Split doAmpOffset into measurement and application components

python/lsst/ip/isr/ampOffset.py

@@ -120,6 +120,11 @@ def setDefaults(self):
         dtype=bool,
         default=True,
     )
+    doApplyAmpOffset = Field(
+        doc="Apply amp offset corrections to the input exposure?",
+        dtype=bool,
+        default=False,
+    )
 
 
 class AmpOffsetTask(Task):
@@ -235,22 +240,28 @@ def run(self, exposure):
             # ensuring that no values are erroneously added/subtracted.
             pedestals = np.nan_to_num(np.linalg.lstsq(A, B, rcond=None)[0])
 
-        metadata = exposure.getMetadata()  # Exposure metadata.
+        if self.config.doApplyAmpOffset:
+            metadata = exposure.getMetadata()  # Exposure metadata.
+            status = "applied"
+        else:
+            status = "not applied"
+
         self.metadata["AMPOFFSET_PEDESTALS"] = {}  # Task metadata.
         for amp, pedestal in zip(amps, pedestals):
-            ampIm = exposure.image[amp.getBBox()].array
-            ampIm -= pedestal
             ampName = amp.getName()
-            # Add the amp pedestal to the exposure metadata.
-            metadata.set(
-                f"LSST ISR AMPOFFSET PEDESTAL {ampName}",
-                float(pedestal),
-                f"Pedestal level subtracted from amp {ampName}",
-            )
+            if self.config.doApplyAmpOffset:
+                ampIm = exposure.image[amp.getBBox()].array
+                ampIm -= pedestal
+                # Add the amp pedestal to the exposure metadata.
+                metadata.set(
+                    f"LSST ISR AMPOFFSET PEDESTAL {ampName}",
+                    float(pedestal),
+                    f"Pedestal level subtracted from amp {ampName}",
+                )
             # Add the amp pedestal to the "Task" metadata as well.
             # Needed for Sasquatch/Chronograf!
             self.metadata["AMPOFFSET_PEDESTALS"][ampName] = float(pedestal)
-        self.log.info(f"amp pedestal values: {', '.join([f'{x:.4f}' for x in pedestals])}")
+        self.log.info(f"amp pedestal values ({status}): {', '.join([f'{x:.4f}' for x in pedestals])}")
 
         return Struct(pedestals=pedestals)
 

python/lsst/ip/isr/isrTask.py

@@ -53,7 +53,7 @@
 from .overscan import OverscanCorrectionTask
 from .straylight import StrayLightTask
 from .vignette import VignetteTask
-from .ampOffset import AmpOffsetTask
+from .ampOffset import AmpOffsetConfig, AmpOffsetTask
 from .deferredCharge import DeferredChargeTask
 from .isrStatistics import IsrStatisticsTask
 from .ptcDataset import PhotonTransferCurveDataset
@@ -768,10 +768,22 @@ class IsrTaskConfig(pipeBase.PipelineTaskConfig,
     )
 
     # Amp offset correction.
+    # TODO: Remove this config field on DM-45526.
     doAmpOffset = pexConfig.Field(
         doc="Calculate and apply amp offset corrections?",
         dtype=bool,
         default=False,
+        deprecated="This field is no longer used. Will be removed after v28."
+    )
+    doMeasureAmpOffset = pexConfig.Field(
+        doc="Measure amp offset corrections?",
+        dtype=bool,
+        default=False,
+    )
+    doApplyAmpOffset = pexConfig.Field(
+        doc="Apply amp offset corrections?",
+        dtype=bool,
+        default=False,
     )
     ampOffset = pexConfig.ConfigurableField(
         doc="Amp offset correction task.",
@@ -1702,10 +1714,34 @@ def run(self, ccdExposure, *, camera=None, bias=None, linearizer=None,
 
         self.roughZeroPoint(ccdExposure)
 
+        # Add extra config validation logic that checks for compatibility
+        # among the config options for amp offset correction.
+        if self.config.doApplyAmpOffset and not self.config.doMeasureAmpOffset:
+            raise RuntimeError("doApplyAmpOffset requires doMeasureAmpOffset to be True.")
+
+        # Measure amp offset corrections within the CCD.
+        if self.config.doMeasureAmpOffset:
+            ampOffsetConfig = AmpOffsetConfig()
+            ampOffsetConfig.doMeasureAmpOffset = True
+            if self.config.doApplyAmpOffset:
+                # Correct for amp offsets within the CCD.
+                ampOffsetConfig.doApplyAmpOffset = True
+                self.log.info("Calculating and applying amp offset corrections.")
+            else:
+                ampOffsetConfig.doApplyAmpOffset = False
+                self.log.info("Calculating amp offset corrections without applying them.")
+            ampOffsetTask = self.ampOffset(config=ampOffsetConfig)
+            ampOffsetTask.run(ccdExposure)
+
         # correct for amp offsets within the CCD
+        # TODO: Remove this whole ``if`` clause on DM-45526.
         if self.config.doAmpOffset:
-            self.log.info("Correcting amp offsets.")
-            self.ampOffset.run(ccdExposure)
+            if self.config.doMeasureBackground or self.config.doApplyAmpOffset:
+                raise RuntimeError("Enabling doMeasureBackground or doApplyAmpOffset "
+                                   "requires doAmpOffset to be False.")
+            else:
+                self.log.info("Correcting amp offsets.")
+                self.ampOffset.run(ccdExposure)
 
         if self.config.doMeasureBackground:
             self.log.info("Measuring background level.")

python/lsst/ip/isr/isrTaskLSST.py

@@ -17,6 +17,7 @@
 import lsst.pipe.base.connectionTypes as cT
 from lsst.meas.algorithms.detection import SourceDetectionTask
 
+from .ampOffset import AmpOffsetConfig, AmpOffsetTask
 from .overscan import SerialOverscanCorrectionTask, ParallelOverscanCorrectionTask
 from .overscanAmpConfig import OverscanCameraConfig
 from .assembleCcdTask import AssembleCcdTask
@@ -369,6 +370,22 @@ class IsrTaskLSSTConfig(pipeBase.PipelineTaskConfig,
         default=False,
     )
 
+    # Amp offset correction.
+    doMeasureAmpOffset = pexConfig.Field(
+        doc="Measure amp offset corrections?",
+        dtype=bool,
+        default=False,
+    )
+    doApplyAmpOffset = pexConfig.Field(
+        doc="Apply amp offset corrections?",
+        dtype=bool,
+        default=False,
+    )
+    ampOffset = pexConfig.ConfigurableField(
+        doc="Amp offset correction task.",
+        target=AmpOffsetTask,
+    )
+
     # Initial masking options.
     doSetBadRegions = pexConfig.Field(
         dtype=bool,
@@ -1523,6 +1540,25 @@ def run(self, ccdExposure, *, dnlLUT=None, bias=None, deferredChargeCalib=None,
                 maskNameList=list(self.config.maskListToInterpolate)
             )
 
+        # Add extra config validation logic that checks for compatibility
+        # among the config options for amp offset correction.
+        if self.config.doApplyAmpOffset and not self.config.doMeasureAmpOffset:
+            raise RuntimeError("doApplyAmpOffset requires doMeasureAmpOffset to be True.")
+
+        # Measure amp offset corrections within the CCD.
+        if self.config.doMeasureAmpOffset:
+            ampOffsetConfig = AmpOffsetConfig()
+            ampOffsetConfig.doMeasureAmpOffset = True
+            if self.config.doApplyAmpOffset:
+                # Correct for amp offsets within the CCD.
+                ampOffsetConfig.doApplyAmpOffset = True
+                self.log.info("Calculating and applying amp offset corrections.")
+            else:
+                ampOffsetConfig.doApplyAmpOffset = False
+                self.log.info("Calculating amp offset corrections without applying them.")
+            ampOffsetTask = self.ampOffset(config=ampOffsetConfig)
+            ampOffsetTask.run(ccdExposure)
+
         # Calculate standard image quality statistics
         if self.config.doStandardStatistics:
             metadata = ccdExposure.getMetadata()

tests/test_ampOffset.py

@@ -305,6 +305,7 @@ def runAmpOffsetWithBackground(self, valueType, rampBackground=False):
             config.doDetection = True
             config.ampEdgeWidth = 12
             config.applyWeights = applyWeights
+            config.doApplyAmpOffset = True  # Updates the exposure in place.
             if valueType == "random":
                 # For this specific case, the fraction of unmasked pixels for
                 # amp interface 01 is unusually small.
@@ -372,6 +373,7 @@ def testAmpOffset(self, valueType):
             config.doBackground = False
             config.doDetection = False
             config.ampEdgeWidth = 12  # Given 100x51 amps in our mock detector.
+            config.doApplyAmpOffset = True  # Updates the exposure in place.
             if valueType == "artificial":
                 # For this extreme case, we expect the interface offsets to be
                 # unusually large.