lsst.ip.diffim  20.0.0-6-g47d5604+533d6aded8
getTemplate.py
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22 
23 import numpy as np
24 
25 import lsst.afw.image as afwImage
26 import lsst.geom as geom
27 import lsst.pex.config as pexConfig
28 import lsst.pipe.base as pipeBase
29 from lsst.ip.diffim.dcrModel import DcrModel
30 
31 __all__ = ["GetCoaddAsTemplateTask", "GetCoaddAsTemplateConfig",
32  "GetCalexpAsTemplateTask", "GetCalexpAsTemplateConfig"]
33 
34 
35 class GetCoaddAsTemplateConfig(pexConfig.Config):
36  templateBorderSize = pexConfig.Field(
37  dtype=int,
38  default=10,
39  doc="Number of pixels to grow the requested template image to account for warping"
40  )
41  coaddName = pexConfig.Field(
42  doc="coadd name: typically one of 'deep', 'goodSeeing', or 'dcr'",
43  dtype=str,
44  default="deep",
45  )
46  numSubfilters = pexConfig.Field(
47  doc="Number of subfilters in the DcrCoadd, used only if ``coaddName``='dcr'",
48  dtype=int,
49  default=3,
50  )
51  warpType = pexConfig.Field(
52  doc="Warp type of the coadd template: one of 'direct' or 'psfMatched'",
53  dtype=str,
54  default="direct",
55  )
56 
57 
58 class GetCoaddAsTemplateTask(pipeBase.Task):
59  """Subtask to retrieve coadd for use as an image difference template.
60 
61  This is the default getTemplate Task to be run as a subtask by
62  ``pipe.tasks.ImageDifferenceTask``. The main methods are ``run()`` and
63  ``runGen3()``.
64 
65  Notes
66  -----
67  From the given skymap, the closest tract is selected; multiple tracts are
68  not supported. The assembled template inherits the WCS of the selected
69  skymap tract and the resolution of the template exposures. Overlapping box
70  regions of the input template patches are pixel by pixel copied into the
71  assembled template image. There is no warping or pixel resampling.
72 
73  Pixels with no overlap of any available input patches are set to ``nan`` value
74  and ``NO_DATA`` flagged.
75  """
76 
77  ConfigClass = GetCoaddAsTemplateConfig
78  _DefaultName = "GetCoaddAsTemplateTask"
79 
80  def runDataRef(self, exposure, sensorRef, templateIdList=None):
81  """Gen2 task entry point. Retrieve and mosaic a template coadd exposure
82  that overlaps the science exposure.
83 
84  Parameters
85  ----------
86  exposure: `lsst.afw.image.Exposure`
87  an exposure for which to generate an overlapping template
88  sensorRef : TYPE
89  a Butler data reference that can be used to obtain coadd data
90  templateIdList : TYPE, optional
91  list of data ids, unused here, in the case of coadd template
92 
93  Returns
94  -------
95  result : `lsst.pipe.base.Struct`
96  - ``exposure`` : `lsst.afw.image.ExposureF`
97  a template coadd exposure assembled out of patches
98  - ``sources`` : None for this subtask
99  """
100  skyMap = sensorRef.get(datasetType=self.config.coaddName + "Coadd_skyMap")
101  tractInfo, patchList, skyCorners = self.getOverlapPatchList(exposure, skyMap)
102 
103  availableCoaddRefs = dict()
104  for patchInfo in patchList:
105  patchNumber = tractInfo.getSequentialPatchIndex(patchInfo)
106  patchArgDict = dict(
107  datasetType=self.getCoaddDatasetName() + "_sub",
108  bbox=patchInfo.getOuterBBox(),
109  tract=tractInfo.getId(),
110  patch="%s,%s" % (patchInfo.getIndex()[0], patchInfo.getIndex()[1]),
111  subfilter=0,
112  numSubfilters=self.config.numSubfilters,
113  )
114 
115  if sensorRef.datasetExists(**patchArgDict):
116  self.log.info("Reading patch %s" % patchArgDict)
117  availableCoaddRefs[patchNumber] = patchArgDict
118 
119  templateExposure = self.run(
120  tractInfo, patchList, skyCorners, availableCoaddRefs,
121  sensorRef=sensorRef, visitInfo=exposure.getInfo().getVisitInfo()
122  )
123  return pipeBase.Struct(exposure=templateExposure, sources=None)
124 
125  def runQuantum(self, exposure, butlerQC, skyMapRef, coaddExposureRefs):
126  """Gen3 task entry point. Retrieve and mosaic a template coadd exposure
127  that overlaps the science exposure.
128 
129  Parameters
130  ----------
131  exposure : `lsst.afw.image.Exposure`
132  The science exposure to define the sky region of the template coadd.
133  butlerQC : `lsst.pipe.base.ButlerQuantumContext`
134  Butler like object that supports getting data by DatasetRef.
135  skyMapRef : `lsst.daf.butler.DatasetRef`
136  Reference to SkyMap object that corresponds to the template coadd.
137  coaddExposureRefs : iterable of `lsst.daf.butler.DeferredDatasetRef`
138  Iterable of references to the available template coadd patches.
139 
140  Returns
141  -------
142  result : `lsst.pipe.base.Struct`
143  - ``exposure`` : `lsst.afw.image.ExposureF`
144  a template coadd exposure assembled out of patches
145  - ``sources`` : `None` for this subtask
146  """
147  skyMap = butlerQC.get(skyMapRef)
148  tractInfo, patchList, skyCorners = self.getOverlapPatchList(exposure, skyMap)
149  patchNumFilter = frozenset(tractInfo.getSequentialPatchIndex(p) for p in patchList)
150 
151  availableCoaddRefs = dict()
152  for coaddRef in coaddExposureRefs:
153  dataId = coaddRef.datasetRef.dataId
154  if dataId['tract'] == tractInfo.getId() and dataId['patch'] in patchNumFilter:
155  if self.config.coaddName == 'dcr':
156  self.log.info("Using template input tract=%s, patch=%s, subfilter=%s" %
157  (tractInfo.getId(), dataId['patch'], dataId['subfilter']))
158  if dataId['patch'] in availableCoaddRefs:
159  availableCoaddRefs[dataId['patch']].append(butlerQC.get(coaddRef))
160  else:
161  availableCoaddRefs[dataId['patch']] = [butlerQC.get(coaddRef), ]
162  else:
163  self.log.info("Using template input tract=%s, patch=%s" %
164  (tractInfo.getId(), dataId['patch']))
165  availableCoaddRefs[dataId['patch']] = butlerQC.get(coaddRef)
166 
167  templateExposure = self.run(tractInfo, patchList, skyCorners, availableCoaddRefs,
168  visitInfo=exposure.getInfo().getVisitInfo())
169  return pipeBase.Struct(exposure=templateExposure, sources=None)
170 
171  def getOverlapPatchList(self, exposure, skyMap):
172  """Select the relevant tract and its patches that overlap with the science exposure.
173 
174  Parameters
175  ----------
176  exposure : `lsst.afw.image.Exposure`
177  The science exposure to define the sky region of the template coadd.
178 
179  skyMap : `lsst.skymap.BaseSkyMap`
180  SkyMap object that corresponds to the template coadd.
181 
182  Returns
183  -------
184  result : `tuple` of
185  - ``tractInfo`` : `lsst.skymap.TractInfo`
186  The selected tract.
187  - ``patchList`` : `list` of `lsst.skymap.PatchInfo`
188  List of all overlap patches of the selected tract.
189  - ``skyCorners`` : `list` of `lsst.geom.SpherePoint`
190  Corners of the exposure in the sky in the order given by `lsst.geom.Box2D.getCorners`.
191  """
192  expWcs = exposure.getWcs()
193  expBoxD = geom.Box2D(exposure.getBBox())
194  expBoxD.grow(self.config.templateBorderSize)
195  ctrSkyPos = expWcs.pixelToSky(expBoxD.getCenter())
196  tractInfo = skyMap.findTract(ctrSkyPos)
197  self.log.info("Using skyMap tract %s" % (tractInfo.getId(),))
198  skyCorners = [expWcs.pixelToSky(pixPos) for pixPos in expBoxD.getCorners()]
199  patchList = tractInfo.findPatchList(skyCorners)
200 
201  if not patchList:
202  raise RuntimeError("No suitable tract found")
203 
204  self.log.info("Assembling %s coadd patches" % (len(patchList),))
205  self.log.info("exposure dimensions=%s" % exposure.getDimensions())
206 
207  return (tractInfo, patchList, skyCorners)
208 
209  def run(self, tractInfo, patchList, skyCorners, availableCoaddRefs,
210  sensorRef=None, visitInfo=None):
211  """Gen2 and gen3 shared code: determination of exposure dimensions and
212  copying of pixels from overlapping patch regions.
213 
214  Parameters
215  ----------
216  skyMap : `lsst.skymap.BaseSkyMap`
217  SkyMap object that corresponds to the template coadd.
218  tractInfo : `lsst.skymap.TractInfo`
219  The selected tract.
220  patchList : iterable of `lsst.skymap.patchInfo.PatchInfo`
221  Patches to consider for making the template exposure.
222  skyCorners : list of `lsst.geom.SpherePoint`
223  Sky corner coordinates to be covered by the template exposure.
224  availableCoaddRefs : `dict` of `int` : `lsst.daf.butler.DeferredDatasetHandle` (Gen3)
225  `dict` (Gen2)
226  Dictionary of spatially relevant retrieved coadd patches,
227  indexed by their sequential patch number. In Gen3 mode, .get() is called,
228  in Gen2 mode, sensorRef.get(**coaddef) is called to retrieve the coadd.
229  sensorRef : `lsst.daf.persistence.ButlerDataRef`, Gen2 only
230  Butler data reference to get coadd data.
231  Must be `None` for Gen3.
232  visitInfo : `lsst.afw.image.VisitInfo`, Gen2 only
233  VisitInfo to make dcr model.
234 
235  Returns
236  -------
237  templateExposure: `lsst.afw.image.ExposureF`
238  The created template exposure.
239  """
240  coaddWcs = tractInfo.getWcs()
241 
242  # compute coadd bbox
243  coaddBBox = geom.Box2D()
244  for skyPos in skyCorners:
245  coaddBBox.include(coaddWcs.skyToPixel(skyPos))
246  coaddBBox = geom.Box2I(coaddBBox)
247  self.log.info("coadd dimensions=%s" % coaddBBox.getDimensions())
248 
249  coaddExposure = afwImage.ExposureF(coaddBBox, coaddWcs)
250  coaddExposure.maskedImage.set(np.nan, afwImage.Mask.getPlaneBitMask("NO_DATA"), np.nan)
251  nPatchesFound = 0
252  coaddFilter = None
253  coaddPsf = None
254  coaddPhotoCalib = None
255  for patchInfo in patchList:
256  patchNumber = tractInfo.getSequentialPatchIndex(patchInfo)
257  patchSubBBox = patchInfo.getOuterBBox()
258  patchSubBBox.clip(coaddBBox)
259  if patchSubBBox.isEmpty():
260  self.log.info(f"skip tract={availableCoaddRefs[patchNumber]['tract']}, "
261  f"patch={patchNumber}; no overlapping pixels")
262  continue
263 
264  if self.config.coaddName == 'dcr':
265  patchInnerBBox = patchInfo.getInnerBBox()
266  patchInnerBBox.clip(coaddBBox)
267  if np.min(patchInnerBBox.getDimensions()) <= 2*self.config.templateBorderSize:
268  self.log.info("skip tract=%(tract)s, patch=%(patch)s; too few pixels."
269  % availableCoaddRefs[patchNumber])
270  continue
271  self.log.info("Constructing DCR-matched template for patch %s"
272  % availableCoaddRefs[patchNumber])
273 
274  if sensorRef:
275  dcrModel = DcrModel.fromDataRef(sensorRef, **availableCoaddRefs[patchNumber])
276  else:
277  dcrModel = DcrModel.fromQuantum(availableCoaddRefs[patchNumber])
278  # The edge pixels of the DcrCoadd may contain artifacts due to missing data.
279  # Each patch has significant overlap, and the contaminated edge pixels in
280  # a new patch will overwrite good pixels in the overlap region from
281  # previous patches.
282  # Shrink the BBox to remove the contaminated pixels,
283  # but make sure it is only the overlap region that is reduced.
284  dcrBBox = geom.Box2I(patchSubBBox)
285  dcrBBox.grow(-self.config.templateBorderSize)
286  dcrBBox.include(patchInnerBBox)
287  coaddPatch = dcrModel.buildMatchedExposure(bbox=dcrBBox,
288  wcs=coaddWcs,
289  visitInfo=visitInfo)
290  else:
291  if sensorRef is None:
292  # Gen3
293  coaddPatch = availableCoaddRefs[patchNumber].get()
294  else:
295  # Gen2
296  coaddPatch = sensorRef.get(**availableCoaddRefs[patchNumber])
297  nPatchesFound += 1
298 
299  # Gen2 get() seems to clip based on bbox kwarg but we removed bbox
300  # calculation from caller code. Gen3 also does not do this.
301  overlapBox = coaddPatch.getBBox()
302  overlapBox.clip(coaddBBox)
303  coaddExposure.maskedImage.assign(coaddPatch.maskedImage[overlapBox], overlapBox)
304 
305  if coaddFilter is None:
306  coaddFilter = coaddPatch.getFilter()
307 
308  # Retrieve the PSF for this coadd tract, if not already retrieved
309  if coaddPsf is None and coaddPatch.hasPsf():
310  coaddPsf = coaddPatch.getPsf()
311 
312  # Retrieve the calibration for this coadd tract, if not already retrieved
313  if coaddPhotoCalib is None:
314  coaddPhotoCalib = coaddPatch.getPhotoCalib()
315 
316  if coaddPhotoCalib is None:
317  raise RuntimeError("No coadd PhotoCalib found!")
318  if nPatchesFound == 0:
319  raise RuntimeError("No patches found!")
320  if coaddPsf is None:
321  raise RuntimeError("No coadd Psf found!")
322 
323  coaddExposure.setPhotoCalib(coaddPhotoCalib)
324  coaddExposure.setPsf(coaddPsf)
325  coaddExposure.setFilter(coaddFilter)
326  return coaddExposure
327 
329  """Return coadd name for given task config
330 
331  Returns
332  -------
333  CoaddDatasetName : `string`
334 
335  TODO: This nearly duplicates a method in CoaddBaseTask (DM-11985)
336  """
337  warpType = self.config.warpType
338  suffix = "" if warpType == "direct" else warpType[0].upper() + warpType[1:]
339  return self.config.coaddName + "Coadd" + suffix
340 
341 
342 class GetCalexpAsTemplateConfig(pexConfig.Config):
343  doAddCalexpBackground = pexConfig.Field(
344  dtype=bool,
345  default=True,
346  doc="Add background to calexp before processing it."
347  )
348 
349 
350 class GetCalexpAsTemplateTask(pipeBase.Task):
351  """Subtask to retrieve calexp of the same ccd number as the science image SensorRef
352  for use as an image difference template. Only gen2 supported.
353 
354  To be run as a subtask by pipe.tasks.ImageDifferenceTask.
355  Intended for use with simulations and surveys that repeatedly visit the same pointing.
356  This code was originally part of Winter2013ImageDifferenceTask.
357  """
358 
359  ConfigClass = GetCalexpAsTemplateConfig
360  _DefaultName = "GetCalexpAsTemplateTask"
361 
362  def run(self, exposure, sensorRef, templateIdList):
363  """Return a calexp exposure with based on input sensorRef.
364 
365  Construct a dataId based on the sensorRef.dataId combined
366  with the specifications from the first dataId in templateIdList
367 
368  Parameters
369  ----------
370  exposure : `lsst.afw.image.Exposure`
371  exposure (unused)
372  sensorRef : `list` of `lsst.daf.persistence.ButlerDataRef`
373  Data reference of the calexp(s) to subtract from.
374  templateIdList : `list` of `lsst.daf.persistence.ButlerDataRef`
375  Data reference of the template calexp to be subtraced.
376  Can be incomplete, fields are initialized from `sensorRef`.
377  If there are multiple items, only the first one is used.
378 
379  Returns
380  -------
381  result : `struct`
382 
383  return a pipeBase.Struct:
384 
385  - ``exposure`` : a template calexp
386  - ``sources`` : source catalog measured on the template
387  """
388 
389  if len(templateIdList) == 0:
390  raise RuntimeError("No template data reference supplied.")
391  if len(templateIdList) > 1:
392  self.log.warn("Multiple template data references supplied. Using the first one only.")
393 
394  templateId = sensorRef.dataId.copy()
395  templateId.update(templateIdList[0])
396 
397  self.log.info("Fetching calexp (%s) as template." % (templateId))
398 
399  butler = sensorRef.getButler()
400  template = butler.get(datasetType="calexp", dataId=templateId)
401  if self.config.doAddCalexpBackground:
402  templateBg = butler.get(datasetType="calexpBackground", dataId=templateId)
403  mi = template.getMaskedImage()
404  mi += templateBg.getImage()
405 
406  if not template.hasPsf():
407  raise pipeBase.TaskError("Template has no psf")
408 
409  templateSources = butler.get(datasetType="src", dataId=templateId)
410  return pipeBase.Struct(exposure=template,
411  sources=templateSources)
412 
413  def runDataRef(self, *args, **kwargs):
414  return self.run(*args, **kwargs)
415 
416  def runQuantum(self, **kwargs):
417  raise NotImplementedError("Calexp template is not supported with gen3 middleware")
lsst::ip::diffim.getTemplate.GetCoaddAsTemplateTask.runQuantum
def runQuantum(self, exposure, butlerQC, skyMapRef, coaddExposureRefs)
Definition: getTemplate.py:125
lsst::afw::image
lsst::ip::diffim.getTemplate.GetCalexpAsTemplateConfig
Definition: getTemplate.py:342
lsst::ip::diffim.getTemplate.GetCalexpAsTemplateTask.runQuantum
def runQuantum(self, **kwargs)
Definition: getTemplate.py:416
lsst::ip::diffim.dcrModel
Definition: dcrModel.py:1
lsst::ip::diffim.getTemplate.GetCoaddAsTemplateTask.getCoaddDatasetName
def getCoaddDatasetName(self)
Definition: getTemplate.py:328
lsst::ip::diffim.getTemplate.GetCalexpAsTemplateTask
Definition: getTemplate.py:350
lsst::ip::diffim.getTemplate.GetCoaddAsTemplateConfig
Definition: getTemplate.py:35
lsst::ip::diffim.getTemplate.GetCalexpAsTemplateTask.run
def run(self, exposure, sensorRef, templateIdList)
Definition: getTemplate.py:362
lsst::pex::config
lsst::ip::diffim.getTemplate.GetCoaddAsTemplateTask.getOverlapPatchList
def getOverlapPatchList(self, exposure, skyMap)
Definition: getTemplate.py:171
lsst::ip::diffim.getTemplate.GetCalexpAsTemplateTask.runDataRef
def runDataRef(self, *args, **kwargs)
Definition: getTemplate.py:413
lsst::geom
lsst::ip::diffim.getTemplate.GetCoaddAsTemplateTask.runDataRef
def runDataRef(self, exposure, sensorRef, templateIdList=None)
Definition: getTemplate.py:80
lsst::ip::diffim.getTemplate.GetCoaddAsTemplateTask
Definition: getTemplate.py:58
lsst::geom::Box2I
lsst::ip::diffim.getTemplate.GetCoaddAsTemplateTask.run
def run(self, tractInfo, patchList, skyCorners, availableCoaddRefs, sensorRef=None, visitInfo=None)
Definition: getTemplate.py:209
lsst::geom::Box2D