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DM-5081: Mark amplifier edges SUSPECT if brighter-fatter is applied. #104

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Aug 7, 2019
Merged

DM-5081: Mark amplifier edges SUSPECT if brighter-fatter is applied. #104

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5c12f8e
Split edge masking from defect masking.
czwa Jun 27, 2019
bc0130e
Mask edges when doBrighterFatter=True.
czwa Jul 15, 2019
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51 changes: 44 additions & 7 deletions python/lsst/ip/isr/isrTask.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1277,6 +1277,11 @@ def run(self, ccdExposure, camera=None, bias=None, linearizer=None, crosstalkSou
self.log.info("Masking defects.")
self.maskDefect(ccdExposure, defects)

if self.config.numEdgeSuspect > 0:
self.log.info("Masking edges as SUSPECT.")
self.maskEdges(ccdExposure, numEdgePixels=self.config.numEdgeSuspect,
maskPlane="SUSPECT")

if self.config.doNanMasking:
self.log.info("Masking NAN value pixels.")
self.maskNan(ccdExposure)
Expand Down Expand Up @@ -1325,6 +1330,16 @@ def run(self, ccdExposure, camera=None, bias=None, linearizer=None, crosstalkSou
bfCorr -= interpExp.getMaskedImage().getImage()
image += bfCorr

# Applying the brighter-fatter correction applies a
# convolution to the science image. At the edges this
# convolution may not have sufficient valid pixels to
# produce a valid correction. Mark pixels within the size
# of the brighter-fatter kernel as EDGE to warn of this
# fact.
self.maskEdges(ccdExposure, numEdgePixels=numpy.max(bfKernel.shape) // 2,
maskPlane="EDGE")
self.log.warn("Ensuring image edges are masked as SUSPECT to the brighter-fatter kernel size.")

self.debugView(ccdExposure, "doBrighterFatter")

if self.config.doDark:
Expand Down Expand Up @@ -2070,7 +2085,7 @@ def maskDefect(self, exposure, defectBaseList):
Exposure to process.
defectBaseList : `lsst.meas.algorithms.Defects` or `list` of
`lsst.afw.image.DefectBase`.
List of defects to mask and interpolate.
List of defects to mask.

Notes
-----
Expand All @@ -2084,15 +2099,30 @@ def maskDefect(self, exposure, defectBaseList):
defectList = defectBaseList
defectList.maskPixels(maskedImage, maskName="BAD")

if self.config.numEdgeSuspect > 0:
def maskEdges(self, exposure, numEdgePixels=0, maskPlane="SUSPECT"):
"""!Mask edge pixels with applicable mask plane.

Parameters
----------
exposure : `lsst.afw.image.Exposure`
Exposure to process.
numEdgePixels : `int`, optional
Number of edge pixels to mask.
maskPlane : `str`, optional
Mask plane name to use.
"""
maskedImage = exposure.getMaskedImage()
maskBitMask = maskedImage.getMask().getPlaneBitMask(maskPlane)

if numEdgePixels > 0:
goodBBox = maskedImage.getBBox()
# This makes a bbox numEdgeSuspect pixels smaller than the image on each side
goodBBox.grow(-self.config.numEdgeSuspect)
# Mask pixels outside goodBBox as SUSPECT
goodBBox.grow(-numEdgePixels)
# Mask pixels outside goodBBox
SourceDetectionTask.setEdgeBits(
maskedImage,
goodBBox,
maskedImage.getMask().getPlaneBitMask("SUSPECT")
maskBitMask
)

def maskAndInterpolateDefects(self, exposure, defectBaseList):
Expand All @@ -2102,10 +2132,17 @@ def maskAndInterpolateDefects(self, exposure, defectBaseList):
----------
exposure : `lsst.afw.image.Exposure`
Exposure to process.
defectBaseList : `List` of `Defects`
defectBaseList : `lsst.meas.algorithms.Defects` or `list` of
`lsst.afw.image.DefectBase`.
List of defects to mask and interpolate.

See Also
--------
lsst.ip.isr.isrTask.maskDefect()
"""
self.maskDefects(exposure, defectBaseList)
self.maskDefect(exposure, defectBaseList)
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...how did this work before? Did this work before?

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I don't have a clear answer.

self.maskEdges(exposure, numEdgePixels=self.config.numEdgeSuspect,
maskPlane="SUSPECT")
isrFunctions.interpolateFromMask(
maskedImage=exposure.getMaskedImage(),
fwhm=self.config.fwhm,
Expand Down