lsst.pipe.tasks g84bf843041+a7098f5eaf
coaddBase.py
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22import lsst.pex.config as pexConfig
23import lsst.geom as geom
24import lsst.afw.geom as afwGeom
25import lsst.afw.image as afwImage
26import lsst.pipe.base as pipeBase
27import lsst.meas.algorithms as measAlg
28
29from lsst.afw.fits import FitsError
30from lsst.coadd.utils import CoaddDataIdContainer
31from .selectImages import WcsSelectImagesTask, SelectStruct
32from .coaddInputRecorder import CoaddInputRecorderTask
33from .scaleVariance import ScaleVarianceTask
34
35__all__ = ["CoaddBaseTask", "getSkyInfo", "makeSkyInfo", "makeCoaddSuffix"]
36
37
38class CoaddBaseConfig(pexConfig.Config):
39 """!Configuration parameters for CoaddBaseTask
40
41 @anchor CoaddBaseConfig_
42
43 @brief Configuration parameters shared between MakeCoaddTempExp and AssembleCoadd
44 """
45 coaddName = pexConfig.Field(
46 doc="Coadd name: typically one of deep or goodSeeing.",
47 dtype=str,
48 default="deep",
49 )
50 select = pexConfig.ConfigurableField(
51 doc="Image selection subtask.",
52 target=WcsSelectImagesTask,
53 )
54 badMaskPlanes = pexConfig.ListField(
55 dtype=str,
56 doc="Mask planes that, if set, the associated pixel should not be included in the coaddTempExp.",
57 default=("NO_DATA",),
58 )
59 inputRecorder = pexConfig.ConfigurableField(
60 doc="Subtask that helps fill CoaddInputs catalogs added to the final Exposure",
61 target=CoaddInputRecorderTask
62 )
63 doPsfMatch = pexConfig.Field(
64 dtype=bool,
65 doc="Match to modelPsf? Deprecated. Sets makePsfMatched=True, makeDirect=False",
66 default=False
67 )
68 modelPsf = measAlg.GaussianPsfFactory.makeField(doc="Model Psf factory")
69 doApplyExternalPhotoCalib = pexConfig.Field(
70 dtype=bool,
71 default=False,
72 doc=("Whether to apply external photometric calibration via an "
73 "`lsst.afw.image.PhotoCalib` object. Uses the "
74 "`externalPhotoCalibName` field to determine which calibration "
75 "to load.")
76 )
77 useGlobalExternalPhotoCalib = pexConfig.Field(
78 dtype=bool,
79 default=True,
80 doc=("When using doApplyExternalPhotoCalib, use 'global' calibrations "
81 "that are not run per-tract. When False, use per-tract photometric "
82 "calibration files.")
83 )
84 externalPhotoCalibName = pexConfig.ChoiceField(
85 # TODO: Remove this config with the removal of Gen2 in DM-20572.
86 dtype=str,
87 doc=("Type of external PhotoCalib if `doApplyExternalPhotoCalib` is True. "
88 "This field is only used for Gen2 middleware."),
89 default="jointcal",
90 allowed={
91 "jointcal": "Use jointcal_photoCalib",
92 "fgcm": "Use fgcm_photoCalib",
93 "fgcm_tract": "Use fgcm_tract_photoCalib"
94 }
95 )
96 doApplyExternalSkyWcs = pexConfig.Field(
97 dtype=bool,
98 default=False,
99 doc=("Whether to apply external astrometric calibration via an "
100 "`lsst.afw.geom.SkyWcs` object. Uses `externalSkyWcsName` "
101 "field to determine which calibration to load.")
102 )
103 useGlobalExternalSkyWcs = pexConfig.Field(
104 dtype=bool,
105 default=False,
106 doc=("When using doApplyExternalSkyWcs, use 'global' calibrations "
107 "that are not run per-tract. When False, use per-tract wcs "
108 "files.")
109 )
110 externalSkyWcsName = pexConfig.ChoiceField(
111 # TODO: Remove this config with the removal of Gen2 in DM-20572.
112 dtype=str,
113 doc=("Type of external SkyWcs if `doApplyExternalSkyWcs` is True. "
114 "This field is only used for Gen2 middleware."),
115 default="jointcal",
116 allowed={
117 "jointcal": "Use jointcal_wcs"
118 }
119 )
120 includeCalibVar = pexConfig.Field(
121 dtype=bool,
122 doc="Add photometric calibration variance to warp variance plane.",
123 default=False
124 )
125 matchingKernelSize = pexConfig.Field(
126 dtype=int,
127 doc="Size in pixels of matching kernel. Must be odd.",
128 default=21,
129 check=lambda x: x % 2 == 1
130 )
131
132
133class CoaddTaskRunner(pipeBase.TaskRunner):
134
135 @staticmethod
136 def getTargetList(parsedCmd, **kwargs):
137 return pipeBase.TaskRunner.getTargetList(parsedCmd, selectDataList=parsedCmd.selectId.dataList,
138 **kwargs)
139
140
141class CoaddBaseTask(pipeBase.CmdLineTask, pipeBase.PipelineTask):
142 """!Base class for coaddition.
143
144 Subclasses must specify _DefaultName
145 """
146 ConfigClass = CoaddBaseConfig
147 RunnerClass = CoaddTaskRunner
148
149 def __init__(self, **kwargs):
150 super().__init__(**kwargs)
151 self.makeSubtask("select")
152 self.makeSubtask("inputRecorder")
153
154 def selectExposures(self, patchRef, skyInfo=None, selectDataList=[]):
155 """!
156 @brief Select exposures to coadd
157
158 Get the corners of the bbox supplied in skyInfo using @ref geom.Box2D and convert the pixel
159 positions of the bbox corners to sky coordinates using @ref skyInfo.wcs.pixelToSky. Use the
160 @ref WcsSelectImagesTask_ "WcsSelectImagesTask" to select exposures that lie inside the patch
161 indicated by the dataRef.
162
163 @param[in] patchRef data reference for sky map patch. Must include keys "tract", "patch",
164 plus the camera-specific filter key (e.g. "filter" or "band")
165 @param[in] skyInfo geometry for the patch; output from getSkyInfo
166 @return a list of science exposures to coadd, as butler data references
167 """
168 if skyInfo is None:
169 skyInfo = self.getSkyInfogetSkyInfo(patchRef)
170 cornerPosList = geom.Box2D(skyInfo.bbox).getCorners()
171 coordList = [skyInfo.wcs.pixelToSky(pos) for pos in cornerPosList]
172 return self.select.runDataRef(patchRef, coordList, selectDataList=selectDataList).dataRefList
173
174 def getSkyInfo(self, patchRef):
175 """!
176 @brief Use @ref getSkyinfo to return the skyMap, tract and patch information, wcs and the outer bbox
177 of the patch.
178
179 @param[in] patchRef data reference for sky map. Must include keys "tract" and "patch"
180
181 @return pipe_base Struct containing:
182 - skyMap: sky map
183 - tractInfo: information for chosen tract of sky map
184 - patchInfo: information about chosen patch of tract
185 - wcs: WCS of tract
186 - bbox: outer bbox of patch, as an geom Box2I
187 """
188 return getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
189
190 def getCoaddDatasetName(self, warpType="direct"):
191 """Return coadd name for given warpType and task config
192
193 Parameters
194 ----------
195 warpType : string
196 Either 'direct' or 'psfMatched'
197
198 Returns
199 -------
200 CoaddDatasetName : `string`
201 """
202 return self.config.coaddName + "Coadd" + makeCoaddSuffix(warpType)
203
204 def getTempExpDatasetName(self, warpType="direct"):
205 """Return warp name for given warpType and task config
206
207 Parameters
208 ----------
209 warpType : string
210 Either 'direct' or 'psfMatched'
211
212 Returns
213 -------
214 WarpDatasetName : `string`
215 """
216 return self.config.coaddName + "Coadd_" + warpType + "Warp"
217
218 @classmethod
219 def _makeArgumentParser(cls):
220 """Create an argument parser
221 """
222 parser = pipeBase.ArgumentParser(name=cls._DefaultName)
223 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2",
224 ContainerClass=CoaddDataIdContainer)
225 parser.add_id_argument("--selectId", "calexp", help="data ID, e.g. --selectId visit=6789 ccd=0..9",
226 ContainerClass=SelectDataIdContainer)
227 return parser
228
229 def _getConfigName(self):
230 """Return the name of the config dataset
231 """
232 return "%s_%s_config" % (self.config.coaddName, self._DefaultName)
233
234 def _getMetadataName(self):
235 """Return the name of the metadata dataset
236 """
237 return "%s_%s_metadata" % (self.config.coaddName, self._DefaultName)
238
240 """!
241 @brief Convenience method to provide the bitmask from the mask plane names
242 """
243 return afwImage.Mask.getPlaneBitMask(self.config.badMaskPlanes)
244
245
246class SelectDataIdContainer(pipeBase.DataIdContainer):
247 """!
248 @brief A dataId container for inputs to be selected.
249
250 Read the header (including the size and Wcs) for all specified
251 inputs and pass those along, ultimately for the SelectImagesTask.
252 This is most useful when used with multiprocessing, as input headers are
253 only read once.
254 """
255
256 def makeDataRefList(self, namespace):
257 """Add a dataList containing useful information for selecting images"""
258 super(SelectDataIdContainer, self).makeDataRefList(namespace)
259 self.dataListdataList = []
260 for ref in self.refList:
261 try:
262 md = ref.get("calexp_md", immediate=True)
263 wcs = afwGeom.makeSkyWcs(md)
264 data = SelectStruct(dataRef=ref, wcs=wcs, bbox=afwImage.bboxFromMetadata(md))
265 except FitsError:
266 namespace.log.warning("Unable to construct Wcs from %s", ref.dataId)
267 continue
268 self.dataListdataList.append(data)
269
270
271def getSkyInfo(coaddName, patchRef):
272 """!
273 @brief Return the SkyMap, tract and patch information, wcs, and outer bbox of the patch to be coadded.
274
275 @param[in] coaddName coadd name; typically one of deep or goodSeeing
276 @param[in] patchRef data reference for sky map. Must include keys "tract" and "patch"
277
278 @return pipe_base Struct containing:
279 - skyMap: sky map
280 - tractInfo: information for chosen tract of sky map
281 - patchInfo: information about chosen patch of tract
282 - wcs: WCS of tract
283 - bbox: outer bbox of patch, as an geom Box2I
284 """
285 skyMap = patchRef.get(coaddName + "Coadd_skyMap")
286 return makeSkyInfo(skyMap, patchRef.dataId["tract"], patchRef.dataId["patch"])
287
288
289def makeSkyInfo(skyMap, tractId, patchId):
290 """Return SkyInfo Struct
291
292 Constructs SkyInfo used by coaddition tasks for multiple
293 patchId formats.
294
295 Parameters
296 ----------
297 skyMap : `lsst.skyMap.SkyMap`
298 tractId : int
299 patchId : str or int or tuple of int
300 Either Gen2-style comma delimited string (e.g. '4,5'),
301 tuple of integers (e.g (4, 5), Gen3-style integer.
302 """
303 tractInfo = skyMap[tractId]
304
305 if isinstance(patchId, str) and ',' in patchId:
306 # patch format is "xIndex,yIndex"
307 patchIndex = tuple(int(i) for i in patchId.split(","))
308 else:
309 patchIndex = patchId
310
311 patchInfo = tractInfo.getPatchInfo(patchIndex)
312
313 return pipeBase.Struct(
314 skyMap=skyMap,
315 tractInfo=tractInfo,
316 patchInfo=patchInfo,
317 wcs=tractInfo.getWcs(),
318 bbox=patchInfo.getOuterBBox(),
319 )
320
321
322def scaleVariance(maskedImage, maskPlanes, log=None):
323 """!
324 @brief Scale the variance in a maskedImage
325
326 The variance plane in a convolved or warped image (or a coadd derived
327 from warped images) does not accurately reflect the noise properties of
328 the image because variance has been lost to covariance. This function
329 attempts to correct for this by scaling the variance plane to match
330 the observed variance in the image. This is not perfect (because we're
331 not tracking the covariance) but it's simple and is often good enough.
332
333 @deprecated Use the ScaleVarianceTask instead.
334
335 @param maskedImage MaskedImage to operate on; variance will be scaled
336 @param maskPlanes List of mask planes for pixels to reject
337 @param log Log for reporting the renormalization factor; or None
338 @return renormalisation factor
339 """
340 config = ScaleVarianceTask.ConfigClass()
341 config.maskPlanes = maskPlanes
342 task = ScaleVarianceTask(config=config, name="scaleVariance", log=log)
343 return task.run(maskedImage)
344
345
346def makeCoaddSuffix(warpType="direct"):
347 """Return coadd suffix for warpType
348
349 Parameters
350 ----------
351 warpType : string
352 Either 'direct' or 'psfMatched'
353
354 Returns
355 -------
356 CoaddSuffix : `string`
357 """
358 suffix = "" if warpType == "direct" else warpType[0].upper() + warpType[1:]
359 return suffix
360
361
362def reorderAndPadList(inputList, inputKeys, outputKeys, padWith=None):
363 """Match the order of one list to another, padding if necessary
364
365 Parameters
366 ----------
367 inputList : list
368 List to be reordered and padded. Elements can be any type.
369 inputKeys : iterable
370 Iterable of values to be compared with outputKeys.
371 Length must match `inputList`
372 outputKeys : iterable
373 Iterable of values to be compared with inputKeys.
374 padWith :
375 Any value to be inserted where inputKey not in outputKeys
376
377 Returns
378 -------
379 list
380 Copy of inputList reordered per outputKeys and padded with `padWith`
381 so that the length matches length of outputKeys.
382 """
383 outputList = []
384 for d in outputKeys:
385 if d in inputKeys:
386 outputList.append(inputList[inputKeys.index(d)])
387 else:
388 outputList.append(padWith)
389 return outputList
Configuration parameters for CoaddBaseTask.
Definition: coaddBase.py:38
Base class for coaddition.
Definition: coaddBase.py:141
def getTempExpDatasetName(self, warpType="direct")
Definition: coaddBase.py:204
def selectExposures(self, patchRef, skyInfo=None, selectDataList=[])
Select exposures to coadd.
Definition: coaddBase.py:154
def getCoaddDatasetName(self, warpType="direct")
Definition: coaddBase.py:190
def getSkyInfo(self, patchRef)
Use getSkyinfo to return the skyMap, tract and patch information, wcs and the outer bbox of the patch...
Definition: coaddBase.py:174
def getBadPixelMask(self)
Convenience method to provide the bitmask from the mask plane names.
Definition: coaddBase.py:239
def getTargetList(parsedCmd, **kwargs)
Definition: coaddBase.py:136
A dataId container for inputs to be selected.
Definition: coaddBase.py:246
def reorderAndPadList(inputList, inputKeys, outputKeys, padWith=None)
Definition: coaddBase.py:362
def makeCoaddSuffix(warpType="direct")
Definition: coaddBase.py:346
def makeSkyInfo(skyMap, tractId, patchId)
Definition: coaddBase.py:289
def scaleVariance(maskedImage, maskPlanes, log=None)
Scale the variance in a maskedImage.
Definition: coaddBase.py:322
def getSkyInfo(coaddName, patchRef)
Return the SkyMap, tract and patch information, wcs, and outer bbox of the patch to be coadded.
Definition: coaddBase.py:271