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DM-36358: "broken" amplifiers trigger a failure in setting the threshold for defects #155

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merged 2 commits into from
Oct 5, 2022
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DM-36358: "broken" amplifiers trigger a failure in setting the threshold for defects #155

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bfed809
Handle exception caused by a single constant pixel value.
czwa Sep 26, 2022
d96a0d6
Add defect test for fully bad images.
czwa Sep 27, 2022
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11 changes: 10 additions & 1 deletion python/lsst/cp/pipe/defects.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
from lsst.geom import Box2I, Point2I
from lsst.meas.algorithms import SourceDetectionTask
from lsst.ip.isr import Defects, countMaskedPixels
from lsst.pex.exceptions import InvalidParameterError

from ._lookupStaticCalibration import lookupStaticCalibration

Expand Down Expand Up @@ -246,7 +247,15 @@ def findHotAndColdPixels(self, exp, nSigma):

threshold = afwDetection.createThreshold(nSig, 'stdev', polarity=polarity)

footprintSet = afwDetection.FootprintSet(ampImg, threshold)
try:
footprintSet = afwDetection.FootprintSet(ampImg, threshold)
except InvalidParameterError:
# This occurs if the image sigma value is 0.0.
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Is there any other way this could happen? Testing exceptions should be the last resort. Can't the threshold value be checked?

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The threshold itself is fine. It's the image sigma value coming out as zero that causes the InvalidParameterError. Manually calculating the image statistics seemed to be less efficient than doing the try/except, as most amplifiers should work fine.

# Let's mask the whole area.
minValue = np.nanmin(ampImg.image.array) - 1.0
threshold = afwDetection.createThreshold(minValue, 'value', polarity=True)
footprintSet = afwDetection.FootprintSet(ampImg, threshold)
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This seems like a pretty complicated (and expensive) way to create a FootprintSet covering the whole area. Since a FootprintSet can be created from a Box2I, wouldn't that be simpler and faster?

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I think I got lost in the FootprintSet definition before I saw that it could have a Box passed to it. I'll refactor for that instead.

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After coding this and sending to Jenkins, I'm now discovering that the box definition only sets the region, and does not create a footprint set containing footprints that can be used to mask the image.


footprintSet.setMask(maskedIm.mask, ("DETECTED" if polarity else "DETECTED_NEGATIVE"))

if mergedSet is None:
Expand Down
22 changes: 20 additions & 2 deletions tests/test_defects.py
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Expand Up @@ -591,7 +591,6 @@ def test_pixelCounting(self):
def test_getNumGoodPixels(self):
"""Test the the number of pixels in the image not masked is as
expected.

"""
testImage = self.flatExp.clone()
mi = testImage.maskedImage
Expand Down Expand Up @@ -622,7 +621,6 @@ def test_getNumGoodPixels(self):
def test_edgeMasking(self):
"""Check that the right number of edge pixels are masked by
_setEdgeBits().

"""
testImage = self.flatExp.clone()
mi = testImage.maskedImage
Expand All @@ -638,6 +636,26 @@ def test_edgeMasking(self):

self.assertEqual(countMaskedPixels(mi, 'EDGE'), nEdge)

def test_badImage(self):
"""Check that fully-bad images do not fail.
"""
testImage = self.flatExp.clone()
testImage.image.array[:, :] = 125000

config = copy.copy(self.defaultConfig)
# Do not exclude any pixels, so the areas match.
config.nPixBorderUpDown = 0
config.nPixBorderLeftRight = 0

task = cpPipe.defects.MeasureDefectsTask(config=config)
defects = task.findHotAndColdPixels(testImage, [config.nSigmaBright,
config.nSigmaDark])

defectArea = 0
for defect in defects:
defectArea += defect.getBBox().getArea()
self.assertEqual(defectArea, testImage.getBBox().getArea())


class TestMemory(lsst.utils.tests.MemoryTestCase):
pass
Expand Down