Merge branch 'tickets/DM-47195'

python/lsst/ip/isr/crosstalk.py

@@ -563,7 +563,7 @@ def calculateBackground(mi, badPixels=["BAD"]):
 
     def subtractCrosstalk(self, thisExposure, sourceExposure=None, crosstalkCoeffs=None,
                           crosstalkCoeffsSqr=None, crosstalkCoeffsValid=None,
-                          badPixels=["BAD"], minPixelToMask=45000,
+                          badPixels=["BAD"], minPixelToMask=45000, doSubtrahendMasking=False,
                           crosstalkStr="CROSSTALK", isTrimmed=False,
                           backgroundMethod="None", doSqrCrosstalk=False, fullAmplifier=False,
                           parallelOverscan=False, detectorConfig=None, badAmpDict=None):
@@ -773,12 +773,26 @@ def subtractCrosstalk(self, thisExposure, sourceExposure=None, crosstalkCoeffs=N
                         fullAmplifier=fullAmplifier,
                         parallelOverscan=parallelOverscan,
                     )
+                    tImageSqr.getMask().getArray()[:] &= crosstalk  # Remove all other masks
+                    tImageSqr -= backgrounds[tt]**2
                     sImage.scaledPlus(coeffsSqr[ss, tt], tImageSqr)
 
         # Set crosstalkStr bit only for those pixels that have been
         # significantly modified (i.e., those masked as such in 'subtrahend'),
         # not necessarily those that are bright originally.
         mask.clearMaskPlane(crosstalkPlane)
+
+        if doSubtrahendMasking:
+            subtrahend.mask.clearMaskPlane(crosstalkPlane)
+            # Run detection twice to avoid needing an absolute value image
+            threshold = lsst.afw.detection.Threshold(minPixelToMask, polarity=True)
+            footprints = lsst.afw.detection.FootprintSet(subtrahend, threshold)
+            footprints.setMask(subtrahend.mask, crosstalkStr)
+
+            threshold = lsst.afw.detection.Threshold(minPixelToMask, polarity=False)
+            footprints = lsst.afw.detection.FootprintSet(subtrahend, threshold)
+            footprints.setMask(subtrahend.mask, crosstalkStr)
+
         mi -= subtrahend  # also sets crosstalkStr bit for bright pixels
 
 
@@ -794,6 +808,11 @@ class CrosstalkConfig(Config):
         doc="Name for crosstalk mask plane.",
         default="CROSSTALK"
     )
+    doSubtrahendMasking = Field(
+        dtype=bool,
+        doc="Use subtrahend image thresholding instead of input image thesholding to set crosstalk mask?",
+        default=False,
+    )
     crosstalkBackgroundMethod = ChoiceField(
         dtype=str,
         doc="Type of background subtraction to use when applying correction.",
@@ -1037,6 +1056,7 @@ def run(
                 crosstalkCoeffsSqr=crosstalkCoeffsSqr,
                 crosstalkCoeffsValid=crosstalk.coeffValid,
                 minPixelToMask=self.config.minPixelToMask,
+                doSubtrahendMasking=self.config.doSubtrahendMasking,
                 crosstalkStr=self.config.crosstalkMaskPlane,
                 isTrimmed=isTrimmed,
                 backgroundMethod=self.config.crosstalkBackgroundMethod,

tests/test_crosstalk.py

@@ -162,6 +162,10 @@ def construct(imageList):
         self.exposure = lsst.afw.image.makeExposure(lsst.afw.image.makeMaskedImage(construct(withCrosstalk)))
         self.exposure.setDetector(ccd1)
 
+        # Add a saturated region so we can confirm it doesn't get duplicated.
+        saturatedBit = self.exposure.mask.getPlaneBitMask("SAT")
+        self.exposure.mask.array[0:5, 0:5] |= saturatedBit
+
         # Create a single ctSource that will be used for interChip CT
         # correction.
         self.ctSource = lsst.afw.image.makeExposure(lsst.afw.image.makeMaskedImage(construct(withCrosstalk)))
@@ -218,21 +222,28 @@ def checkSubtracted(self, exposure):
         self.assertFloatsAlmostEqual(image.getArray(), self.corrected.getArray(), atol=2.0e-2)
         self.assertIn(self.crosstalkStr, mask.getMaskPlaneDict())
         self.assertGreater((mask.getArray() & mask.getPlaneBitMask(self.crosstalkStr) > 0).sum(), 0)
+        self.assertEqual((mask.getArray() & mask.getPlaneBitMask("SAT") > 0).sum(), 25)
 
-    def checkTaskAPI_NL(self, this_isr_task):
+    def checkTaskAPI_NL(self, this_isr_task, doSubtrahendMasking=False):
         """Check the the crosstalk task under different ISR tasks.
         (e.g., IsrTask and IsrTaskLSST)
 
         Parameters
         ----------
         this_isr_task : `lsst.pipe.base.PipelineTask`
+            The ISR Task instance to use.
+        doSubtrahendMasking : `bool`
+            Enable subtrahend masking code.
         """
         self.setUp_general(doSqrCrosstalk=True)
         coeff = np.array(self.crosstalk).transpose()
         coeffSqr = np.array(self.crosstalk_sqr).transpose()
         config = this_isr_task.ConfigClass()
         config.crosstalk.minPixelToMask = self.value - 1
         config.crosstalk.crosstalkMaskPlane = self.crosstalkStr
+        if doSubtrahendMasking:
+            config.crosstalk.doSubtrahendMasking = True
+            config.crosstalk.minPixelToMask = 1.0
         # Turn on the NL correction
         config.crosstalk.doQuadraticCrosstalkCorrection = True
         isr = this_isr_task(config=config)
@@ -282,7 +293,8 @@ def testTaskAPI_NL(self):
         correction.
         """
         for this_isr_task in [IsrTask, IsrTaskLSST]:
-            self.checkTaskAPI_NL(this_isr_task)
+            for subtrahendMasking in [False, True]:
+                self.checkTaskAPI_NL(this_isr_task, subtrahendMasking)
 
     def test_nullCrosstalkTask(self):
         """Test that the null crosstalk task does not create an error.