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DM-17446: overscan improperly sets bounding boxes when leading/trailing columns are skipped #73

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Jan 30, 2019
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DM-17446: overscan improperly sets bounding boxes when leading/trailing columns are skipped #73

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868e9b1
Fix overscan bounding box issue.
czwa Jan 24, 2019
e404c11
Proposed fix; see slack #dm-lsstcam
RobertLuptonTheGood Jan 23, 2019
f685ab5
Cleaned up bbox code
RobertLuptonTheGood Jan 28, 2019
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53 changes: 21 additions & 32 deletions python/lsst/ip/isr/isrTask.py
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Expand Up @@ -1570,30 +1570,22 @@ def overscanCorrection(self, ccdExposure, amp):
self.log.info("ISR_OSCAN: No overscan region. Not performing overscan correction.")
return None

# Construct views
ampImage = afwImage.MaskedImageF(ccdExposure.getMaskedImage(), amp.getRawDataBBox(),
afwImage.PARENT)
overscanImage = afwImage.MaskedImageF(ccdExposure.getMaskedImage(),
amp.getRawHorizontalOverscanBBox(),
afwImage.PARENT)
overscanArray = overscanImage.getImage().getArray()

statControl = afwMath.StatisticsControl()
statControl.setAndMask(ccdExposure.getMaskedImage().getMask().getPlaneBitMask("SAT"))
statControl.setAndMask(ccdExposure.mask.getPlaneBitMask("SAT"))

# Determine the bounding boxes
dataBBox = amp.getRawDataBBox()
oscanBBox = amp.getRawHorizontalOverscanBBox()
x0 = 0
x1 = 0
dx0 = 0
dx1 = 0

prescanBBox = amp.getRawPrescanBBox()
if (oscanBBox.getBeginX() > prescanBBox.getBeginX()): # amp is at the right
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x0 += self.config.overscanNumLeadingColumnsToSkip
x1 -= self.config.overscanNumTrailingColumnsToSkip
dx0 += self.config.overscanNumLeadingColumnsToSkip
dx1 -= self.config.overscanNumTrailingColumnsToSkip
else:
x0 += self.config.overscanNumTrailingColumnsToSkip
x1 -= self.config.overscanNumLeadingColumnsToSkip
dx0 += self.config.overscanNumTrailingColumnsToSkip
dx1 -= self.config.overscanNumLeadingColumnsToSkip

# Determine if we need to work on subregions of the amplifier and overscan.
imageBBoxes = []
Expand All @@ -1614,37 +1606,34 @@ def overscanCorrection(self, ccdExposure, amp):
imageBBoxes.append(afwGeom.Box2I(dataBBox.getBegin(),
afwGeom.Extent2I(dataBBox.getWidth(), yLower)))
overscanBBoxes.append(afwGeom.Box2I(oscanBBox.getBegin() +
afwGeom.Extent2I(x0, 0),
afwGeom.Extent2I(oscanBBox.getWidth() + x1, yLower)))
afwGeom.Extent2I(dx0, 0),
afwGeom.Extent2I(oscanBBox.getWidth() - dx0 + dx1,
yLower)))

imageBBoxes.append(afwGeom.Box2I(dataBBox.getBegin() + afwGeom.Extent2I(0, yLower),
afwGeom.Extent2I(dataBBox.getWidth(), yUpper)))

overscanBBoxes.append(afwGeom.Box2I(oscanBBox.getBegin() + afwGeom.Extent2I(x0, yLower),
afwGeom.Extent2I(oscanBBox.getWidth() + x1, yUpper)))
overscanBBoxes.append(afwGeom.Box2I(oscanBBox.getBegin() + afwGeom.Extent2I(dx0, yLower),
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afwGeom.Extent2I(oscanBBox.getWidth() - dx0 + dx1,
yUpper)))
else:
imageBBoxes.append(afwGeom.Box2I(dataBBox.getBegin(),
afwGeom.Extent2I(dataBBox.getWidth(), dataBBox.getHeight())))

overscanBBoxes.append(afwGeom.Box2I(oscanBBox.getBegin() + afwGeom.Extent2I(x0, 0),
afwGeom.Extent2I(oscanBBox.getWidth() + x1,
overscanBBoxes.append(afwGeom.Box2I(oscanBBox.getBegin() + afwGeom.Extent2I(dx0, 0),
afwGeom.Extent2I(oscanBBox.getWidth() - dx0 + dx1,
oscanBBox.getHeight())))

# Perform overscan correction on subregions, ensuring saturated pixels are masked.
for imageBBox, overscanBBox in zip(imageBBoxes, overscanBBoxes):
ampImage = afwImage.MaskedImageF(ccdExposure.getMaskedImage(), imageBBox,
afwImage.PARENT)
overscanImage = afwImage.MaskedImageF(ccdExposure.getMaskedImage(), overscanBBox,
afwImage.PARENT)
ampImage = ccdExposure.maskedImage[imageBBox]
overscanImage = ccdExposure.maskedImage[overscanBBox]

overscanArray = overscanImage.getImage().getArray()
median = numpy.ma.median(numpy.ma.masked_where(overscanImage.getMask().getArray(),
overscanArray))
overscanArray = overscanImage.image.array
median = numpy.ma.median(numpy.ma.masked_where(overscanImage.mask.array, overscanArray))
bad = numpy.where(numpy.abs(overscanArray - median) > self.config.overscanMaxDev)
overscanImage.getMask().getArray()[bad] = overscanImage.getMask().getPlaneBitMask("SAT")
overscanImage.mask.array[bad] = overscanImage.mask.getPlaneBitMask("SAT")

statControl = afwMath.StatisticsControl()
statControl.setAndMask(ccdExposure.getMaskedImage().getMask().getPlaneBitMask("SAT"))
statControl.setAndMask(ccdExposure.mask.getPlaneBitMask("SAT"))

overscanResults = isrFunctions.overscanCorrection(ampMaskedImage=ampImage,
overscanImage=overscanImage,
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