Allow using external cals even if calexp WCS is None

This also reorders the selection of suitable calexps such that the
selection based on patch overlap is based on the final calibrated
WCS (i.e. if an external calibration is being applied, this one will
be used instead of the calibration based on single frame measurement).

python/lsst/pipe/tasks/makeCoaddTempExp.py

@@ -30,6 +30,7 @@
 import lsst.pipe.base.connectionTypes as connectionTypes
 import lsst.utils as utils
 import lsst.geom
+from lsst.daf.butler import DeferredDatasetHandle
 from lsst.meas.algorithms import CoaddPsf, CoaddPsfConfig
 from lsst.skymap import BaseSkyMap
 from lsst.utils.timer import timeMethod
@@ -790,20 +791,6 @@ def runQuantum(self, butlerQC, inputRefs, outputRefs):
         # Construct list of packed integer IDs expected by `run`
         ccdIdList = [dataId.pack("visit_detector") for dataId in dataIdList]
 
-        # Run the selector and filter out calexps that were not selected
-        # primarily because they do not overlap the patch
-        cornerPosList = lsst.geom.Box2D(skyInfo.bbox).getCorners()
-        coordList = [skyInfo.wcs.pixelToSky(pos) for pos in cornerPosList]
-        goodIndices = self.select.run(**inputs, coordList=coordList, dataIds=dataIdList)
-        inputs = self.filterInputs(indices=goodIndices, inputs=inputs)
-
-        # Read from disk only the selected calexps
-        inputs['calExpList'] = [ref.get() for ref in inputs['calExpList']]
-
-        # Extract integer visitId requested by `run`
-        visits = [dataId['visit'] for dataId in dataIdList]
-        visitId = visits[0]
-
         if self.config.doApplyExternalSkyWcs:
             if self.config.useGlobalExternalSkyWcs:
                 externalSkyWcsCatalog = inputs.pop("externalSkyWcsGlobalCatalog")
@@ -825,13 +812,25 @@ def runQuantum(self, butlerQC, inputRefs, outputRefs):
         else:
             finalizedPsfApCorrCatalog = None
 
+        # Do an initial selection on inputs with complete wcs/photoCalib info.
+        # Qualifying calexps will be read in the following call.
         completeIndices = self.prepareCalibratedExposures(**inputs,
                                                           externalSkyWcsCatalog=externalSkyWcsCatalog,
                                                           externalPhotoCalibCatalog=externalPhotoCalibCatalog,
                                                           finalizedPsfApCorrCatalog=finalizedPsfApCorrCatalog)
-        # Redo the input selection with inputs with complete wcs/photocalib info.
         inputs = self.filterInputs(indices=completeIndices, inputs=inputs)
 
+        # Do another selection based on the configured selection task
+        # (using updated WCSs to determine patch overlap if an external
+        # calibration was applied).
+        cornerPosList = lsst.geom.Box2D(skyInfo.bbox).getCorners()
+        coordList = [skyInfo.wcs.pixelToSky(pos) for pos in cornerPosList]
+        goodIndices = self.select.run(**inputs, coordList=coordList, dataIds=dataIdList)
+        inputs = self.filterInputs(indices=goodIndices, inputs=inputs)
+
+        # Extract integer visitId requested by `run`
+        visitId = dataIdList[0]["visit"]
+
         results = self.run(**inputs, visitId=visitId,
                            ccdIdList=[ccdIdList[i] for i in goodIndices],
                            dataIdList=[dataIdList[i] for i in goodIndices],
@@ -855,16 +854,23 @@ def filterInputs(self, indices, inputs):
                 inputs[key] = [inputs[key][ind] for ind in indices]
         return inputs
 
-    def prepareCalibratedExposures(self, calExpList, backgroundList=None, skyCorrList=None,
+    def prepareCalibratedExposures(self, calExpList, wcsList, backgroundList=None, skyCorrList=None,
                                    externalSkyWcsCatalog=None, externalPhotoCalibCatalog=None,
                                    finalizedPsfApCorrCatalog=None,
                                    **kwargs):
         """Calibrate and add backgrounds to input calExpList in place
 
         Parameters
         ----------
-        calExpList : `list` of `lsst.afw.image.Exposure`
+        calExpList : `list` of `lsst.afw.image.Exposure` or
+                     `lsst.daf.butler.DeferredDatasetHandle`
             Sequence of calexps to be modified in place
+        wcsList : `list` of `lsst.afw.geom.SkyWcs`
+            The WCSs of the calexps in ``calExpList``.  When
+            ``externalSkyCatalog`` is `None`, these are used to determine if
+            the calexp should be included in the warp, namely checking that it
+            is not `None`.  If ``externalSkyCatalog`` is not `None`, this list
+            will be dynamically updates with the external sky WCS.
         backgroundList : `list` of `lsst.afw.math.backgroundList`, optional
             Sequence of backgrounds to be added back in if bgSubtracted=False
         skyCorrList : `list` of `lsst.afw.math.backgroundList`, optional
@@ -896,6 +902,14 @@ def prepareCalibratedExposures(self, calExpList, backgroundList=None, skyCorrLis
         for index, (calexp, background, skyCorr) in enumerate(zip(calExpList,
                                                                   backgroundList,
                                                                   skyCorrList)):
+            if externalSkyWcsCatalog is None and wcsList[index] is None:
+                self.log.warning("Detector id %d for visit %d has None for skyWcs and will not be "
+                                 "used in the warp", calexp.dataId["detector"], calexp.dataId["visit"])
+                continue
+
+            if isinstance(calexp, DeferredDatasetHandle):
+                calexp = calexp.get()
+
             if not self.config.bgSubtracted:
                 calexp.maskedImage += background.getImage()
 
@@ -929,13 +943,15 @@ def prepareCalibratedExposures(self, calExpList, backgroundList=None, skyCorrLis
                                      "and will not be used in the warp.", detectorId)
                     continue
                 skyWcs = row.getWcs()
+                wcsList[index] = skyWcs
                 if skyWcs is None:
                     self.log.warning("Detector id %s has None for skyWcs in externalSkyWcsCatalog "
                                      "and will not be used in the warp.", detectorId)
                     continue
                 calexp.setWcs(skyWcs)
             else:
                 skyWcs = calexp.getWcs()
+                wcsList[index] = skyWcs
                 if skyWcs is None:
                     self.log.warning("Detector id %s has None for skyWcs in the calexp "
                                      "and will not be used in the warp.", detectorId)
@@ -973,6 +989,7 @@ def prepareCalibratedExposures(self, calExpList, backgroundList=None, skyCorrLis
                 calexp.maskedImage -= skyCorr.getImage()
 
             indices.append(index)
+            calExpList[index] = calexp
 
         return indices