExpRef.dataId, 

354 tract=skyInfo.tractInfo.getId()) 

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

356 except Exception as e: 

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

358 continue 

359 

360 if self.config.doApplySkyCorr: 360 ↛ 361line 360 didn't jump to line 361, because the condition on line 360 was never true

361 self.applySkyCorr(calExpRef, calExp) 

362 

363 calExpList.append(calExp) 

364 ccdIdList.append(ccdId) 

365 dataIdList.append(calExpRef.dataId) 

366 

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

368 

369 if any(exps.values()): 

370 dataRefList.append(tempExpRef) 

371 else: 

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

373 

374 if self.config.doWrite: 374 ↛ 320line 374 didn't jump to line 320, because the condition on line 374 was never false

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

376 if exposure is not None: 

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

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

379 

380 return dataRefList 

381 

382 @pipeBase.timeMethod 

383 def run(self, calExpList, ccdIdList, skyInfo, visitId=0, dataIdList=None): 

384 """Create a Warp from inputs 

385 

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

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

388 supplied tract/patch. 

389 

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

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

392 interpolating after the coaddition. 

393 

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

395 overlap the patch of interest 

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

397 information about the patch 

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

399 produce the CoaddPsf 

400 @return a pipeBase Struct containing: 

401 - exposures: a dictionary containing the warps requested: 

402 "direct": direct warp if config.makeDirect 

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

404 """ 

405 warpTypeList = self.getWarpTypeList() 

406 

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

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

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

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

411 for warpType in warpTypeList} 

412 

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

414 if dataIdList is None: 414 ↛ 415line 414 didn't jump to line 415, because the condition on line 414 was never true

415 dataIdList = ccdIdList 

416 

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

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

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

420 

421 try: 

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

423 wcs=skyInfo.wcs, maxBBox=skyInfo.bbox, 

424 makeDirect=self.config.makeDirect, 

425 makePsfMatched=self.config.makePsfMatched) 

426 except Exception as e: 

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

428 continue 

429 try: 

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

431 for warpType in warpTypeList: 

432 exposure = warpedAndMatched.getDict()[warpType] 

433 if exposure is None: 

434 continue 

435 coaddTempExp = coaddTempExps[warpType] 

436 if didSetMetadata[warpType]: 

437 mimg = exposure.getMaskedImage() 

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

439 / exposure.getPhotoCalib().getInstFluxAtZeroMagnitude()) 

440 del mimg 

441 numGoodPix[warpType] = coaddUtils.copyGoodPixels( 

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

443 totGoodPix[warpType] += numGoodPix[warpType] 

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

445 dataId, numGoodPix[warpType], 

446 100.0*numGoodPix[warpType]/skyInfo.bbox.getArea(), warpType) 

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

448 coaddTempExp.setPhotoCalib(exposure.getPhotoCalib()) 

449 coaddTempExp.setFilter(exposure.getFilter()) 

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

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

452 coaddTempExp.setPsf(exposure.getPsf()) 

453 didSetMetadata[warpType] = True 

454 

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

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

457 

458 except Exception as e: 

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

460 continue 

461 

462 for warpType in warpTypeList: 

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

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

465 

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

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

468 if warpType == "direct": 

469 coaddTempExps[warpType].setPsf( 

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

471 self.config.coaddPsf.makeControl())) 

472 else: 

473 if not self.config.doWriteEmptyWarps: 473 ↛ 462line 473 didn't jump to line 462, because the condition on line 473 was never false

474 # No good pixels. Exposure still empty 

475 coaddTempExps[warpType] = None 

476 

477 result = pipeBase.Struct(exposures=coaddTempExps) 

478 return result 

479 

480 def getCalibratedExposure(self, dataRef, bgSubtracted): 

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

482 

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

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

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

486 @return calibrated exposure 

487 

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

489 

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

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

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

493 retrieved from the processed exposure. When 

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

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

496 Otherwise, the astrometric calibration is taken from the processed 

497 exposure. 

498 """ 

499 try: 

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

501 except dafPersist.NoResults as e: 

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

503 

504 if not bgSubtracted: 504 ↛ 505line 504 didn't jump to line 505, because the condition on line 504 was never true

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

506 mi = exposure.getMaskedImage() 

507 mi += background.getImage() 

508 del mi 

509 

510 if self.config.doApplyExternalPhotoCalib: 

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

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

513 photoCalib = dataRef.get(source) 

514 exposure.setPhotoCalib(photoCalib) 

515 else: 

516 photoCalib = exposure.getPhotoCalib() 

517 

518 if self.config.doApplyExternalSkyWcs: 

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

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

521 skyWcs = dataRef.get(source) 

522 exposure.setWcs(skyWcs) 

523 

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

525 includeScaleUncertainty=self.config.includeCalibVar) 

526 exposure.maskedImage /= photoCalib.getCalibrationMean() 

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

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

529 return exposure 

530 

531 @staticmethod 

532 def _prepareEmptyExposure(skyInfo): 

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

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

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

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

537 return exp 

538 

539 def getWarpTypeList(self): 

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

541 """ 

542 warpTypeList = [] 

543 if self.config.makeDirect: 543 ↛ 545line 543 didn't jump to line 545, because the condition on line 543 was never false

544 warpTypeList.append("direct") 

545 if self.config.makePsfMatched: 545 ↛ 547line 545 didn't jump to line 547, because the condition on line 545 was never false

546 warpTypeList.append("psfMatched") 

547 return warpTypeList 

548 

549 def applySkyCorr(self, dataRef, calexp): 

550 """Apply correction to the sky background level 

551 

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

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

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

555 better sky subtraction. 

556 

557 The calexp is updated in-place. 

558 

559 Parameters 

560 ---------- 

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

562 Data reference for calexp. 

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

564 Calibrated exposure. 

565 """ 

566 bg = dataRef.get("skyCorr") 

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

568 if isinstance(calexp, afwImage.Exposure): 

569 calexp = calexp.getMaskedImage() 

570 calexp -= bg.getImage() 

571 

572 

573class MakeWarpConnections(pipeBase.PipelineTaskConnections, 

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

575 defaultTemplates={"coaddName": "deep"}): 

576 calExpList = cT.Input( 

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

578 name="calexp", 

579 storageClass="ExposureF", 

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

581 multiple=True, 

582 ) 

583 backgroundList = cT.Input( 

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

585 name="calexpBackground", 

586 storageClass="Background", 

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

588 multiple=True, 

589 ) 

590 skyCorrList = cT.Input( 

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

592 name="skyCorr", 

593 storageClass="Background", 

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

595 multiple=True, 

596 ) 

597 skyMap = cT.Input( 

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

599 name="{coaddName}Coadd_skyMap", 

600 storageClass="SkyMap", 

601 dimensions=("skymap",), 

602 ) 

603 direct = cT.Output( 

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

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

606 name="{coaddName}Coadd_directWarp", 

607 storageClass="ExposureF", 

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

609 ) 

610 psfMatched = cT.Output( 

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

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

613 name="{coaddName}Coadd_psfMatchedWarp", 

614 storageClass="ExposureF", 

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

616 ) 

617 

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

619 super().__init__(config=config) 

620 if config.bgSubtracted: 

621 self.inputs.remove("backgroundList") 

622 if not config.doApplySkyCorr: 

623 self.inputs.remove("skyCorrList") 

624 if not config.makeDirect: 

625 self.outputs.remove("direct") 

626 if not config.makePsfMatched: 

627 self.outputs.remove("psfMatched") 

628 

629 

630class MakeWarpConfig(pipeBase.PipelineTaskConfig, MakeCoaddTempExpConfig, 

631 pipelineConnections=MakeWarpConnections): 

632 

633 def validate(self): 

634 super().validate() 

635 # TODO: Remove this constraint after DM-17062 

636 if self.doApplyExternalPhotoCalib: 

637 raise RuntimeError("Gen3 MakeWarpTask cannot apply external PhotoCalib results. " 

638 "Please set doApplyExternalPhotoCalib=False.") 

639 if self.doApplyExternalSkyWcs: 

640 raise RuntimeError("Gen3 MakeWarpTask cannot apply external SkyWcs results. " 

641 "Please set doApplyExternalSkyWcs=False.") 

642 

643 

644class MakeWarpTask(MakeCoaddTempExpTask, pipeBase.PipelineTask): 

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

646 

647 First Draft of a Gen3 compatible MakeWarpTask which 

648 currently does not handle doApplyExternalPhotoCalib=True or 

649 doApplyExternalSkyWcs=True. 

650 """ 

651 ConfigClass = MakeWarpConfig 

652 _DefaultName = "makeWarp" 

653 

654 @utils.inheritDoc(pipeBase.PipelineTask) 

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

656 """ 

657 Notes 

658 ---- 

659 Construct warps for requested warp type for single epoch 

660 

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

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

663 """ 

664 # Read in all inputs. 

665 inputs = butlerQC.get(inputRefs) 

666 

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

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

669 skyMap = inputs.pop("skyMap") 

670 quantumDataId = butlerQC.quantum.dataId 

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

672 

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

674 dataIdList = [ref.dataId for ref in inputRefs.calExpList] 

675 

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

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

678 

679 # Extract integer visitId requested by `run` 

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

681 assert(all(visits[0] == visit for visit in visits)) 

682 visitId = visits[0] 

683 

684 self.prepareCalibratedExposures(**inputs) 

685 results = self.run(**inputs, visitId=visitId, ccdIdList=ccdIdList, dataIdList=dataIdList, 

686 skyInfo=skyInfo) 

687 if self.config.makeDirect: 

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

689 if self.config.makePsfMatched: 

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

691 

692 def prepareCalibratedExposures(self, calExpList, backgroundList=None, skyCorrList=None): 

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

694 

695 TODO DM-17062: apply jointcal/meas_mosaic here 

696 

697 Parameters 

698 ---------- 

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

700 Sequence of calexps to be modified in place 

701 backgroundList : `list` of `lsst.afw.math.backgroundList` 

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

703 skyCorrList : `list` of `lsst.afw.math.backgroundList` 

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

705 """ 

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

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

708 for calexp, background, skyCorr in zip(calExpList, backgroundList, skyCorrList): 

709 mi = calexp.maskedImage 

710 if not self.config.bgSubtracted: 

711 mi += background.getImage() 

712 if self.config.doApplySkyCorr: 

713 mi -= skyCorr.getImage()