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

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1#
2# LSST Data Management System
3# Copyright 2008-2015 AURA/LSST.
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 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 doApplyUberCal = pexConfig.Field(
70 dtype=bool,
71 doc=("Apply ubercalibrated WCS and PhotoCalib results to input calexps? "
72 "This field is no longer used, and has been deprecated by DM-21308. "
73 "It will be removed after v20. Use doApplyExternalPhotoCalib and "
74 "doApplyExternalSkyWcs instead."),
75 default=False
76 )
77 doApplyExternalPhotoCalib = pexConfig.Field(
78 dtype=bool,
79 default=False,
80 doc=("Whether to apply external photometric calibration via an "
81 "`lsst.afw.image.PhotoCalib` object. Uses the "
82 "`externalPhotoCalibName` field to determine which calibration "
83 "to load.")
84 )
85 externalPhotoCalibName = pexConfig.ChoiceField(
86 dtype=str,
87 doc="Type of external PhotoCalib if `doApplyExternalPhotoCalib` is True.",
88 default="jointcal",
89 allowed={
90 "jointcal": "Use jointcal_photoCalib",
91 "fgcm": "Use fgcm_photoCalib",
92 "fgcm_tract": "Use fgcm_tract_photoCalib"
93 }
94 )
95 doApplyExternalSkyWcs = pexConfig.Field(
96 dtype=bool,
97 default=False,
98 doc=("Whether to apply external astrometric calibration via an "
99 "`lsst.afw.geom.SkyWcs` object. Uses `externalSkyWcsName` "
100 "field to determine which calibration to load.")
101 )
102 externalSkyWcsName = pexConfig.ChoiceField(
103 dtype=str,
104 doc="Type of external SkyWcs if `doApplyExternalSkyWcs` is True.",
105 default="jointcal",
106 allowed={
107 "jointcal": "Use jointcal_wcs"
108 }
109 )
110 includeCalibVar = pexConfig.Field(
111 dtype=bool,
112 doc="Add photometric calibration variance to warp variance plane.",
113 default=False
114 )
115 matchingKernelSize = pexConfig.Field( 115 ↛ exitline 115 didn't jump to the function exit
116 dtype=int,
117 doc="Size in pixels of matching kernel. Must be odd.",
118 default=21,
119 check=lambda x: x % 2 == 1
120 )
123class CoaddTaskRunner(pipeBase.TaskRunner):
125 @staticmethod
126 def getTargetList(parsedCmd, **kwargs):
127 return pipeBase.TaskRunner.getTargetList(parsedCmd, selectDataList=parsedCmd.selectId.dataList,
128 **kwargs)
131class CoaddBaseTask(pipeBase.CmdLineTask):
132 """!Base class for coaddition.
134 Subclasses must specify _DefaultName
135 """
136 ConfigClass = CoaddBaseConfig
137 RunnerClass = CoaddTaskRunner
139 def __init__(self, **kwargs):
140 super().__init__(**kwargs)
141 self.makeSubtask("select")
142 self.makeSubtask("inputRecorder")
144 def selectExposures(self, patchRef, skyInfo=None, selectDataList=[]):
145 """!
146 @brief Select exposures to coadd
148 Get the corners of the bbox supplied in skyInfo using @ref geom.Box2D and convert the pixel
149 positions of the bbox corners to sky coordinates using @ref skyInfo.wcs.pixelToSky. Use the
150 @ref WcsSelectImagesTask_ "WcsSelectImagesTask" to select exposures that lie inside the patch
151 indicated by the dataRef.
153 @param[in] patchRef data reference for sky map patch. Must include keys "tract", "patch",
154 plus the camera-specific filter key (e.g. "filter" or "band")
155 @param[in] skyInfo geometry for the patch; output from getSkyInfo
156 @return a list of science exposures to coadd, as butler data references
157 """
158 if skyInfo is None:
159 skyInfo = self.getSkyInfo(patchRef)
160 cornerPosList = geom.Box2D(skyInfo.bbox).getCorners()
161 coordList = [skyInfo.wcs.pixelToSky(pos) for pos in cornerPosList]
162 return self.select.runDataRef(patchRef, coordList, selectDataList=selectDataList).dataRefList
164 def getSkyInfo(self, patchRef):
165 """!
166 @brief Use @ref getSkyinfo to return the skyMap, tract and patch information, wcs and the outer bbox
167 of the patch.
169 @param[in] patchRef data reference for sky map. Must include keys "tract" and "patch"
171 @return pipe_base Struct containing:
172 - skyMap: sky map
173 - tractInfo: information for chosen tract of sky map
174 - patchInfo: information about chosen patch of tract
175 - wcs: WCS of tract
176 - bbox: outer bbox of patch, as an geom Box2I
177 """
178 return getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
180 def getCoaddDatasetName(self, warpType="direct"):
181 """Return coadd name for given warpType and task config
183 Parameters
184 ----------
185 warpType : string
186 Either 'direct' or 'psfMatched'
188 Returns
189 -------
190 CoaddDatasetName : `string`
191 """
192 return self.config.coaddName + "Coadd" + makeCoaddSuffix(warpType)
194 def getTempExpDatasetName(self, warpType="direct"):
195 """Return warp name for given warpType and task config
197 Parameters
198 ----------
199 warpType : string
200 Either 'direct' or 'psfMatched'
202 Returns
203 -------
204 WarpDatasetName : `string`
205 """
206 return self.config.coaddName + "Coadd_" + warpType + "Warp"
208 @classmethod
209 def _makeArgumentParser(cls):
210 """Create an argument parser
211 """
212 parser = pipeBase.ArgumentParser(name=cls._DefaultName)
213 parser.add_id_argument("--id", "deepCoadd", help="data ID, e.g. --id tract=12345 patch=1,2",
214 ContainerClass=CoaddDataIdContainer)
215 parser.add_id_argument("--selectId", "calexp", help="data ID, e.g. --selectId visit=6789 ccd=0..9",
216 ContainerClass=SelectDataIdContainer)
217 return parser
219 def _getConfigName(self):
220 """Return the name of the config dataset
221 """
222 return "%s_%s_config" % (self.config.coaddName, self._DefaultName)
224 def _getMetadataName(self):
225 """Return the name of the metadata dataset
226 """
227 return "%s_%s_metadata" % (self.config.coaddName, self._DefaultName)
229 def getBadPixelMask(self):
230 """!
231 @brief Convenience method to provide the bitmask from the mask plane names
232 """
233 return afwImage.Mask.getPlaneBitMask(self.config.badMaskPlanes)
236class SelectDataIdContainer(pipeBase.DataIdContainer):
237 """!
238 @brief A dataId container for inputs to be selected.
240 Read the header (including the size and Wcs) for all specified
241 inputs and pass those along, ultimately for the SelectImagesTask.
242 This is most useful when used with multiprocessing, as input headers are
243 only read once.
244 """
246 def makeDataRefList(self, namespace):
247 """Add a dataList containing useful information for selecting images"""
248 super(SelectDataIdContainer, self).makeDataRefList(namespace)
249 self.dataList = []
250 for ref in self.refList:
251 try:
252 md = ref.get("calexp_md", immediate=True)
253 wcs = afwGeom.makeSkyWcs(md)
254 data = SelectStruct(dataRef=ref, wcs=wcs, bbox=afwImage.bboxFromMetadata(md))
255 except FitsError:
256 namespace.log.warn("Unable to construct Wcs from %s" % (ref.dataId))
257 continue
258 self.dataList.append(data)
261def getSkyInfo(coaddName, patchRef):
262 """!
263 @brief Return the SkyMap, tract and patch information, wcs, and outer bbox of the patch to be coadded.
265 @param[in] coaddName coadd name; typically one of deep or goodSeeing
266 @param[in] patchRef data reference for sky map. Must include keys "tract" and "patch"
268 @return pipe_base Struct containing:
269 - skyMap: sky map
270 - tractInfo: information for chosen tract of sky map
271 - patchInfo: information about chosen patch of tract
272 - wcs: WCS of tract
273 - bbox: outer bbox of patch, as an geom Box2I
274 """
275 skyMap = patchRef.get(coaddName + "Coadd_skyMap")
276 return makeSkyInfo(skyMap, patchRef.dataId["tract"], patchRef.dataId["patch"])
279def makeSkyInfo(skyMap, tractId, patchId):
280 """Return SkyInfo Struct
282 Constructs SkyInfo used by coaddition tasks for multiple
283 patchId formats.
285 Parameters
286 ----------
287 skyMap : `lsst.skyMap.SkyMap`
288 tractId : int
289 patchId : str or int or tuple of int
290 Either Gen2-style comma delimited string (e.g. '4,5'),
291 tuple of integers (e.g (4, 5), Gen3-style integer.
292 """
293 tractInfo = skyMap[tractId]
295 if isinstance(patchId, str) and ',' in patchId:
296 # patch format is "xIndex,yIndex"
297 patchIndex = tuple(int(i) for i in patchId.split(","))
298 else:
299 patchIndex = patchId
301 patchInfo = tractInfo.getPatchInfo(patchIndex)
303 return pipeBase.Struct(
304 skyMap=skyMap,
305 tractInfo=tractInfo,
306 patchInfo=patchInfo,
307 wcs=tractInfo.getWcs(),
308 bbox=patchInfo.getOuterBBox(),
309 )
312def scaleVariance(maskedImage, maskPlanes, log=None):
313 """!
314 @brief Scale the variance in a maskedImage
316 The variance plane in a convolved or warped image (or a coadd derived
317 from warped images) does not accurately reflect the noise properties of
318 the image because variance has been lost to covariance. This function
319 attempts to correct for this by scaling the variance plane to match
320 the observed variance in the image. This is not perfect (because we're
321 not tracking the covariance) but it's simple and is often good enough.
323 @deprecated Use the ScaleVarianceTask instead.
325 @param maskedImage MaskedImage to operate on; variance will be scaled
326 @param maskPlanes List of mask planes for pixels to reject
327 @param log Log for reporting the renormalization factor; or None
328 @return renormalisation factor
329 """
330 config = ScaleVarianceTask.ConfigClass()
331 config.maskPlanes = maskPlanes
332 task = ScaleVarianceTask(config=config, name="scaleVariance", log=log)
333 return task.run(maskedImage)
336def makeCoaddSuffix(warpType="direct"):
337 """Return coadd suffix for warpType
339 Parameters
340 ----------
341 warpType : string
342 Either 'direct' or 'psfMatched'
344 Returns
345 -------
346 CoaddSuffix : `string`
347 """
348 suffix = "" if warpType == "direct" else warpType[0].upper() + warpType[1:]
349 return suffix