Implement amp-to-amp offset correction task

This commit adds a placeholder amp offset task which is not implemented
here, and instead should be retargeted by a camera specific version.

python/lsst/ip/isr/ampOffset.py

@@ -0,0 +1,103 @@
+# This file is part of ip_isr.
+#
+# Developed for the LSST Data Management System.
+# This product includes software developed by the LSST Project
+# (https://www.lsst.org).
+# See the COPYRIGHT file at the top-level directory of this distribution
+# for details of code ownership.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+# import os
+
+import lsst.pex.config as pexConfig
+import lsst.pipe.base as pipeBase
+from lsst.meas.algorithms import (SubtractBackgroundTask, SourceDetectionTask)
+
+
+class AmpOffsetConfig(pexConfig.Config):
+    """Configuration parameters for AmpOffsetTask.
+    """
+    ampEdgeInset = pexConfig.Field(
+        doc="Number of pixels the amp edge strip is inset from the amp edge. A thin strip of pixels running "
+        "parallel to the edge of the amp is used to characterize the average flux level at the amp edge.",
+        dtype=int,
+        default=5,
+    )
+    ampEdgeWidth = pexConfig.Field(
+        doc="Pixel width of the amp edge strip, starting at ampEdgeInset and extending inwards.",
+        dtype=int,
+        default=64,
+    )
+    ampEdgeMinFrac = pexConfig.Field(
+        doc="Minimum allowed fraction of viable pixel rows along an amp edge. No amp offset estimate will be "
+        "generated for amp edges that do not have at least this fraction of unmasked pixel rows.",
+        dtype=float,
+        default=0.5,
+    )
+    ampEdgeMaxOffset = pexConfig.Field(
+        doc="Maximum allowed amp offset ADU value. If a measured amp offset value is larger than this, the "
+        "result will be discarded and therefore not used to determine amp pedestal corrections.",
+        dtype=float,
+        default=5.0,
+    )
+    ampEdgeWindow = pexConfig.Field(
+        doc="Pixel size of the sliding window used to generate rolling average amp offset values.",
+        dtype=int,
+        default=512,
+    )
+    doBackground = pexConfig.Field(
+        doc="Estimate and subtract background prior to amp offset estimation?",
+        dtype=bool,
+        default=True,
+    )
+    background = pexConfig.ConfigurableField(
+        doc="An initial background estimation step run prior to amp offset calculation.",
+        target=SubtractBackgroundTask,
+    )
+    doDetection = pexConfig.Field(
+        doc="Detect sources and update cloned exposure prior to amp offset estimation?",
+        dtype=bool,
+        default=True,
+    )
+    detection = pexConfig.ConfigurableField(
+        doc="Source detection to add temporary detection footprints prior to amp offset calculation.",
+        target=SourceDetectionTask,
+    )
+
+
+class AmpOffsetTask(pipeBase.Task):
+    """Calculate and apply amp offset corrections to an exposure.
+    """
+    ConfigClass = AmpOffsetConfig
+    _DefaultName = "isrAmpOffset"
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(**kwargs)
+        # always load background subtask, even if doBackground=False;
+        # this allows for default plane bit masks to be defined
+        self.makeSubtask("background")
+        if self.config.doDetection:
+            self.makeSubtask("detection")
+
+    def run(self, exposure):
+        """Calculate amp offset values, determine corrective pedestals for each
+        amp, and update the input exposure in-place. This task is currently not
+        implemented, and should be retargeted by a camera specific version.
+
+        Parameters
+        ----------
+        exposure : `lsst.afw.image.Exposure`
+            Exposure to be corrected for any amp offsets.
+        """
+        raise NotImplementedError("Amp offset task should be retargeted by a camera specific version.")

python/lsst/ip/isr/isrTask.py

@@ -53,6 +53,7 @@
 from .overscan import OverscanCorrectionTask
 from .straylight import StrayLightTask
 from .vignette import VignetteTask
+from .ampOffset import AmpOffsetTask
 from lsst.daf.butler import DimensionGraph
 
 
@@ -445,7 +446,6 @@ class IsrTaskConfig(pipeBase.PipelineTaskConfig,
         target=OverscanCorrectionTask,
         doc="Overscan subtraction task for image segments.",
     )
-
     overscanFitType = pexConfig.ChoiceField(
         dtype=str,
         doc="The method for fitting the overscan bias level.",
@@ -776,6 +776,17 @@ class IsrTaskConfig(pipeBase.PipelineTaskConfig,
         default=True,
     )
 
+    # Amp offset correction.
+    doAmpOffset = pexConfig.Field(
+        doc="Calculate and apply amp offset corrections?",
+        dtype=bool,
+        default=False,
+    )
+    ampOffset = pexConfig.ConfigurableField(
+        doc="Amp offset correction task.",
+        target=AmpOffsetTask,
+    )
+
     # Initial CCD-level background statistics options.
     doMeasureBackground = pexConfig.Field(
         dtype=bool,
@@ -795,7 +806,6 @@ class IsrTaskConfig(pipeBase.PipelineTaskConfig,
     )
 
     # Interpolation options.
-
     doInterpolate = pexConfig.Field(
         dtype=bool,
         doc="Interpolate masked pixels?",
@@ -967,6 +977,7 @@ def __init__(self, **kwargs):
         self.makeSubtask("masking")
         self.makeSubtask("overscan")
         self.makeSubtask("vignette")
+        self.makeSubtask("ampOffset")
 
     def runQuantum(self, butlerQC, inputRefs, outputRefs):
         inputs = butlerQC.get(inputRefs)
@@ -1709,6 +1720,11 @@ def run(self, ccdExposure, *, camera=None, bias=None, linearizer=None,
 
         self.roughZeroPoint(ccdExposure)
 
+        # correct for amp offsets within the CCD
+        if self.config.doAmpOffset:
+            self.log.info("Correcting amp offsets.")
+            self.ampOffset.run(ccdExposure)
+
         if self.config.doMeasureBackground:
             self.log.info("Measuring background level.")
             self.measureBackground(ccdExposure, self.config.qa)