Coverage for python/lsst/pipe/tasks/coaddBase.py: 76%
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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
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
35__all__ = ["CoaddBaseTask", "getSkyInfo", "makeSkyInfo", "makeCoaddSuffix"]
38class CoaddBaseConfig(pexConfig.Config):
39 """!Configuration parameters for CoaddBaseTask
41 @anchor CoaddBaseConfig_
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 )
133class CoaddTaskRunner(pipeBase.TaskRunner):
135 @staticmethod
136 def getTargetList(parsedCmd, **kwargs):
137 return pipeBase.TaskRunner.getTargetList(parsedCmd, selectDataList=parsedCmd.selectId.dataList,
138 **kwargs)
141class CoaddBaseTask(pipeBase.CmdLineTask, pipeBase.PipelineTask):
142 """!Base class for coaddition.
144 Subclasses must specify _DefaultName
145 """
146 ConfigClass = CoaddBaseConfig
147 RunnerClass = CoaddTaskRunner
149 def __init__(self, **kwargs):
150 super().__init__(**kwargs)
151 self.makeSubtask("select")
152 self.makeSubtask("inputRecorder")
154 def selectExposures(self, patchRef, skyInfo=None, selectDataList=[]):
155 """!
156 @brief Select exposures to coadd
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.
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: 168 ↛ 169line 168 didn't jump to line 169, because the condition on line 168 was never true
169 skyInfo = self.getSkyInfo(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
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.
179 @param[in] patchRef data reference for sky map. Must include keys "tract" and "patch"
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)
190 def getCoaddDatasetName(self, warpType="direct"):
191 """Return coadd name for given warpType and task config
193 Parameters
194 ----------
195 warpType : string
196 Either 'direct' or 'psfMatched'
198 Returns
199 -------
200 CoaddDatasetName : `string`
201 """
202 return self.config.coaddName + "Coadd" + makeCoaddSuffix(warpType)
204 def getTempExpDatasetName(self, warpType="direct"):
205 """Return warp name for given warpType and task config
207 Parameters
208 ----------
209 warpType : string
210 Either 'direct' or 'psfMatched'
212 Returns
213 -------
214 WarpDatasetName : `string`
215 """
216 return self.config.coaddName + "Coadd_" + warpType + "Warp"
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
229 def _getConfigName(self):
230 """Return the name of the config dataset
231 """
232 return "%s_%s_config" % (self.config.coaddName, self._DefaultName)
234 def _getMetadataName(self):
235 """Return the name of the metadata dataset
236 """
237 return "%s_%s_metadata" % (self.config.coaddName, self._DefaultName)
239 def getBadPixelMask(self):
240 """!
241 @brief Convenience method to provide the bitmask from the mask plane names
242 """
243 return afwImage.Mask.getPlaneBitMask(self.config.badMaskPlanes)
246class SelectDataIdContainer(pipeBase.DataIdContainer):
247 """!
248 @brief A dataId container for inputs to be selected.
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 """
256 def makeDataRefList(self, namespace):
257 """Add a dataList containing useful information for selecting images"""
258 super(SelectDataIdContainer, self).makeDataRefList(namespace)
259 self.dataList = []
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.dataList.append(data)
271def getSkyInfo(coaddName, patchRef):
272 """!
273 @brief Return the SkyMap, tract and patch information, wcs, and outer bbox of the patch to be coadded.
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"
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"])
289def makeSkyInfo(skyMap, tractId, patchId):
290 """Return SkyInfo Struct
292 Constructs SkyInfo used by coaddition tasks for multiple
293 patchId formats.
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]
305 if isinstance(patchId, str) and ',' in patchId: 305 ↛ 309line 305 didn't jump to line 309, because the condition on line 305 was never false
306 # patch format is "xIndex,yIndex"
307 patchIndex = tuple(int(i) for i in patchId.split(","))
308 else:
309 patchIndex = patchId
311 patchInfo = tractInfo.getPatchInfo(patchIndex)
313 return pipeBase.Struct(
314 skyMap=skyMap,
315 tractInfo=tractInfo,
316 patchInfo=patchInfo,
317 wcs=tractInfo.getWcs(),
318 bbox=patchInfo.getOuterBBox(),
319 )
322def scaleVariance(maskedImage, maskPlanes, log=None):
323 """!
324 @brief Scale the variance in a maskedImage
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.
333 @deprecated Use the ScaleVarianceTask instead.
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)
346def makeCoaddSuffix(warpType="direct"):
347 """Return coadd suffix for warpType
349 Parameters
350 ----------
351 warpType : string
352 Either 'direct' or 'psfMatched'
354 Returns
355 -------
356 CoaddSuffix : `string`
357 """
358 suffix = "" if warpType == "direct" else warpType[0].upper() + warpType[1:]
359 return suffix
362def reorderAndPadList(inputList, inputKeys, outputKeys, padWith=None):
363 """Match the order of one list to another, padding if necessary
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
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