def testRenamedMasking(self):
"""Test that masking works using some other mask name instead of the default
"""
AltMaskName = "BAD" # pick something that exists for simplicity
isrConfig = ipIsr.IsrTask.ConfigClass()
isrConfig.suspectMaskName = AltMaskName
isrTask = ipIsr.IsrTask(config=isrConfig)
maxVal = 32000
fracSuspect = 0.3
suspectLevel = maxVal * (1 - fracSuspect)
bbox = self.ampInfo.getRawBBox()
self.ampInfo.setSuspectLevel(suspectLevel)
maskedImage = makeRampMaskedImage(bbox, 0, maxVal)
imArr = maskedImage.getImage().getArray()
desSetArr = imArr >= suspectLevel
exposure = afwImage.ExposureF(maskedImage)
inMaskedImage = maskedImage.Factory(maskedImage, True) # deep copy
isrTask.suspectDetection(exposure, self.ampInfo)
maskArr = maskedImage.getMask().getArray()
suspectMask = maskedImage.getMask().getPlaneBitMask(AltMaskName)
measSetArr = maskArr == suspectMask
self.assertImagesEqual(desSetArr, measSetArr)
self.assertMaskedImagesAlmostEqual(inMaskedImage,
maskedImage,
doMask=False)
def testDarkWithDarktimeNan(self):
darkTime = 128.0
nan = float("NAN")
exp = afwImage.ExposureF(1, 1)
exp.getMaskedImage().getImage().set(1.0)
exp.getMaskedImage().getMask().set(0)
exp.getMaskedImage().getVariance().set(1.0)
dark = afwImage.ExposureF(1, 1)
dark.getMaskedImage().getImage().set(1.0/darkTime)
dark.getMaskedImage().getMask().set(0)
dark.getMaskedImage().getVariance().set(0.0)
dark.getInfo().setVisitInfo(afwImage.VisitInfo())
task = ipIsr.IsrTask()
# scale with darkScale=1 if the dark has darkTime=NaN.
exp.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=darkTime))
dark.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=nan))
task.darkCorrection(exp, dark)
self.assertEqual(exp.image[0, 0, afwImage.LOCAL], 0.0)
self.assertEqual(exp.mask[0, 0, afwImage.LOCAL], 0)
self.assertEqual(exp.variance[0, 0, afwImage.LOCAL], 1.0)
self.assertEqual(exp.getInfo().getVisitInfo().getDarkTime(), darkTime) # Hasn't been modified
def checkOverscanCorrectionX(self, **kwargs):
bbox = lsst.geom.Box2I(lsst.geom.Point2I(0, 0),
lsst.geom.Point2I(12, 9))
maskedImage = afwImage.MaskedImageF(bbox)
maskedImage.set(10, 0x0, 1)
dataBox = lsst.geom.Box2I(lsst.geom.Point2I(0, 0), lsst.geom.Extent2I(10, 10))
dataImage = afwImage.MaskedImageF(maskedImage, dataBox)
# these should be functionally equivalent
bbox = lsst.geom.Box2I(lsst.geom.Point2I(10, 0),
lsst.geom.Point2I(12, 9))
biassec = '[11:13,1:10]'
overscan = afwImage.MaskedImageF(maskedImage, bbox)
overscan.set(2, 0x0, 1)
exposure = afwImage.ExposureF(maskedImage, None)
metadata = exposure.getMetadata()
metadata.setString(self.overscanKeyword, biassec)
config = ipIsr.IsrTask.ConfigClass()
self.updateConfigFromKwargs(config, **kwargs)
isrTask = ipIsr.IsrTask(config=config)
isrTask.overscan.run(dataImage, overscan.getImage())
height = maskedImage.getHeight()
width = maskedImage.getWidth()
for j in range(height):
for i in range(width):
if i >= 10:
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL], 0)
else:
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL], 8)
def checkPolyOverscanCorrectionX(self, **kwargs):
bbox = lsst.geom.Box2I(lsst.geom.Point2I(0, 0),
lsst.geom.Point2I(12, 9))
maskedImage = afwImage.MaskedImageF(bbox)
maskedImage.set(10, 0x0, 1)
dataBox = lsst.geom.Box2I(lsst.geom.Point2I(0, 0), lsst.geom.Extent2I(10, 10))
dataImage = afwImage.MaskedImageF(maskedImage, dataBox)
# these should be functionally equivalent
bbox = lsst.geom.Box2I(lsst.geom.Point2I(10, 0),
lsst.geom.Point2I(12, 9))
overscan = afwImage.MaskedImageF(maskedImage, bbox)
overscan.set(2, 0x0, 1)
for i in range(bbox.getDimensions()[1]):
for j, off in enumerate([-0.5, 0.0, 0.5]):
overscan.image[j, i, afwImage.LOCAL] = 2+i+off
config = ipIsr.IsrTask.ConfigClass()
self.updateConfigFromKwargs(config, **kwargs)
isrTask = ipIsr.IsrTask(config=config)
isrTask.overscan.run(dataImage, overscan.getImage())
height = maskedImage.getHeight()
width = maskedImage.getWidth()
for j in range(height):
for i in range(width):
if i == 10:
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL], -0.5)
elif i == 11:
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL], 0)
elif i == 12:
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL], 0.5)
else:
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL], 10 - 2 - j)
def setUpClass(cls):
"""Setup butler, and generate an ISR processed exposure.
Notes
-----
DMTN-101 4.1:
Process an independent bias frame through the ISR including
overscan correction and bias subtraction
"""
repoDir = os.path.join("DATA/")
butler = dafButler.Butler(
repoDir,
collections=['LATISS/raw/all', 'LATISS/calib', 'calib/v00'])
config = ipIsr.IsrTaskConfig()
config.doSaturation = True
config.doSuspect = True
config.doSetBadRegions = True
config.doOverscan = True
config.doBias = True
config.doVariance = True
config.doLinearize = False
config.doCrosstalk = False
config.doWidenSaturationTrails = False
config.doBrighterFatter = False
config.doDefect = False
config.doSaturationInterpolation = False
config.doDark = False
config.doStrayLight = False
config.doFlat = False
config.doApplyGains = False
config.doFringe = False
config.doMeasureBackground = False
config.doVignette = False
config.doAttachTransmissionCurve = False
config.doUseOpticsTransmission = False
config.doUseFilterTransmission = False
config.doUseSensorTransmission = False
config.doUseAtmosphereTransmission = False
isrTask = ipIsr.IsrTask(config=config)
rawDataId = {
'detector': 0,
'exposure': 2020012800007,
'instrument': 'LATISS'
}
# TODO: DM-26396
# This is not an independent frame.
cls.raw = butler.get('raw', dataId=rawDataId)
cls.bias = butler.get('bias', rawDataId)
cls.camera = butler.get('camera', rawDataId)
results = isrTask.run(cls.raw, camera=cls.camera, bias=cls.bias)
cls.exposure = results.outputExposure
def setUp(self):
ampInfoShema = afwTable.AmpInfoTable.makeMinimalSchema()
ampInfoCat = afwTable.AmpInfoCatalog(ampInfoShema)
ampInfo = ampInfoCat.addNew()
ampInfo.setRawBBox(
afwGeom.Box2I(afwGeom.Point2I(-5, 7), afwGeom.Extent2I(53, 104)))
ampInfo.setSuspectLevel(25000)
self.ampInfo = ampInfo
self.isrTask = ipIsr.IsrTask()
def setUp(self):
ampInfo = cameraGeom.Amplifier.Builder()
ampInfo.setRawBBox(
lsst.geom.Box2I(lsst.geom.Point2I(-5, 7),
lsst.geom.Extent2I(53, 104)))
ampInfo.setSuspectLevel(25000)
self.ampInfo = ampInfo
self.isrTask = ipIsr.IsrTask()
def testBrighterFatterInterface(self):
"""Test brighter fatter correction interface using a delta function kernel on a flat image"""
image = afwImage.ImageF(100, 100)
image.set(100)
ref_image = afwImage.ImageF(image, True)
mi = afwImage.makeMaskedImage(image)
exp = afwImage.makeExposure(mi)
isrTask = ipIsr.IsrTask()
with open(self.filename, 'rb') as f:
bfKernel = pickle.load(f)
isrTask.brighterFatterCorrection(exp, bfKernel, 5, 100, False)
self.assertImagesEqual(ref_image, image)
def checkOverscanCorrectionY(self, **kwargs):
bbox = lsst.geom.Box2I(lsst.geom.Point2I(0, 0),
lsst.geom.Point2I(9, 12))
maskedImage = afwImage.MaskedImageF(bbox)
maskedImage.set(10, 0x0, 1)
dataBox = lsst.geom.Box2I(lsst.geom.Point2I(0, 0),
lsst.geom.Extent2I(10, 10))
dataImage = afwImage.MaskedImageF(maskedImage, dataBox)
# these should be functionally equivalent
bbox = lsst.geom.Box2I(lsst.geom.Point2I(0, 10),
lsst.geom.Point2I(9, 12))
biassec = '[1:10,11:13]'
overscan = afwImage.MaskedImageF(maskedImage, bbox)
overscan.set(2, 0x0, 1)
exposure = afwImage.ExposureF(maskedImage, None)
metadata = exposure.getMetadata()
metadata.setString(self.overscanKeyword, biassec)
config = ipIsr.IsrTask.ConfigClass()
self.updateConfigFromKwargs(config, **kwargs)
if kwargs['fitType'] == "MEDIAN_PER_ROW":
# Add a bad point to test outlier rejection.
overscan.getImage().getArray()[0, 0] = 12345
# Shrink the sigma clipping limit to handle the fact that the
# bad point is not be rejected at higher thresholds (2/0.74).
config.overscan.numSigmaClip = 2.7
isrTask = ipIsr.IsrTask(config=config)
isrTask.overscan.run(dataImage.getImage(), overscan.getImage())
height = maskedImage.getHeight()
width = maskedImage.getWidth()
for j in range(height):
for i in range(width):
if j == 10 and i == 0 and kwargs['fitType'] == "MEDIAN_PER_ROW":
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL],
12343)
elif j >= 10:
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL],
0)
else:
self.assertEqual(maskedImage.image[i, j, afwImage.LOCAL],
8)
def testDarkWithDarktime(self):
darkTime = 128.0
nan = float("NAN")
exp = afwImage.ExposureF(1, 1)
exp.getMaskedImage().getImage().set(1.0)
exp.getMaskedImage().getMask().set(0)
exp.getMaskedImage().getVariance().set(1.0)
dark = afwImage.ExposureF(1, 1)
dark.getMaskedImage().getImage().set(1.0 / darkTime)
dark.getMaskedImage().getMask().set(0)
dark.getMaskedImage().getVariance().set(0.0)
dark.getInfo().setVisitInfo(afwImage.VisitInfo())
task = ipIsr.IsrTask()
# No darktime set in at least one of the inputs
exp.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=nan))
dark.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=nan))
with self.assertRaises(RuntimeError):
task.darkCorrection(exp, dark)
exp.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=nan))
dark.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=1.0))
with self.assertRaises(RuntimeError):
task.darkCorrection(exp, dark)
exp.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=1.0))
dark.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=nan))
with self.assertRaises(RuntimeError):
task.darkCorrection(exp, dark)
# With darktime set
exp.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=darkTime))
dark.getInfo().setVisitInfo(afwImage.VisitInfo(darkTime=1.0))
task.darkCorrection(exp, dark)
self.assertEqual(exp.getMaskedImage().getImage().get(0, 0), 0.0)
self.assertEqual(exp.getMaskedImage().getMask().get(0, 0), 0)
self.assertEqual(exp.getMaskedImage().getVariance().get(0, 0), 1.0)
self.assertEqual(exp.getInfo().getVisitInfo().getDarkTime(),
darkTime) # Hasn't been modified
