Tickets/dm 42572: Add background subtraction to pipeline

doc/versionHistory.rst

@@ -6,6 +6,14 @@
 Version History
 ##################
 
+.. _lsst.ts.wep-8.2.0:
+
+-------------
+8.2.0
+-------------
+
+* Add background subtraction to cutOutDonutsBase.
+
 .. _lsst.ts.wep-8.1.1:
 
 -------------

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

@@ -149,6 +149,10 @@ class CutOutDonutsBaseTaskConfig(
         dtype=int,
         default=6,
     )
+    subtractBackground = pexConfig.ConfigurableField(
+        target=lsst.meas.algorithms.SubtractBackgroundTask,
+        doc="Task to perform background subtraction.",
+    )
 
 
 class CutOutDonutsBaseTask(pipeBase.PipelineTask):
@@ -185,6 +189,8 @@ def __init__(self, **kwargs):
         # Parameters for mask multiplication (for deblending)
         self.multiplyMask = self.config.multiplyMask
         self.maskGrowthIter = self.config.maskGrowthIter
+        # Set up background subtraction task
+        self.makeSubtask("subtractBackground")
 
     def _checkAndSetOffset(self, dataOffsetValue):
         """Check offset in instParams dictionary and if it
@@ -384,6 +390,10 @@ def cutOutStamps(self, exposure, donutCatalog, defocalType, cameraName):
         pixelScale = exposure.getWcs().getPixelScale().asArcseconds()
         camType = getCamTypeFromButlerName(cameraName, detectorType)
         bandpass = exposure.filter.bandLabel
+
+        # Run background subtraction
+        self.subtractBackground.run(exposure=exposure).background
+
         # Get template
         template = self.getTemplate(
             detectorName,

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

@@ -269,17 +269,14 @@ def makeMasks(self, inst, model, boundaryT, maskScalingFactorLocal):
 
         self.comp_im.makeBlendedMask(inst, model, boundaryT, maskScalingFactorLocal)
 
-        # 0 flag in mask is part of image that is not donut
-        # 1 flag in mask means it is part of the model donut
-        maskDict = {"BKGRD": 0, "DONUT": 1}
-
         # Set masks
-        self.mask_comp = afwImage.Mask(np.array(self.comp_im.mask_comp, dtype=np.int32))
-        self.mask_comp.clearMaskPlaneDict()
-        self.mask_comp.conformMaskPlanes(maskDict)
-        # Will inherit conformed MaskPlaneDict
+        afwImage.Mask.addMaskPlane("DONUT")
+        donutMaskVal = afwImage.Mask.getPlaneBitMask("DONUT")
+        self.mask_comp = afwImage.Mask(
+            np.array(self.comp_im.mask_comp, dtype=np.int32) * donutMaskVal
+        )
         self.mask_pupil = afwImage.Mask(
-            np.array(self.comp_im.mask_pupil, dtype=np.int32)
+            np.array(self.comp_im.mask_pupil, dtype=np.int32) * donutMaskVal
         )
 
     def getLinearWCS(self):

tests/task/test_cutOutDonutsBase.py

@@ -247,13 +247,52 @@ def testCalculateFinalCentroid(self):
         self.assertEqual(cornerX, 0)
         self.assertEqual(cornerY, 0)
 
-    def testCutOutStamps(self):
+    def _getExpAndCatalog(self, defocalType):
+        """
+        Helper function to get exposure and donutCatalog for
+        testing cutOutStamps.
+
+        Parameters
+        ----------
+        defocalType : lsst.ts.wep.utils.DefocalType
+            Defocal type of stamp to cut out.
+
+        Returns
+        -------
+        lsst.afw.image.Exposure
+            Exposure related to given defocal type
+        pandas.DataFrame
+            Donut Catalog for exposure
+        """
+
+        if defocalType is DefocalType.Extra:
+            dataId = self.dataIdExtra
+        else:
+            dataId = self.dataIdIntra
+
         exposure = self.butler.get(
-            "postISRCCD", dataId=self.dataIdExtra, collections=[self.runName]
+            "postISRCCD", dataId=dataId, collections=[self.runName]
         )
         donutCatalog = self.butler.get(
-            "donutCatalog", dataId=self.dataIdExtra, collections=[self.runName]
+            "donutCatalog", dataId=dataId, collections=[self.runName]
+        )
+
+        return exposure, donutCatalog
+
+    def testBackgroundSubtractionApplied(self):
+        exposure, donutCatalog = self._getExpAndCatalog(DefocalType.Extra)
+        with self.assertRaises(KeyError):
+            exposure.getMetadata()["BGMEAN"]
+        self.task.cutOutStamps(
+            exposure, donutCatalog, DefocalType.Extra, self.cameraName
         )
+        # cutOutStamps runs background subtraction which is automatically
+        # applied to the exposure. Thus, BGMEAN should now exist in the
+        # exposure metadata.
+        self.assertIsInstance(exposure.getMetadata()["BGMEAN"], float)
+
+    def testCutOutStamps(self):
+        exposure, donutCatalog = self._getExpAndCatalog(DefocalType.Extra)
         donutStamps = self.task.cutOutStamps(
             exposure, donutCatalog, DefocalType.Extra, self.cameraName
         )
@@ -287,13 +326,7 @@ def testCutOutStamps(self):
                 )
 
     def testCutOutStampsBlended(self):
-        exposure = self.butler.get(
-            "postISRCCD", dataId=self.dataIdExtra, collections=[self.runName]
-        )
-        donutCatalog = self.butler.get(
-            "donutCatalog", dataId=self.dataIdExtra, collections=[self.runName]
-        )
-
+        exposure, donutCatalog = self._getExpAndCatalog(DefocalType.Extra)
         donutStampsNoBlend = self.task.cutOutStamps(
             exposure, donutCatalog, DefocalType.Extra, self.cameraName
         )

tests/task/test_donutStamp.py

@@ -267,12 +267,8 @@ def testMakeMasks(self):
         donutStamp.makeMasks(inst, "offAxis", 0, 1)
         self.assertEqual(afwImage.MaskX, type(donutStamp.mask_comp))
         self.assertEqual(afwImage.MaskX, type(donutStamp.mask_pupil))
-        self.assertDictEqual(
-            {"BKGRD": 0, "DONUT": 1}, donutStamp.mask_comp.getMaskPlaneDict()
-        )
-        self.assertDictEqual(
-            {"BKGRD": 0, "DONUT": 1}, donutStamp.mask_pupil.getMaskPlaneDict()
-        )
+        self.assertIn("DONUT", list(donutStamp.mask_comp.getMaskPlaneDict().keys()))
+        self.assertIn("DONUT", list(donutStamp.mask_pupil.getMaskPlaneDict().keys()))
         maskC = donutStamp.mask_comp.getArray()
         maskP = donutStamp.mask_pupil.getArray()
         # Donut should match
@@ -281,6 +277,15 @@ def testMakeMasks(self):
         # Make sure not just an empty array
         self.assertTrue(np.sum(maskC) > 0.0)
         self.assertTrue(np.sum(maskP) > 0.0)
+        # Make sure bits set are donut bits
+        self.assertCountEqual(
+            [0, afwImage.Mask.getPlaneBitMask("DONUT")],
+            list(np.unique(donutStamp.mask_comp.array)),
+        )
+        self.assertCountEqual(
+            [0, afwImage.Mask.getPlaneBitMask("DONUT")],
+            list(np.unique(donutStamp.mask_pupil.array)),
+        )
         # Donut at center of focal plane should be symmetric
         np.testing.assert_array_equal(maskC[:63], maskC[-63:][::-1])
         np.testing.assert_array_equal(maskP[:63], maskP[-63:][::-1])