DM-10299: Apply crosstalk correction in decam

python/lsst/ip/isr/crosstalk.py

@@ -24,19 +24,14 @@
 """
 from __future__ import absolute_import, division, print_function
 
-__all__ = ["CrosstalkConfig", "CrosstalkTask", "subtractCrosstalk"]
-
-from builtins import zip
-
-import numpy as np
-
 import lsst.afw.math
 import lsst.afw.table
 import lsst.afw.detection
-
-from lsst.pex.config import Config, Field, ListField
+from lsst.pex.config import Config, Field
 from lsst.pipe.base import Task
 
+__all__ = ["CrosstalkConfig", "CrosstalkTask", "subtractCrosstalk"]
+
 
 class CrosstalkConfig(Config):
     """Configuration for intra-CCD crosstalk removal"""
@@ -49,13 +44,26 @@ class CrosstalkTask(Task):
     """Apply intra-CCD crosstalk correction"""
     ConfigClass = CrosstalkConfig
 
-    def run(self, exposure):
+    def prepCrosstalk(self, dataRef):
+        """Placeholder for crosstalk preparation method, e.g., for inter-CCD crosstalk.
+
+        See also
+        --------
+        lsst.obs.decam.crosstalk.DecamCrosstalkTask.prepCrosstalk
+        """
+        return
+
+    def run(self, exposure, crosstalkSources=None):
         """Apply intra-CCD crosstalk correction
 
         Parameters
         ----------
         exposure : `lsst.afw.image.Exposure`
             Exposure for which to remove crosstalk.
+        crosstalkSources : `defaultdict`, optional
+            Image data and crosstalk coefficients from other CCDs/amps that are
+            sources of crosstalk in exposure.
+            The default for intra-CCD crosstalk here is None.
         """
         detector = exposure.getDetector()
         if not detector.hasCrosstalk():

python/lsst/ip/isr/isrTask.py

@@ -81,6 +81,21 @@ class IsrTaskConfig(pexConfig.Config):
         doc="Persist postISRCCD?",
         default=True,
     )
+    biasDataProductName = pexConfig.Field(
+        dtype=str,
+        doc="Name of the bias data product",
+        default="bias",
+    )
+    darkDataProductName = pexConfig.Field(
+        dtype=str,
+        doc="Name of the dark data product",
+        default="dark",
+    )
+    flatDataProductName = pexConfig.Field(
+        dtype=str,
+        doc="Name of the flat data product",
+        default="flat",
+    )
     assembleCcd = pexConfig.ConfigurableField(
         target=AssembleCcdTask,
         doc="CCD assembly task",
@@ -392,14 +407,22 @@ def readIsrData(self, dataRef, rawExposure):
         """
         ccd = rawExposure.getDetector()
 
-        biasExposure = self.getIsrExposure(dataRef, "bias") if self.config.doBias else None
+        biasExposure = self.getIsrExposure(dataRef, self.config.biasDataProductName) \
+            if self.config.doBias else None
         # immediate=True required for functors and linearizers are functors; see ticket DM-6515
         linearizer = dataRef.get("linearizer", immediate=True) if self.doLinearize(ccd) else None
-        darkExposure = self.getIsrExposure(dataRef, "dark") if self.config.doDark else None
-        flatExposure = self.getIsrExposure(dataRef, "flat") if self.config.doFlat else None
+        darkExposure = self.getIsrExposure(dataRef, self.config.darkDataProductName) \
+            if self.config.doDark else None
+        flatExposure = self.getIsrExposure(dataRef, self.config.flatDataProductName) \
+            if self.config.doFlat else None
         brighterFatterKernel = dataRef.get("brighterFatterKernel") if self.config.doBrighterFatter else None
         defectList = dataRef.get("defects") if self.config.doDefect else None
 
+        if self.config.doCrosstalk:
+            crosstalkSources = self.crosstalk.prepCrosstalk(dataRef)
+        else:
+            crosstalkSources = None
+
         if self.config.doFringe and self.fringe.checkFilter(rawExposure):
             fringeStruct = self.fringe.readFringes(dataRef, assembler=self.assembleCcd
                                                    if self.config.doAssembleIsrExposures else None)
@@ -433,13 +456,15 @@ def readIsrData(self, dataRef, rawExposure):
                                filterTransmission=filterTransmission,
                                sensorTransmission=sensorTransmission,
                                atmosphereTransmission=atmosphereTransmission,
+                               crosstalkSources=crosstalkSources,
                                )
 
     @pipeBase.timeMethod
     def run(self, ccdExposure, bias=None, linearizer=None, dark=None, flat=None, defects=None,
             fringes=None, bfKernel=None, camera=None,
             opticsTransmission=None, filterTransmission=None,
-            sensorTransmission=None, atmosphereTransmission=None):
+            sensorTransmission=None, atmosphereTransmission=None,
+            crosstalkSources=None):
         """!Perform instrument signature removal on an exposure
 
         Steps include:
@@ -462,6 +487,7 @@ def run(self, ccdExposure, bias=None, linearizer=None, dark=None, flat=None, def
         @param[in] filterTransmission  a TransmissionCurve for the filter
         @param[in] sensorTransmission  a TransmissionCurve for the sensor
         @param[in] atmosphereTransmission  a TransmissionCurve for the atmosphere
+        @param[in] crosstalkSources  a defaultdict used for DECam inter-CCD crosstalk
 
         @return a pipeBase.Struct with field:
          - exposure
@@ -505,6 +531,9 @@ def run(self, ccdExposure, bias=None, linearizer=None, dark=None, flat=None, def
                 self.suspectDetection(ccdExposure, amp)
                 self.overscanCorrection(ccdExposure, amp)
 
+        if self.config.doCrosstalk:
+            self.crosstalk.run(ccdExposure, crosstalkSources)
+
         if self.config.doAssembleCcd:
             ccdExposure = self.assembleCcd.assembleCcd(ccdExposure)
             if self.config.expectWcs and not ccdExposure.getWcs():
@@ -516,9 +545,6 @@ def run(self, ccdExposure, bias=None, linearizer=None, dark=None, flat=None, def
         if self.doLinearize(ccd):
             linearizer(image=ccdExposure.getMaskedImage().getImage(), detector=ccd, log=self.log)
 
-        if self.config.doCrosstalk:
-            self.crosstalk.run(ccdExposure)
-
         for amp in ccd:
             # if ccdExposure is one amp, check for coverage to prevent performing ops multiple times
             if ccdExposure.getBBox().contains(amp.getBBox()):
@@ -589,16 +615,21 @@ def run(self, ccdExposure, bias=None, linearizer=None, dark=None, flat=None, def
 
     @pipeBase.timeMethod
     def runDataRef(self, sensorRef):
-        """!Perform instrument signature removal on a ButlerDataRef of a Sensor
+        """Perform instrument signature removal on a ButlerDataRef of a Sensor
 
         - Read in necessary detrending/isr/calibration data
         - Process raw exposure in run()
         - Persist the ISR-corrected exposure as "postISRCCD" if config.doWrite is True
 
-        @param[in] sensorRef    daf.persistence.butlerSubset.ButlerDataRef of the
-                                detector data to be processed
-        @return a pipeBase.Struct with fields:
-        - exposure: the exposure after application of ISR
+        Parameters
+        ----------
+        sensorRef : `daf.persistence.butlerSubset.ButlerDataRef`
+            DataRef of the detector data to be processed
+
+        Returns
+        -------
+        result : `pipeBase.Struct`
+            Struct contains field "exposure," which is the exposure after application of ISR
         """
         self.log.info("Performing ISR on sensor %s" % (sensorRef.dataId))
         ccdExposure = sensorRef.get('raw')