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DM-25934: MeasurePhotonTransferCurveTask appears to ignore the defect mask #42

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Jul 14, 2020
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DM-25934: MeasurePhotonTransferCurveTask appears to ignore the defect mask #42

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32 changes: 26 additions & 6 deletions python/lsst/cp/pipe/ptc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,11 @@ class MeasurePhotonTransferCurveTaskConfig(pexConfig.Config):
doc="Sigma cut for outlier rejection in PTC.",
default=5.0,
)
maskNameList = pexConfig.ListField(
dtype=str,
doc="Mask list to exclude from statistics calculations.",
default=['DETECTED', 'BAD', 'NO_DATA'],
)
nSigmaClipPtc = pexConfig.Field(
dtype=float,
doc="Sigma cut for afwMath.StatisticsControl()",
Expand Down Expand Up @@ -598,12 +603,21 @@ def measureMeanVarCov(self, exposure1, exposure2, region=None, covAstierRealSpac
im1Area = afwMath.binImage(im1Area, self.config.binSize)
im2Area = afwMath.binImage(im2Area, self.config.binSize)

statsCtrl = afwMath.StatisticsControl()
statsCtrl.setNumSigmaClip(self.config.nSigmaClipPtc)
statsCtrl.setNumIter(self.config.nIterSigmaClipPtc)
im1MaskVal = exposure1.getMask().getPlaneBitMask(self.config.maskNameList)
im1StatsCtrl = afwMath.StatisticsControl(self.config.nSigmaClipPtc,
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I think setting things with the statsCtrl.setXYZ() methods is clearer, but this is perfectly fine as the config options state what they are.

self.config.nIterSigmaClipPtc,
im1MaskVal)
im1StatsCtrl.setAndMask(im1MaskVal)

im2MaskVal = exposure2.getMask().getPlaneBitMask(self.config.maskNameList)
im2StatsCtrl = afwMath.StatisticsControl(self.config.nSigmaClipPtc,
self.config.nIterSigmaClipPtc,
im2MaskVal)
im2StatsCtrl.setAndMask(im2MaskVal)

# Clipped mean of images; then average of mean.
mu1 = afwMath.makeStatistics(im1Area, afwMath.MEANCLIP, statsCtrl).getValue()
mu2 = afwMath.makeStatistics(im2Area, afwMath.MEANCLIP, statsCtrl).getValue()
mu1 = afwMath.makeStatistics(im1Area, afwMath.MEANCLIP, im1StatsCtrl).getValue()
mu2 = afwMath.makeStatistics(im2Area, afwMath.MEANCLIP, im2StatsCtrl).getValue()
mu = 0.5*(mu1 + mu2)

# Take difference of pairs
Expand All @@ -615,7 +629,13 @@ def measureMeanVarCov(self, exposure1, exposure2, region=None, covAstierRealSpac
diffIm -= temp
diffIm /= mu

varDiff = 0.5*(afwMath.makeStatistics(diffIm, afwMath.VARIANCECLIP, statsCtrl).getValue())
diffImMaskVal = diffIm.getMask().getPlaneBitMask(self.config.maskNameList)
diffImStatsCtrl = afwMath.StatisticsControl(self.config.nSigmaClipPtc,
self.config.nIterSigmaClipPtc,
diffImMaskVal)
diffImStatsCtrl.setAndMask(diffImMaskVal)

varDiff = 0.5*(afwMath.makeStatistics(diffIm, afwMath.VARIANCECLIP, diffImStatsCtrl).getValue())

# Get the mask and identify good pixels as '1', and the rest as '0'.
w1 = np.where(im1Area.getMask().getArray() == 0, 1, 0)
Expand Down