Fixed bug where original mask bits aren't persisted in stamps.

python/lsst/ts/wep/task/cutOutDonutsBase.py

@@ -343,7 +343,6 @@ def calculateSN(self, stamp):
              A dictionary of calculated quantities
         """
 
-        stamp.makeMask(self.instConfigFile, self.opticalModel)
         imageArray = stamp.stamp_im.image.array
         mask = stamp.stamp_im.mask
         varianceArray = stamp.stamp_im.variance.array
@@ -437,6 +436,7 @@ def calculateSN(self, stamp):
             "ttl_noise_bkgnd_variance": ttlNoiseBkgndVariance,
             "ttl_noise_donut_variance": ttlNoiseDonutVariance,
         }
+
         return snDict
 
     def filterBadRecentering(self, xShifts, yShifts):
@@ -672,6 +672,9 @@ def cutOutStamps(self, exposure, donutCatalog, defocalType, cameraName):
                 archive_element=linear_wcs,
             )
 
+            # Create image mask
+            donutStamp.makeMask(self.instConfigFile, self.opticalModel)
+
             # Calculate the S/N per stamp
             snQuant.append(self.calculateSN(donutStamp))
 

python/lsst/ts/wep/task/donutStamp.py

@@ -301,12 +301,7 @@ def makeMask(
     ):
         """Create the mask for the image.
 
-        Note the mask is returned in the original coordinate system of the info
-        that came from the butler (i.e. the DVCS, and the CWFSs are rotated
-        with respect to the science sensors). See sitcomtn-003.lsst.io for more
-        information.
-
-        Also note that technically the image masks depend on the optical
+        Note that technically the image masks depend on the optical
         aberrations, but this function assumes the aberrations are zero.
 
         Parameters
@@ -363,6 +358,9 @@ def makeMask(
         nRot = int(eulerZ // 90)
         stampMask = np.rot90(stampMask, -nRot)
 
+        # Add back to the original mask
+        stampMask += self.stamp_im.mask.array
+
         # Save mask
         self.stamp_im.setMask(afwImage.Mask(stampMask.copy()))