Coverage for python/lsst/pipe/tasks/makeCoaddTempExp.py : 46%

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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
23import logging
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 .warpAndPsfMatch import WarpAndPsfMatchTask
38from .coaddHelpers import groupPatchExposures, getGroupDataRef
39from collections.abc import Iterable
41__all__ = ["MakeCoaddTempExpTask", "MakeWarpTask", "MakeWarpConfig"]
43log = logging.getLogger(__name__.partition(".")[2])
46class MissingExposureError(Exception):
47 """Raised when data cannot be retrieved for an exposure.
48 When processing patches, sometimes one exposure is missing; this lets us
49 distinguish bewteen that case, and other errors.
50 """
51 pass
54class MakeCoaddTempExpConfig(CoaddBaseTask.ConfigClass):
55 """Config for MakeCoaddTempExpTask
56 """
57 warpAndPsfMatch = pexConfig.ConfigurableField(
58 target=WarpAndPsfMatchTask,
59 doc="Task to warp and PSF-match calexp",
60 )
61 doWrite = pexConfig.Field(
62 doc="persist <coaddName>Coadd_<warpType>Warp",
63 dtype=bool,
64 default=True,
65 )
66 bgSubtracted = pexConfig.Field(
67 doc="Work with a background subtracted calexp?",
68 dtype=bool,
69 default=True,
70 )
71 coaddPsf = pexConfig.ConfigField(
72 doc="Configuration for CoaddPsf",
73 dtype=CoaddPsfConfig,
74 )
75 makeDirect = pexConfig.Field(
76 doc="Make direct Warp/Coadds",
77 dtype=bool,
78 default=True,
79 )
80 makePsfMatched = pexConfig.Field(
81 doc="Make Psf-Matched Warp/Coadd?",
82 dtype=bool,
83 default=False,
84 )
86 doWriteEmptyWarps = pexConfig.Field(
87 dtype=bool,
88 default=False,
89 doc="Write out warps even if they are empty"
90 )
92 hasFakes = pexConfig.Field(
93 doc="Should be set to True if fake sources have been inserted into the input data.",
94 dtype=bool,
95 default=False,
96 )
97 doApplySkyCorr = pexConfig.Field(dtype=bool, default=False, doc="Apply sky correction?")
99 def validate(self):
100 CoaddBaseTask.ConfigClass.validate(self)
101 if not self.makePsfMatched and not self.makeDirect:
102 raise RuntimeError("At least one of config.makePsfMatched and config.makeDirect must be True")
103 if self.doPsfMatch:
104 # Backwards compatibility.
105 log.warning("Config doPsfMatch deprecated. Setting makePsfMatched=True and makeDirect=False")
106 self.makePsfMatched = True
107 self.makeDirect = False
109 def setDefaults(self):
110 CoaddBaseTask.ConfigClass.setDefaults(self)
111 self.warpAndPsfMatch.psfMatch.kernel.active.kernelSize = self.matchingKernelSize
113## \addtogroup LSST_task_documentation
114## \{
115## \page MakeCoaddTempExpTask
116## \ref MakeCoaddTempExpTask_ "MakeCoaddTempExpTask"
117## \copybrief MakeCoaddTempExpTask
118## \}
121class MakeCoaddTempExpTask(CoaddBaseTask):
122 r"""!Warp and optionally PSF-Match calexps onto an a common projection.
124 @anchor MakeCoaddTempExpTask_
126 @section pipe_tasks_makeCoaddTempExp_Contents Contents
128 - @ref pipe_tasks_makeCoaddTempExp_Purpose
129 - @ref pipe_tasks_makeCoaddTempExp_Initialize
130 - @ref pipe_tasks_makeCoaddTempExp_IO
131 - @ref pipe_tasks_makeCoaddTempExp_Config
132 - @ref pipe_tasks_makeCoaddTempExp_Debug
133 - @ref pipe_tasks_makeCoaddTempExp_Example
135 @section pipe_tasks_makeCoaddTempExp_Purpose Description
137 Warp and optionally PSF-Match calexps onto a common projection, by
138 performing the following operations:
139 - Group calexps by visit/run
140 - For each visit, generate a Warp by calling method @ref makeTempExp.
141 makeTempExp loops over the visit's calexps calling @ref WarpAndPsfMatch
142 on each visit
144 The result is a `directWarp` (and/or optionally a `psfMatchedWarp`).
146 @section pipe_tasks_makeCoaddTempExp_Initialize Task Initialization
148 @copydoc \_\_init\_\_
150 This task has one special keyword argument: passing reuse=True will cause
151 the task to skip the creation of warps that are already present in the
152 output repositories.
154 @section pipe_tasks_makeCoaddTempExp_IO Invoking the Task
156 This task is primarily designed to be run from the command line.
158 The main method is `runDataRef`, which takes a single butler data reference for the patch(es)
159 to process.
161 @copydoc run
163 WarpType identifies the types of convolutions applied to Warps (previously CoaddTempExps).
164 Only two types are available: direct (for regular Warps/Coadds) and psfMatched
165 (for Warps/Coadds with homogenized PSFs). We expect to add a third type, likelihood,
166 for generating likelihood Coadds with Warps that have been correlated with their own PSF.
168 @section pipe_tasks_makeCoaddTempExp_Config Configuration parameters
170 See @ref MakeCoaddTempExpConfig and parameters inherited from
171 @link lsst.pipe.tasks.coaddBase.CoaddBaseConfig CoaddBaseConfig @endlink
173 @subsection pipe_tasks_MakeCoaddTempExp_psfMatching Guide to PSF-Matching Configs
175 To make `psfMatchedWarps`, select `config.makePsfMatched=True`. The subtask
176 @link lsst.ip.diffim.modelPsfMatch.ModelPsfMatchTask ModelPsfMatchTask @endlink
177 is responsible for the PSF-Matching, and its config is accessed via `config.warpAndPsfMatch.psfMatch`.
178 The optimal configuration depends on aspects of dataset: the pixel scale, average PSF FWHM and
179 dimensions of the PSF kernel. These configs include the requested model PSF, the matching kernel size,
180 padding of the science PSF thumbnail and spatial sampling frequency of the PSF.
182 *Config Guidelines*: The user must specify the size of the model PSF to which to match by setting
183 `config.modelPsf.defaultFwhm` in units of pixels. The appropriate values depends on science case.
184 In general, for a set of input images, this config should equal the FWHM of the visit
185 with the worst seeing. The smallest it should be set to is the median FWHM. The defaults
186 of the other config options offer a reasonable starting point.
187 The following list presents the most common problems that arise from a misconfigured
188 @link lsst.ip.diffim.modelPsfMatch.ModelPsfMatchTask ModelPsfMatchTask @endlink
189 and corresponding solutions. All assume the default Alard-Lupton kernel, with configs accessed via
190 ```config.warpAndPsfMatch.psfMatch.kernel['AL']```. Each item in the list is formatted as:
191 Problem: Explanation. *Solution*
193 *Troublshooting PSF-Matching Configuration:*
194 - Matched PSFs look boxy: The matching kernel is too small. _Increase the matching kernel size.
195 For example:_
197 config.warpAndPsfMatch.psfMatch.kernel['AL'].kernelSize=27 # default 21
199 Note that increasing the kernel size also increases runtime.
200 - Matched PSFs look ugly (dipoles, quadropoles, donuts): unable to find good solution
201 for matching kernel. _Provide the matcher with more data by either increasing
202 the spatial sampling by decreasing the spatial cell size,_
204 config.warpAndPsfMatch.psfMatch.kernel['AL'].sizeCellX = 64 # default 128
205 config.warpAndPsfMatch.psfMatch.kernel['AL'].sizeCellY = 64 # default 128
207 _or increasing the padding around the Science PSF, for example:_
209 config.warpAndPsfMatch.psfMatch.autoPadPsfTo=1.6 # default 1.4
211 Increasing `autoPadPsfTo` increases the minimum ratio of input PSF dimensions to the
212 matching kernel dimensions, thus increasing the number of pixels available to fit
213 after convolving the PSF with the matching kernel.
214 Optionally, for debugging the effects of padding, the level of padding may be manually
215 controlled by setting turning off the automatic padding and setting the number
216 of pixels by which to pad the PSF:
218 config.warpAndPsfMatch.psfMatch.doAutoPadPsf = False # default True
219 config.warpAndPsfMatch.psfMatch.padPsfBy = 6 # pixels. default 0
221 - Deconvolution: Matching a large PSF to a smaller PSF produces
222 a telltale noise pattern which looks like ripples or a brain.
223 _Increase the size of the requested model PSF. For example:_
225 config.modelPsf.defaultFwhm = 11 # Gaussian sigma in units of pixels.
227 - High frequency (sometimes checkered) noise: The matching basis functions are too small.
228 _Increase the width of the Gaussian basis functions. For example:_
230 config.warpAndPsfMatch.psfMatch.kernel['AL'].alardSigGauss=[1.5, 3.0, 6.0]
231 # from default [0.7, 1.5, 3.0]
234 @section pipe_tasks_makeCoaddTempExp_Debug Debug variables
236 MakeCoaddTempExpTask has no debug output, but its subtasks do.
238 @section pipe_tasks_makeCoaddTempExp_Example A complete example of using MakeCoaddTempExpTask
240 This example uses the package ci_hsc to show how MakeCoaddTempExp fits
241 into the larger Data Release Processing.
242 Set up by running:
244 setup ci_hsc
245 cd $CI_HSC_DIR
246 # if not built already:
247 python $(which scons) # this will take a while
249 The following assumes that `processCcd.py` and `makeSkyMap.py` have previously been run
250 (e.g. by building `ci_hsc` above) to generate a repository of calexps and an
251 output respository with the desired SkyMap. The command,
253 makeCoaddTempExp.py $CI_HSC_DIR/DATA --rerun ci_hsc \
254 --id patch=5,4 tract=0 filter=HSC-I \
255 --selectId visit=903988 ccd=16 --selectId visit=903988 ccd=17 \
256 --selectId visit=903988 ccd=23 --selectId visit=903988 ccd=24 \
257 --config doApplyExternalPhotoCalib=False doApplyExternalSkyWcs=False \
258 makePsfMatched=True modelPsf.defaultFwhm=11
260 writes a direct and PSF-Matched Warp to
261 - `$CI_HSC_DIR/DATA/rerun/ci_hsc/deepCoadd/HSC-I/0/5,4/warp-HSC-I-0-5,4-903988.fits` and
262 - `$CI_HSC_DIR/DATA/rerun/ci_hsc/deepCoadd/HSC-I/0/5,4/psfMatchedWarp-HSC-I-0-5,4-903988.fits`
263 respectively.
265 @note PSF-Matching in this particular dataset would benefit from adding
266 `--configfile ./matchingConfig.py` to
267 the command line arguments where `matchingConfig.py` is defined by:
269 echo "
270 config.warpAndPsfMatch.psfMatch.kernel['AL'].kernelSize=27
271 config.warpAndPsfMatch.psfMatch.kernel['AL'].alardSigGauss=[1.5, 3.0, 6.0]" > matchingConfig.py
274 Add the option `--help` to see more options.
275 """
276 ConfigClass = MakeCoaddTempExpConfig
277 _DefaultName = "makeCoaddTempExp"
279 def __init__(self, reuse=False, **kwargs):
280 CoaddBaseTask.__init__(self, **kwargs)
281 self.reuse = reuse
282 self.makeSubtask("warpAndPsfMatch")
283 if self.config.hasFakes: 283 ↛ 284line 283 didn't jump to line 284, because the condition on line 283 was never true
284 self.calexpType = "fakes_calexp"
285 else:
286 self.calexpType = "calexp"
288 @timeMethod
289 def runDataRef(self, patchRef, selectDataList=[]):
290 """!Produce <coaddName>Coadd_<warpType>Warp images by warping and optionally PSF-matching.
292 @param[in] patchRef: data reference for sky map patch. Must include keys "tract", "patch",
293 plus the camera-specific filter key (e.g. "filter" or "band")
294 @return: dataRefList: a list of data references for the new <coaddName>Coadd_directWarps
295 if direct or both warp types are requested and <coaddName>Coadd_psfMatchedWarps if only psfMatched
296 warps are requested.
298 @warning: this task assumes that all exposures in a warp (coaddTempExp) have the same filter.
300 @warning: this task sets the PhotoCalib of the coaddTempExp to the PhotoCalib of the first calexp
301 with any good pixels in the patch. For a mosaic camera the resulting PhotoCalib should be ignored
302 (assembleCoadd should determine zeropoint scaling without referring to it).
303 """
304 skyInfo = self.getSkyInfo(patchRef)
306 # DataRefs to return are of type *_directWarp unless only *_psfMatchedWarp requested
307 if self.config.makePsfMatched and not self.config.makeDirect: 307 ↛ 308line 307 didn't jump to line 308, because the condition on line 307 was never true
308 primaryWarpDataset = self.getTempExpDatasetName("psfMatched")
309 else:
310 primaryWarpDataset = self.getTempExpDatasetName("direct")
312 calExpRefList = self.selectExposures(patchRef, skyInfo, selectDataList=selectDataList)
314 if len(calExpRefList) == 0: 314 ↛ 315line 314 didn't jump to line 315, because the condition on line 314 was never true
315 self.log.warning("No exposures to coadd for patch %s", patchRef.dataId)
316 return None
317 self.log.info("Selected %d calexps for patch %s", len(calExpRefList), patchRef.dataId)
318 calExpRefList = [calExpRef for calExpRef in calExpRefList if calExpRef.datasetExists(self.calexpType)]
319 self.log.info("Processing %d existing calexps for patch %s", len(calExpRefList), patchRef.dataId)
321 groupData = groupPatchExposures(patchRef, calExpRefList, self.getCoaddDatasetName(),
322 primaryWarpDataset)
323 self.log.info("Processing %d warp exposures for patch %s", len(groupData.groups), patchRef.dataId)
325 dataRefList = []
326 for i, (tempExpTuple, calexpRefList) in enumerate(groupData.groups.items()):
327 tempExpRef = getGroupDataRef(patchRef.getButler(), primaryWarpDataset,
328 tempExpTuple, groupData.keys)
329 if self.reuse and tempExpRef.datasetExists(datasetType=primaryWarpDataset, write=True): 329 ↛ 330line 329 didn't jump to line 330, because the condition on line 329 was never true
330 self.log.info("Skipping makeCoaddTempExp for %s; output already exists.", tempExpRef.dataId)
331 dataRefList.append(tempExpRef)
332 continue
333 self.log.info("Processing Warp %d/%d: id=%s", i, len(groupData.groups), tempExpRef.dataId)
335 # TODO: mappers should define a way to go from the "grouping keys" to a numeric ID (#2776).
336 # For now, we try to get a long integer "visit" key, and if we can't, we just use the index
337 # of the visit in the list.
338 try:
339 visitId = int(tempExpRef.dataId["visit"])
340 except (KeyError, ValueError):
341 visitId = i
343 calExpList = []
344 ccdIdList = []
345 dataIdList = []
347 for calExpInd, calExpRef in enumerate(calexpRefList):
348 self.log.info("Reading calexp %s of %s for Warp id=%s", calExpInd+1, len(calexpRefList),
349 calExpRef.dataId)
350 try:
351 ccdId = calExpRef.get("ccdExposureId", immediate=True)
352 except Exception:
353 ccdId = calExpInd
354 try:
355 # We augment the dataRef here with the tract, which is harmless for loading things
356 # like calexps that don't need the tract, and necessary for meas_mosaic outputs,
357 # which do.
358 calExpRef = calExpRef.butlerSubset.butler.dataRef(self.calexpType,
359 dataId=calExpRef.dataId,
360 tract=skyInfo.tractInfo.getId())
361 calExp = self.getCalibratedExposure(calExpRef, bgSubtracted=self.config.bgSubtracted)
362 except Exception as e:
363 self.log.warning("Calexp %s not found; skipping it: %s", calExpRef.dataId, e)
364 continue
366 if self.config.doApplySkyCorr: 366 ↛ 367line 366 didn't jump to line 367, because the condition on line 366 was never true
367 self.applySkyCorr(calExpRef, calExp)
369 calExpList.append(calExp)
370 ccdIdList.append(ccdId)
371 dataIdList.append(calExpRef.dataId)
373 exps = self.run(calExpList, ccdIdList, skyInfo, visitId, dataIdList).exposures
375 if any(exps.values()):
376 dataRefList.append(tempExpRef)
377 else:
378 self.log.warning("Warp %s could not be created", tempExpRef.dataId)
380 if self.config.doWrite: 380 ↛ 326line 380 didn't jump to line 326, because the condition on line 380 was never false
381 for (warpType, exposure) in exps.items(): # compatible w/ Py3
382 if exposure is not None:
383 self.log.info("Persisting %s", self.getTempExpDatasetName(warpType))
384 tempExpRef.put(exposure, self.getTempExpDatasetName(warpType))
386 return dataRefList
388 @timeMethod
389 def run(self, calExpList, ccdIdList, skyInfo, visitId=0, dataIdList=None, **kwargs):
390 """Create a Warp from inputs
392 We iterate over the multiple calexps in a single exposure to construct
393 the warp (previously called a coaddTempExp) of that exposure to the
394 supplied tract/patch.
396 Pixels that receive no pixels are set to NAN; this is not correct
397 (violates LSST algorithms group policy), but will be fixed up by
398 interpolating after the coaddition.
400 @param calexpRefList: List of data references for calexps that (may)
401 overlap the patch of interest
402 @param skyInfo: Struct from CoaddBaseTask.getSkyInfo() with geometric
403 information about the patch
404 @param visitId: integer identifier for visit, for the table that will
405 produce the CoaddPsf
406 @return a pipeBase Struct containing:
407 - exposures: a dictionary containing the warps requested:
408 "direct": direct warp if config.makeDirect
409 "psfMatched": PSF-matched warp if config.makePsfMatched
410 """
411 warpTypeList = self.getWarpTypeList()
413 totGoodPix = {warpType: 0 for warpType in warpTypeList}
414 didSetMetadata = {warpType: False for warpType in warpTypeList}
415 coaddTempExps = {warpType: self._prepareEmptyExposure(skyInfo) for warpType in warpTypeList}
416 inputRecorder = {warpType: self.inputRecorder.makeCoaddTempExpRecorder(visitId, len(calExpList))
417 for warpType in warpTypeList}
419 modelPsf = self.config.modelPsf.apply() if self.config.makePsfMatched else None
420 if dataIdList is None: 420 ↛ 421line 420 didn't jump to line 421, because the condition on line 420 was never true
421 dataIdList = ccdIdList
423 for calExpInd, (calExp, ccdId, dataId) in enumerate(zip(calExpList, ccdIdList, dataIdList)):
424 self.log.info("Processing calexp %d of %d for this Warp: id=%s",
425 calExpInd+1, len(calExpList), dataId)
427 try:
428 warpedAndMatched = self.warpAndPsfMatch.run(calExp, modelPsf=modelPsf,
429 wcs=skyInfo.wcs, maxBBox=skyInfo.bbox,
430 makeDirect=self.config.makeDirect,
431 makePsfMatched=self.config.makePsfMatched)
432 except Exception as e:
433 self.log.warning("WarpAndPsfMatch failed for calexp %s; skipping it: %s", dataId, e)
434 continue
435 try:
436 numGoodPix = {warpType: 0 for warpType in warpTypeList}
437 for warpType in warpTypeList:
438 exposure = warpedAndMatched.getDict()[warpType]
439 if exposure is None:
440 continue
441 coaddTempExp = coaddTempExps[warpType]
442 if didSetMetadata[warpType]:
443 mimg = exposure.getMaskedImage()
444 mimg *= (coaddTempExp.getPhotoCalib().getInstFluxAtZeroMagnitude()
445 / exposure.getPhotoCalib().getInstFluxAtZeroMagnitude())
446 del mimg
447 numGoodPix[warpType] = coaddUtils.copyGoodPixels(
448 coaddTempExp.getMaskedImage(), exposure.getMaskedImage(), self.getBadPixelMask())
449 totGoodPix[warpType] += numGoodPix[warpType]
450 self.log.debug("Calexp %s has %d good pixels in this patch (%.1f%%) for %s",
451 dataId, numGoodPix[warpType],
452 100.0*numGoodPix[warpType]/skyInfo.bbox.getArea(), warpType)
453 if numGoodPix[warpType] > 0 and not didSetMetadata[warpType]:
454 coaddTempExp.setPhotoCalib(exposure.getPhotoCalib())
455 coaddTempExp.setFilterLabel(exposure.getFilterLabel())
456 coaddTempExp.getInfo().setVisitInfo(exposure.getInfo().getVisitInfo())
457 # PSF replaced with CoaddPsf after loop if and only if creating direct warp
458 coaddTempExp.setPsf(exposure.getPsf())
459 didSetMetadata[warpType] = True
461 # Need inputRecorder for CoaddApCorrMap for both direct and PSF-matched
462 inputRecorder[warpType].addCalExp(calExp, ccdId, numGoodPix[warpType])
464 except Exception as e:
465 self.log.warning("Error processing calexp %s; skipping it: %s", dataId, e)
466 continue
468 for warpType in warpTypeList:
469 self.log.info("%sWarp has %d good pixels (%.1f%%)",
470 warpType, totGoodPix[warpType], 100.0*totGoodPix[warpType]/skyInfo.bbox.getArea())
472 if totGoodPix[warpType] > 0 and didSetMetadata[warpType]:
473 inputRecorder[warpType].finish(coaddTempExps[warpType], totGoodPix[warpType])
474 if warpType == "direct":
475 coaddTempExps[warpType].setPsf(
476 CoaddPsf(inputRecorder[warpType].coaddInputs.ccds, skyInfo.wcs,
477 self.config.coaddPsf.makeControl()))
478 else:
479 if not self.config.doWriteEmptyWarps: 479 ↛ 468line 479 didn't jump to line 468, because the condition on line 479 was never false
480 # No good pixels. Exposure still empty
481 coaddTempExps[warpType] = None
482 # NoWorkFound is unnecessary as the downstream tasks will
483 # adjust the quantum accordingly, and it prevents gen2
484 # MakeCoaddTempExp from continuing to loop over visits.
486 result = pipeBase.Struct(exposures=coaddTempExps)
487 return result
489 def getCalibratedExposure(self, dataRef, bgSubtracted):
490 """Return one calibrated Exposure, possibly with an updated SkyWcs.
492 @param[in] dataRef a sensor-level data reference
493 @param[in] bgSubtracted return calexp with background subtracted? If False get the
494 calexp's background background model and add it to the calexp.
495 @return calibrated exposure
497 @raises MissingExposureError If data for the exposure is not available.
499 If config.doApplyExternalPhotoCalib is `True`, the photometric calibration
500 (`photoCalib`) is taken from `config.externalPhotoCalibName` via the
501 `name_photoCalib` dataset. Otherwise, the photometric calibration is
502 retrieved from the processed exposure. When
503 `config.doApplyExternalSkyWcs` is `True`, the astrometric calibration
504 is taken from `config.externalSkyWcsName` with the `name_wcs` dataset.
505 Otherwise, the astrometric calibration is taken from the processed
506 exposure.
507 """
508 try:
509 exposure = dataRef.get(self.calexpType, immediate=True)
510 except dafPersist.NoResults as e:
511 raise MissingExposureError('Exposure not found: %s ' % str(e)) from e
513 if not bgSubtracted: 513 ↛ 514line 513 didn't jump to line 514, because the condition on line 513 was never true
514 background = dataRef.get("calexpBackground", immediate=True)
515 mi = exposure.getMaskedImage()
516 mi += background.getImage()
517 del mi
519 if self.config.doApplyExternalPhotoCalib: 519 ↛ 520line 519 didn't jump to line 520, because the condition on line 519 was never true
520 source = f"{self.config.externalPhotoCalibName}_photoCalib"
521 self.log.debug("Applying external photoCalib to %s from %s", dataRef.dataId, source)
522 photoCalib = dataRef.get(source)
523 exposure.setPhotoCalib(photoCalib)
524 else:
525 photoCalib = exposure.getPhotoCalib()
527 if self.config.doApplyExternalSkyWcs: 527 ↛ 528line 527 didn't jump to line 528, because the condition on line 527 was never true
528 source = f"{self.config.externalSkyWcsName}_wcs"
529 self.log.debug("Applying external skyWcs to %s from %s", dataRef.dataId, source)
530 skyWcs = dataRef.get(source)
531 exposure.setWcs(skyWcs)
533 exposure.maskedImage = photoCalib.calibrateImage(exposure.maskedImage,
534 includeScaleUncertainty=self.config.includeCalibVar)
535 exposure.maskedImage /= photoCalib.getCalibrationMean()
536 # TODO: The images will have a calibration of 1.0 everywhere once RFC-545 is implemented.
537 # exposure.setCalib(afwImage.Calib(1.0))
538 return exposure
540 @staticmethod
541 def _prepareEmptyExposure(skyInfo):
542 """Produce an empty exposure for a given patch"""
543 exp = afwImage.ExposureF(skyInfo.bbox, skyInfo.wcs)
544 exp.getMaskedImage().set(numpy.nan, afwImage.Mask
545 .getPlaneBitMask("NO_DATA"), numpy.inf)
546 return exp
548 def getWarpTypeList(self):
549 """Return list of requested warp types per the config.
550 """
551 warpTypeList = []
552 if self.config.makeDirect: 552 ↛ 554line 552 didn't jump to line 554, because the condition on line 552 was never false
553 warpTypeList.append("direct")
554 if self.config.makePsfMatched: 554 ↛ 556line 554 didn't jump to line 556, because the condition on line 554 was never false
555 warpTypeList.append("psfMatched")
556 return warpTypeList
558 def applySkyCorr(self, dataRef, calexp):
559 """Apply correction to the sky background level
561 Sky corrections can be generated with the 'skyCorrection.py'
562 executable in pipe_drivers. Because the sky model used by that
563 code extends over the entire focal plane, this can produce
564 better sky subtraction.
566 The calexp is updated in-place.
568 Parameters
569 ----------
570 dataRef : `lsst.daf.persistence.ButlerDataRef`
571 Data reference for calexp.
572 calexp : `lsst.afw.image.Exposure` or `lsst.afw.image.MaskedImage`
573 Calibrated exposure.
574 """
575 bg = dataRef.get("skyCorr")
576 self.log.debug("Applying sky correction to %s", dataRef.dataId)
577 if isinstance(calexp, afwImage.Exposure):
578 calexp = calexp.getMaskedImage()
579 calexp -= bg.getImage()
582class MakeWarpConnections(pipeBase.PipelineTaskConnections,
583 dimensions=("tract", "patch", "skymap", "instrument", "visit"),
584 defaultTemplates={"coaddName": "deep",
585 "skyWcsName": "jointcal",
586 "photoCalibName": "fgcm",
587 "calexpType": ""}):
588 calExpList = connectionTypes.Input(
589 doc="Input exposures to be resampled and optionally PSF-matched onto a SkyMap projection/patch",
590 name="{calexpType}calexp",
591 storageClass="ExposureF",
592 dimensions=("instrument", "visit", "detector"),
593 multiple=True,
594 deferLoad=True,
595 )
596 backgroundList = connectionTypes.Input(
597 doc="Input backgrounds to be added back into the calexp if bgSubtracted=False",
598 name="calexpBackground",
599 storageClass="Background",
600 dimensions=("instrument", "visit", "detector"),
601 multiple=True,
602 )
603 skyCorrList = connectionTypes.Input(
604 doc="Input Sky Correction to be subtracted from the calexp if doApplySkyCorr=True",
605 name="skyCorr",
606 storageClass="Background",
607 dimensions=("instrument", "visit", "detector"),
608 multiple=True,
609 )
610 skyMap = connectionTypes.Input(
611 doc="Input definition of geometry/bbox and projection/wcs for warped exposures",
612 name=BaseSkyMap.SKYMAP_DATASET_TYPE_NAME,
613 storageClass="SkyMap",
614 dimensions=("skymap",),
615 )
616 externalSkyWcsTractCatalog = connectionTypes.Input(
617 doc=("Per-tract, per-visit wcs calibrations. These catalogs use the detector "
618 "id for the catalog id, sorted on id for fast lookup."),
619 name="{skyWcsName}SkyWcsCatalog",
620 storageClass="ExposureCatalog",
621 dimensions=("instrument", "visit", "tract"),
622 )
623 externalSkyWcsGlobalCatalog = connectionTypes.Input(
624 doc=("Per-visit wcs calibrations computed globally (with no tract information). "
625 "These catalogs use the detector id for the catalog id, sorted on id for "
626 "fast lookup."),
627 name="{skyWcsName}SkyWcsCatalog",
628 storageClass="ExposureCatalog",
629 dimensions=("instrument", "visit"),
630 )
631 externalPhotoCalibTractCatalog = connectionTypes.Input(
632 doc=("Per-tract, per-visit photometric calibrations. These catalogs use the "
633 "detector id for the catalog id, sorted on id for fast lookup."),
634 name="{photoCalibName}PhotoCalibCatalog",
635 storageClass="ExposureCatalog",
636 dimensions=("instrument", "visit", "tract"),
637 )
638 externalPhotoCalibGlobalCatalog = connectionTypes.Input(
639 doc=("Per-visit photometric calibrations computed globally (with no tract "
640 "information). These catalogs use the detector id for the catalog id, "
641 "sorted on id for fast lookup."),
642 name="{photoCalibName}PhotoCalibCatalog",
643 storageClass="ExposureCatalog",
644 dimensions=("instrument", "visit"),
645 )
646 direct = connectionTypes.Output(
647 doc=("Output direct warped exposure (previously called CoaddTempExp), produced by resampling ",
648 "calexps onto the skyMap patch geometry."),
649 name="{coaddName}Coadd_directWarp",
650 storageClass="ExposureF",
651 dimensions=("tract", "patch", "skymap", "visit", "instrument"),
652 )
653 psfMatched = connectionTypes.Output(
654 doc=("Output PSF-Matched warped exposure (previously called CoaddTempExp), produced by resampling ",
655 "calexps onto the skyMap patch geometry and PSF-matching to a model PSF."),
656 name="{coaddName}Coadd_psfMatchedWarp",
657 storageClass="ExposureF",
658 dimensions=("tract", "patch", "skymap", "visit", "instrument"),
659 )
660 # TODO DM-28769, have selectImages subtask indicate which connections they need:
661 wcsList = connectionTypes.Input(
662 doc="WCSs of calexps used by SelectImages subtask to determine if the calexp overlaps the patch",
663 name="{calexpType}calexp.wcs",
664 storageClass="Wcs",
665 dimensions=("instrument", "visit", "detector"),
666 multiple=True,
667 )
668 bboxList = connectionTypes.Input(
669 doc="BBoxes of calexps used by SelectImages subtask to determine if the calexp overlaps the patch",
670 name="{calexpType}calexp.bbox",
671 storageClass="Box2I",
672 dimensions=("instrument", "visit", "detector"),
673 multiple=True,
674 )
675 srcList = connectionTypes.Input(
676 doc="src catalogs used by PsfWcsSelectImages subtask to further select on PSF stability",
677 name="src",
678 storageClass="SourceCatalog",
679 dimensions=("instrument", "visit", "detector"),
680 multiple=True,
681 )
682 psfList = connectionTypes.Input(
683 doc="PSF models used by BestSeeingWcsSelectImages subtask to futher select on seeing",
684 name="{calexpType}calexp.psf",
685 storageClass="Psf",
686 dimensions=("instrument", "visit", "detector"),
687 multiple=True,
688 )
690 def __init__(self, *, config=None):
691 super().__init__(config=config)
692 if config.bgSubtracted:
693 self.inputs.remove("backgroundList")
694 if not config.doApplySkyCorr:
695 self.inputs.remove("skyCorrList")
696 if config.doApplyExternalSkyWcs:
697 if config.useGlobalExternalSkyWcs:
698 self.inputs.remove("externalSkyWcsTractCatalog")
699 else:
700 self.inputs.remove("externalSkyWcsGlobalCatalog")
701 else:
702 self.inputs.remove("externalSkyWcsTractCatalog")
703 self.inputs.remove("externalSkyWcsGlobalCatalog")
704 if config.doApplyExternalPhotoCalib:
705 if config.useGlobalExternalPhotoCalib:
706 self.inputs.remove("externalPhotoCalibTractCatalog")
707 else:
708 self.inputs.remove("externalPhotoCalibGlobalCatalog")
709 else:
710 self.inputs.remove("externalPhotoCalibTractCatalog")
711 self.inputs.remove("externalPhotoCalibGlobalCatalog")
712 if not config.makeDirect:
713 self.outputs.remove("direct")
714 if not config.makePsfMatched:
715 self.outputs.remove("psfMatched")
716 # TODO DM-28769: add connection per selectImages connections
717 # instead of removing if not PsfWcsSelectImagesTask here:
718 if config.select.target != lsst.pipe.tasks.selectImages.PsfWcsSelectImagesTask:
719 self.inputs.remove("srcList")
720 if config.select.target != lsst.pipe.tasks.selectImages.BestSeeingWcsSelectImagesTask:
721 self.inputs.remove("psfList")
724class MakeWarpConfig(pipeBase.PipelineTaskConfig, MakeCoaddTempExpConfig,
725 pipelineConnections=MakeWarpConnections):
727 def validate(self):
728 super().validate()
731class MakeWarpTask(MakeCoaddTempExpTask):
732 """Warp and optionally PSF-Match calexps onto an a common projection
733 """
734 ConfigClass = MakeWarpConfig
735 _DefaultName = "makeWarp"
737 @utils.inheritDoc(pipeBase.PipelineTask)
738 def runQuantum(self, butlerQC, inputRefs, outputRefs):
739 """
740 Notes
741 ----
742 Construct warps for requested warp type for single epoch
744 PipelineTask (Gen3) entry point to warp and optionally PSF-match
745 calexps. This method is analogous to `runDataRef`.
746 """
748 # Ensure all input lists are in same detector order as the calExpList
749 detectorOrder = [ref.datasetRef.dataId['detector'] for ref in inputRefs.calExpList]
750 inputRefs = reorderRefs(inputRefs, detectorOrder, dataIdKey='detector')
752 # Read in all inputs.
753 inputs = butlerQC.get(inputRefs)
755 # Construct skyInfo expected by `run`. We remove the SkyMap itself
756 # from the dictionary so we can pass it as kwargs later.
757 skyMap = inputs.pop("skyMap")
758 quantumDataId = butlerQC.quantum.dataId
759 skyInfo = makeSkyInfo(skyMap, tractId=quantumDataId['tract'], patchId=quantumDataId['patch'])
761 # Construct list of input DataIds expected by `run`
762 dataIdList = [ref.datasetRef.dataId for ref in inputRefs.calExpList]
763 # Construct list of packed integer IDs expected by `run`
764 ccdIdList = [dataId.pack("visit_detector") for dataId in dataIdList]
766 # Run the selector and filter out calexps that were not selected
767 # primarily because they do not overlap the patch
768 cornerPosList = lsst.geom.Box2D(skyInfo.bbox).getCorners()
769 coordList = [skyInfo.wcs.pixelToSky(pos) for pos in cornerPosList]
770 goodIndices = self.select.run(**inputs, coordList=coordList, dataIds=dataIdList)
771 inputs = self.filterInputs(indices=goodIndices, inputs=inputs)
773 # Read from disk only the selected calexps
774 inputs['calExpList'] = [ref.get() for ref in inputs['calExpList']]
776 # Extract integer visitId requested by `run`
777 visits = [dataId['visit'] for dataId in dataIdList]
778 visitId = visits[0]
780 if self.config.doApplyExternalSkyWcs:
781 if self.config.useGlobalExternalSkyWcs:
782 externalSkyWcsCatalog = inputs.pop("externalSkyWcsGlobalCatalog")
783 else:
784 externalSkyWcsCatalog = inputs.pop("externalSkyWcsTractCatalog")
785 else:
786 externalSkyWcsCatalog = None
788 if self.config.doApplyExternalPhotoCalib:
789 if self.config.useGlobalExternalPhotoCalib:
790 externalPhotoCalibCatalog = inputs.pop("externalPhotoCalibGlobalCatalog")
791 else:
792 externalPhotoCalibCatalog = inputs.pop("externalPhotoCalibTractCatalog")
793 else:
794 externalPhotoCalibCatalog = None
796 completeIndices = self.prepareCalibratedExposures(**inputs,
797 externalSkyWcsCatalog=externalSkyWcsCatalog,
798 externalPhotoCalibCatalog=externalPhotoCalibCatalog)
799 # Redo the input selection with inputs with complete wcs/photocalib info.
800 inputs = self.filterInputs(indices=completeIndices, inputs=inputs)
802 results = self.run(**inputs, visitId=visitId,
803 ccdIdList=[ccdIdList[i] for i in goodIndices],
804 dataIdList=[dataIdList[i] for i in goodIndices],
805 skyInfo=skyInfo)
806 if self.config.makeDirect and results.exposures["direct"] is not None:
807 butlerQC.put(results.exposures["direct"], outputRefs.direct)
808 if self.config.makePsfMatched and results.exposures["psfMatched"] is not None:
809 butlerQC.put(results.exposures["psfMatched"], outputRefs.psfMatched)
811 def filterInputs(self, indices, inputs):
812 """Return task inputs with their lists filtered by indices
814 Parameters
815 ----------
816 indices : `list` of integers
817 inputs : `dict` of `list` of input connections to be passed to run
818 """
819 for key in inputs.keys():
820 # Only down-select on list inputs
821 if isinstance(inputs[key], list):
822 inputs[key] = [inputs[key][ind] for ind in indices]
823 return inputs
825 def prepareCalibratedExposures(self, calExpList, backgroundList=None, skyCorrList=None,
826 externalSkyWcsCatalog=None, externalPhotoCalibCatalog=None,
827 **kwargs):
828 """Calibrate and add backgrounds to input calExpList in place
830 Parameters
831 ----------
832 calExpList : `list` of `lsst.afw.image.Exposure`
833 Sequence of calexps to be modified in place
834 backgroundList : `list` of `lsst.afw.math.backgroundList`, optional
835 Sequence of backgrounds to be added back in if bgSubtracted=False
836 skyCorrList : `list` of `lsst.afw.math.backgroundList`, optional
837 Sequence of background corrections to be subtracted if doApplySkyCorr=True
838 externalSkyWcsCatalog : `lsst.afw.table.ExposureCatalog`, optional
839 Exposure catalog with external skyWcs to be applied
840 if config.doApplyExternalSkyWcs=True. Catalog uses the detector id
841 for the catalog id, sorted on id for fast lookup.
842 externalPhotoCalibCatalog : `lsst.afw.table.ExposureCatalog`, optional
843 Exposure catalog with external photoCalib to be applied
844 if config.doApplyExternalPhotoCalib=True. Catalog uses the detector
845 id for the catalog id, sorted on id for fast lookup.
847 Returns
848 -------
849 indices : `list` [`int`]
850 Indices of calExpList and friends that have valid photoCalib/skyWcs
851 """
852 backgroundList = len(calExpList)*[None] if backgroundList is None else backgroundList
853 skyCorrList = len(calExpList)*[None] if skyCorrList is None else skyCorrList
855 includeCalibVar = self.config.includeCalibVar
857 indices = []
858 for index, (calexp, background, skyCorr) in enumerate(zip(calExpList,
859 backgroundList,
860 skyCorrList)):
861 mi = calexp.maskedImage
862 if not self.config.bgSubtracted:
863 mi += background.getImage()
865 if externalSkyWcsCatalog is not None or externalPhotoCalibCatalog is not None:
866 detectorId = calexp.getInfo().getDetector().getId()
868 # Find the external photoCalib
869 if externalPhotoCalibCatalog is not None:
870 row = externalPhotoCalibCatalog.find(detectorId)
871 if row is None:
872 self.log.warning("Detector id %s not found in externalPhotoCalibCatalog "
873 "and will not be used in the warp.", detectorId)
874 continue
875 photoCalib = row.getPhotoCalib()
876 if photoCalib is None:
877 self.log.warning("Detector id %s has None for photoCalib in externalPhotoCalibCatalog "
878 "and will not be used in the warp.", detectorId)
879 continue
880 calexp.setPhotoCalib(photoCalib)
881 else:
882 photoCalib = calexp.getPhotoCalib()
883 if photoCalib is None:
884 self.log.warning("Detector id %s has None for photoCalib in the calexp "
885 "and will not be used in the warp.", detectorId)
886 continue
888 # Find and apply external skyWcs
889 if externalSkyWcsCatalog is not None:
890 row = externalSkyWcsCatalog.find(detectorId)
891 if row is None:
892 self.log.warning("Detector id %s not found in externalSkyWcsCatalog "
893 "and will not be used in the warp.", detectorId)
894 continue
895 skyWcs = row.getWcs()
896 if skyWcs is None:
897 self.log.warning("Detector id %s has None for skyWcs in externalSkyWcsCatalog "
898 "and will not be used in the warp.", detectorId)
899 continue
900 calexp.setWcs(skyWcs)
901 else:
902 skyWcs = calexp.getWcs()
903 if skyWcs is None:
904 self.log.warning("Detector id %s has None for skyWcs in the calexp "
905 "and will not be used in the warp.", detectorId)
906 continue
908 # Calibrate the image
909 calexp.maskedImage = photoCalib.calibrateImage(calexp.maskedImage,
910 includeScaleUncertainty=includeCalibVar)
911 calexp.maskedImage /= photoCalib.getCalibrationMean()
912 # TODO: The images will have a calibration of 1.0 everywhere once RFC-545 is implemented.
913 # exposure.setCalib(afwImage.Calib(1.0))
915 # Apply skycorr
916 if self.config.doApplySkyCorr:
917 mi -= skyCorr.getImage()
919 indices.append(index)
921 return indices
924def reorderRefs(inputRefs, outputSortKeyOrder, dataIdKey):
925 """Reorder inputRefs per outputSortKeyOrder
927 Any inputRefs which are lists will be resorted per specified key e.g.,
928 'detector.' Only iterables will be reordered, and values can be of type
929 `lsst.pipe.base.connections.DeferredDatasetRef` or
930 `lsst.daf.butler.core.datasets.ref.DatasetRef`.
931 Returned lists of refs have the same length as the outputSortKeyOrder.
932 If an outputSortKey not in the inputRef, then it will be padded with None.
933 If an inputRef contains an inputSortKey that is not in the
934 outputSortKeyOrder it will be removed.
936 Parameters
937 ----------
938 inputRefs : `lsst.pipe.base.connections.QuantizedConnection`
939 Input references to be reordered and padded.
940 outputSortKeyOrder : iterable
941 Iterable of values to be compared with inputRef's dataId[dataIdKey]
942 dataIdKey : `str`
943 dataIdKey in the dataRefs to compare with the outputSortKeyOrder.
945 Returns:
946 --------
947 inputRefs: `lsst.pipe.base.connections.QuantizedConnection`
948 Quantized Connection with sorted DatasetRef values sorted if iterable.
949 """
950 for connectionName, refs in inputRefs:
951 if isinstance(refs, Iterable):
952 if hasattr(refs[0], "dataId"):
953 inputSortKeyOrder = [ref.dataId[dataIdKey] for ref in refs]
954 else:
955 inputSortKeyOrder = [ref.datasetRef.dataId[dataIdKey] for ref in refs]
956 if inputSortKeyOrder != outputSortKeyOrder:
957 setattr(inputRefs, connectionName,
958 reorderAndPadList(refs, inputSortKeyOrder, outputSortKeyOrder))
959 return inputRefs