DM-15862: Reduce ISR code duplication between ip_isr, obs_subaru, and obs_decam

config/isr.py

@@ -1,15 +1,108 @@
 """
 DECam-specific overrides of IsrTask
 """
+import os.path
+
 from lsst.obs.decam.crosstalk import DecamCrosstalkTask
-config.crosstalk.retarget(DecamCrosstalkTask)
 
-config.doCrosstalk = True
-config.doDark = False
-config.doAddDistortionModel = False  # rely on the TPV terms instead
-config.fringe.filters = ['z', 'y']
+config.datasetType = "raw"
+config.fallbackFilterName = None
+config.expectWcs = True
+config.fwhm = 1.0
+
+config.doConvertIntToFloat = False
+
+config.doSaturation=True
+config.saturatedMaskName = "SAT"
+config.saturation = float("NaN")
+config.growSaturationFootprintSize = 1
+
+config.doSuspect=True
+config.suspectMaskName = "SUSPECT"
+config.numEdgeSuspect = 35
+
+config.doSetBadRegions = True
+config.badStatistic = "MEANCLIP"
+
+config.doOverscan = True
+config.overscanFitType = "MEDIAN"
+config.overscanOrder = 1
+config.overscanNumSigmaClip = 3.0
+config.overscanNumLeadingColumnsToSkip = 0
+config.overscanNumTrailingColumnsToSkip = 0
+config.overscanMaxDev = 1000.0
+config.overscanBiasJump = True
+config.overscanBiasJumpKeyword = "FPA"
+config.overscanBiasJumpDevices = ["DECAM_BKP3", "DECAM_BKP5", "DECAM_BKP1", "DECAM_BKP4"]
+config.overscanBiasJumpLocation = 2098
+
+config.doAssembleCcd = True
+# Use default ISR assembleCcdTask
+config.assembleCcd.doTrim = True
 config.assembleCcd.keysToRemove = ['DATASECA', 'DATASECB',
                                    'TRIMSECA', 'TRIMSECB',
                                    'BIASSECA', 'BIASSECB',
                                    'PRESECA', 'PRESECB',
                                    'POSTSECA', 'POSTSECB']
+
+config.doAssembleIsrExposures = False
+config.doTrimToMatchCalib = True
+
+config.doBias = True
+config.biasDataProductName = "cpBias"
+
+config.doVariance = True
+config.gain = float("NaN")
+config.readNoise = 0.0
+config.doEmpiricalReadNoise = False
+
+config.doLinearize = True
+
+config.doCrosstalkBeforeAssemble = True
+config.doCrosstalk = True
+config.crosstalk.retarget(DecamCrosstalkTask)
+config.crosstalk.minPixelToMask=45000.0
+config.crosstalk.crosstalkMaskPlane="CROSSTALK"
+
+config.doWidenSaturationTrails = True
+
+config.doBrighterFatter = False
+
+config.doDefect = True
+config.doSaturationInterpolation = True
+config.numEdgeSuspect=35
+
+config.doDark = False
+config.darkDataProductName = "dark"
+
+config.doStrayLight = False
+
+config.doFlat = True
+config.flatDataProductName = "cpFlat"
+config.flatScalingType = "USER"
+config.flatUserScale = 1.0
+config.doTweakFlat = False
+
+config.doApplyGains = False
+config.normalizeGains = False
+
+config.doFringe = True
+config.fringeAfterFlat = True
+config.fringe.filters = ['z', 'y']
+
+config.doNanInterpAfterFlat = False
+
+config.doAddDistortionModel = False  # rely on the TPV terms instead
+
+config.doMeasureBackground = True
+
+config.doCameraSpecificMasking = False
+
+config.doVignette = False
+config.doAttachTransmissionCurve = False
+config.doUseOpticsTransmission = False
+config.doUseFilterTransmission = False
+config.doUseSensorTransmission = False
+config.doUseAtmosphereTransmission = False
+
+config.doWrite = True

config/processCcd.py

@@ -5,11 +5,9 @@
 
 from lsst.utils import getPackageDir
 from lsst.meas.algorithms import LoadIndexedReferenceObjectsTask
-from lsst.obs.decam.isr import DecamIsrTask
 
 obsConfigDir = os.path.join(getPackageDir('obs_decam'), 'config')
 
-config.isr.retarget(DecamIsrTask)
 config.isr.load(os.path.join(obsConfigDir, 'isr.py'))
 
 config.charImage.repair.cosmicray.nCrPixelMax = 100000

config/processCcdCpIsr.py

@@ -5,11 +5,9 @@
 
 from lsst.utils import getPackageDir
 from lsst.meas.algorithms import LoadIndexedReferenceObjectsTask
-from lsst.obs.decam.decamCpIsr import DecamCpIsrTask
 
 obsConfigDir = os.path.join(getPackageDir('obs_decam'), 'config')
 
-config.isr.retarget(DecamCpIsrTask)
 config.isr.load(os.path.join(obsConfigDir, 'isr.py'))
 
 config.charImage.repair.cosmicray.nCrPixelMax = 100000

config/runIsr.py

@@ -4,9 +4,7 @@
 import os.path
 
 from lsst.utils import getPackageDir
-from lsst.obs.decam.isr import DecamIsrTask
 
 obsConfigDir = os.path.join(getPackageDir("obs_decam"), "config")
 
-config.isr.retarget(DecamIsrTask)
 config.isr.load(os.path.join(obsConfigDir, "isr.py"))

config/runIsrCp.py

@@ -4,9 +4,7 @@
 import os.path
 
 from lsst.utils import getPackageDir
-from lsst.obs.decam.decamCpIsr import DecamCpIsrTask
 
 obsConfigDir = os.path.join(getPackageDir("obs_decam"), "config")
 
-config.isr.retarget(DecamCpIsrTask)
 config.isr.load(os.path.join(obsConfigDir, "isr.py"))

policy/DecamMapper.yaml

@@ -213,7 +213,7 @@ datasets:
     template: '%(visit)07d/metadata/metadata-%(visit)07d_%(ccdnum)02d.yaml'
   isr_config:
     python: lsst.obs.decam.isr.DecamIsrConfig
-  isr_metadata:
+  runIsr_metadata:
     template: '%(visit)07d/metadata/metadata-%(visit)07d_%(ccdnum)02d.yaml'
   characterizeImage_metadata:
     template: '%(visit)07d/metadata/metadata-%(visit)07d_%(ccdnum)02d.yaml'
@@ -264,4 +264,8 @@ datasets:
   dcrDiff_kernelSrc:
     template: dcrDiff/v%(visit)d/kernelSrc-%(ccdnum)02d.fits
   apPipe_metadata:
-    template: '%(visit)07d/apPipe_metadata/metadata-%(visit)07d_%(ccdnum)02d.yaml'
+    template: '%(visit)07d/apPipe_metadata/metadata-%(visit)07d_%(ccdnum)02d.yaml'
+  ossThumb:
+    template: '%(visit)07d/thumbs/oss-%(visit)07d-%(ccdnum)03d.png'
+  flattenedThumb:
+    template: '%(visit)07d/thumbs/flattened-%(visit)07d-%(ccdnum)03d.png'

python/lsst/obs/decam/crosstalk.py

@@ -37,11 +37,11 @@
 
 import lsst.log
 import lsst.pipe.base as pipeBase
-from lsst.ip.isr import CrosstalkConfig, CrosstalkTask
+from lsst.ip.isr import CrosstalkConfig, CrosstalkTask, IsrTask
 from lsst.obs.decam import DecamMapper
 from lsst.utils import getPackageDir
 import lsst.afw.math as afwMath
-from .isr import DecamIsrTask
+
 
 __all__ = ["DecamCrosstalkTask"]
 
@@ -142,7 +142,7 @@ def prepCrosstalk(self, dataRef):
         ccdnum = det.getId()
         ccdnum_str = '%02d' % ccdnum
         crosstalkSources = defaultdict(list)
-        decamisr = DecamIsrTask()  # needed for source_exposure overscan correction
+        decamisr = IsrTask()  # needed for source_exposure overscan correction
         for amp in det:
             victim = ccdnum_str + amp.getName()
             for source in sources[victim]:
@@ -160,15 +160,17 @@ def prepCrosstalk(self, dataRef):
                     else:
                         self.log.fatal('DECam source amp name does not contain A or B, cannot proceed')
                     source_amp = source_exposure.getDetector()[amp_idx]
-                    source_dataBBox = source_amp.getRawDataBBox()
+                    # If doCrosstalkBeforeAssemble=True, then use getRawBBox().  Otherwise, getRawDataBBox().
+                    source_dataBBox = source_amp.getRawBBox()
                     # Check to see if source overscan has been corrected, and if not, correct it first
                     if not source_exposure.getMetadata().exists('OVERSCAN'):
                         decamisr.overscanCorrection(source_exposure, source_amp)
                         self.log.info('Correcting source %s overscan before using to correct crosstalk'
                                       % source)
                     source_image = source_exposure.getMaskedImage().getImage()
+
                     source_data = source_image.Factory(source_image, source_dataBBox, deep=True)
-                    crosstalkSources[victim].append((source_data, coeffs[(victim, source)]))
+                    crosstalkSources[victim].append((source_data, coeffs[(victim, source)], amp_idx))
         return crosstalkSources
 
     @pipeBase.timeMethod
@@ -204,19 +206,28 @@ def run(self, exposure, crosstalkSources=None):
             ccdnum = det.getId()
             ccdnum_str = '%02d' % ccdnum
             victim = ccdnum_str + amp.getName()
-            dataBBox = amp.getRawDataBBox()
+            # If doCrosstalkBeforeAssemble=True, then use getRawBBox().  Otherwise, getBBox().
+            dataBBox = amp.getRawBBox()
             # Check to see if victim overscan has been corrected, and if not, correct it first
             if not exposure.getMetadata().exists('OVERSCAN'):
-                decamisr = DecamIsrTask()
+                decamisr = IsrTask()
                 decamisr.overscanCorrection(exposure, amp)
                 self.log.warn('Overscan correction did not happen prior to crosstalk correction')
                 self.log.info('Correcting victim %s overscan before crosstalk' % victim)
             image = exposure.getMaskedImage().getImage()
             victim_data = image.Factory(image, dataBBox)
             # Load data from crosstalk 'source' exposures
             for source in crosstalkSources[victim]:
-                source_data, source_coeff = source
-                if victim_data.getX0() != source_data.getX0():
+                source_data, source_coeff, source_idx = source
+                victim_idx = 0
+                if 'A' in victim:
+                    victim_idx = 0
+                elif 'B' in victim:
+                    victim_idx = 1
+                else:
+                    self.log.fatal('DECam victim amp name does not contain A or B, cannot proceed')
+
+                if source_idx != victim_idx:
                     # Occurs with amp A and B mismatch; need to flip horizontally
                     source_data = afwMath.flipImage(source_data, flipLR=True, flipTB=False)
                 # Perform the linear crosstalk correction