def runIsr(self, doCrosstalk):
"""Run DecamCpIsrTask with or without crosstalk correction
"""
dataRef = self.butler.dataRef('raw', dataId=self.dataId)
rawExposure = self.butler.get('raw', dataId=self.dataId)
camera = dataRef.get('camera')
config = getObsDecamConfig(IsrTask)
config.doCrosstalk = doCrosstalk
decamCpIsrTask = IsrTask(config=config)
isrData = decamCpIsrTask.readIsrData(dataRef, rawExposure)
isrResult = decamCpIsrTask.run(rawExposure, camera=camera, **isrData.getDict())
return isrResult
class EmpiricalVarianceTestCast(lsst.utils.tests.TestCase):
def setUp(self):
"""Constructs a CCD with two amplifiers and prepares for ISR"""
np.random.seed(12345)
baseValue = 100.0
gain = 1.0
readNoise = 123456789.0
saturation = 987654321.0
height = 234
imageSize = Extent2I(123, height)
overscanSize = Extent2I(16, height)
self.sigma = 1.234
# Set up the various regions
overscan1 = Box2I(Point2I(0, 0), overscanSize)
image1 = Box2I(Point2I(overscanSize[0], 0), imageSize)
image2 = Box2I(Point2I(overscanSize[0] + imageSize[0], 0), imageSize)
overscan2 = Box2I(Point2I(overscanSize[0] + 2*imageSize[0], 0), overscanSize)
leftBox = Box2I(overscan1.getMin(), Extent2I(overscan1.getWidth() + image1.getWidth(), height))
rightBox = Box2I(image2.getMin(), Extent2I(image2.getWidth() + overscan2.getWidth(), height))
target1 = Box2I(Point2I(0, 0), imageSize)
target2 = Box2I(Point2I(image1.getWidth(), 0), imageSize)
# Set the pixels
exposure = ExposureF(Box2I(Point2I(0, 0), Extent2I(imageSize[0]*2 + overscanSize[0]*2, height)))
yy = np.arange(0, height, 1, dtype=np.float32)
leftImage = ExposureF(exposure, leftBox)
leftImage.image.array[:] = baseValue + yy[:, np.newaxis]
rightImage = ExposureF(exposure, rightBox)
rightImage.image.array[:] = baseValue - yy[:, np.newaxis]
leftOverscan = ExposureF(exposure, overscan1)
leftOverscan.image.array += np.random.normal(0.0, self.sigma, leftOverscan.image.array.shape)
rightOverscan = ExposureF(exposure, overscan2)
rightOverscan.image.array += np.random.normal(0.0, self.sigma, leftOverscan.image.array.shape)
exposure.mask.array[:] = 0.0
exposure.variance.array[:] = np.nan
# Construct the detectors
amps = AmpInfoCatalog(AmpInfoTable.makeMinimalSchema())
makeAmplifier(amps, "left", target1, image1, overscan1, gain, readNoise, saturation)
makeAmplifier(amps, "right", target2, image2, overscan2, gain, readNoise, saturation)
ccdBox = Box2I(Point2I(0, 0), Extent2I(image1.getWidth() + image2.getWidth(), height))
ccd = Detector("detector", 1, SCIENCE, "det1", ccdBox, amps, Orientation(), Extent2D(1.0, 1.0), {})
exposure.setDetector(ccd)
header = PropertyList()
header.add("EXPTIME", 0.0)
exposure.getInfo().setVisitInfo(VisitInfo(header))
self.exposure = exposure
self.config = IsrTask.ConfigClass()
# Disable everything we don't care about
self.config.doBias = False
self.config.doDark = False
self.config.doFlat = False
self.config.doFringe = False
self.config.doDefect = False
self.config.doAddDistortionModel = False
self.config.doWrite = False
self.config.expectWcs = False
self.config.doLinearize = False
self.config.doCrosstalk = False
self.config.doBrighterFatter = False
self.config.doAttachTransmissionCurve = False
# Set the things that match our test setup
self.config.overscanFitType = "CHEB"
self.config.overscanOrder = 1
self.config.doEmpiricalReadNoise = True
self.task = IsrTask(config=self.config)
def tearDown(self):
del self.exposure
def testEmpiricalVariance(self):
results = self.task.run(self.exposure)
postIsr = results.exposure
self.assertFloatsEqual(postIsr.mask.array, 0)
# Image is not exactly zero because the noise in the overscan (required to be able to set
# the empirical variance) leads to a slight misestimate in the polynomial fit.
self.assertFloatsAlmostEqual(postIsr.image.array, 0.0, atol=5.0e-2)
self.assertFloatsAlmostEqual(postIsr.variance.array, self.sigma**2, rtol=5.0e-2)
class IsrTaskUnTrimmedTestCases(lsst.utils.tests.TestCase):
"""Test IsrTask methods using untrimmed raw data.
"""
def setUp(self):
self.config = IsrTaskConfig()
self.config.qa = IsrQaConfig()
self.task = IsrTask(config=self.config)
self.mockConfig = isrMock.IsrMockConfig()
self.mockConfig.isTrimmed = False
self.doGenerateImage = True
self.dataRef = isrMock.DataRefMock(config=self.mockConfig)
self.camera = isrMock.IsrMock(config=self.mockConfig).getCamera()
self.inputExp = isrMock.RawMock(config=self.mockConfig).run()
self.amp = self.inputExp.getDetector()[0]
self.mi = self.inputExp.getMaskedImage()
def batchSetConfiguration(self, value):
"""Set the configuration state to a consistent value.
Disable options we do not need as well.
Parameters
----------
value : `bool`
Value to switch common ISR configuration options to.
"""
self.config.qa.flatness.meshX = 20
self.config.qa.flatness.meshY = 20
self.config.doWrite = False
self.config.doLinearize = False
self.config.doCrosstalk = False
self.config.doConvertIntToFloat = value
self.config.doSaturation = value
self.config.doSuspect = value
self.config.doSetBadRegions = value
self.config.doOverscan = value
self.config.doBias = value
self.config.doVariance = value
self.config.doWidenSaturationTrails = value
self.config.doBrighterFatter = value
self.config.doDefect = value
self.config.doSaturationInterpolation = value
self.config.doDark = value
self.config.doStrayLight = value
self.config.doFlat = value
self.config.doFringe = value
self.config.doMeasureBackground = value
self.config.doVignette = value
self.config.doAttachTransmissionCurve = value
self.config.doUseOpticsTransmission = value
self.config.doUseFilterTransmission = value
self.config.doUseSensorTransmission = value
self.config.doUseAtmosphereTransmission = value
self.config.qa.saveStats = value
self.config.qa.doThumbnailOss = value
self.config.qa.doThumbnailFlattened = value
self.config.doApplyGains = not value
self.config.doCameraSpecificMasking = value
def validateIsrResults(self):
"""results should be a struct with components that are
not None if included in the configuration file.
Returns
-------
results : `pipeBase.Struct`
Results struct generated from the current ISR configuration.
"""
self.task = IsrTask(config=self.config)
results = self.task.run(
self.inputExp,
camera=self.camera,
bias=self.dataRef.get("bias"),
dark=self.dataRef.get("dark"),
flat=self.dataRef.get("flat"),
bfKernel=self.dataRef.get("bfKernel"),
defects=self.dataRef.get("defects"),
fringes=Struct(fringes=self.dataRef.get("fringe"), seed=1234),
opticsTransmission=self.dataRef.get("transmission_"),
filterTransmission=self.dataRef.get("transmission_"),
sensorTransmission=self.dataRef.get("transmission_"),
atmosphereTransmission=self.dataRef.get("transmission_"))
self.assertIsInstance(results, Struct)
self.assertIsInstance(results.exposure, afwImage.Exposure)
return results
def test_overscanCorrection(self):
"""Expect that this should reduce the image variance with a full fit.
The default fitType of MEDIAN will reduce the median value.
This needs to operate on a RawMock() to have overscan data to use.
The output types may be different when fitType != MEDIAN.
"""
statBefore = computeImageMedianAndStd(
self.inputExp.image[self.amp.getRawDataBBox()])
oscanResults = self.task.overscanCorrection(self.inputExp, self.amp)
self.assertIsInstance(oscanResults, Struct)
self.assertIsInstance(oscanResults.imageFit, float)
self.assertIsInstance(oscanResults.overscanFit, float)
self.assertIsInstance(oscanResults.overscanImage,
afwImage.MaskedImageF)
statAfter = computeImageMedianAndStd(
self.inputExp.image[self.amp.getRawDataBBox()])
self.assertLess(statAfter[0], statBefore[0])
def test_overscanCorrectionMedianPerRow(self):
"""Expect that this should reduce the image variance with a full fit.
fitType of MEDIAN_PER_ROW will reduce the median value.
This needs to operate on a RawMock() to have overscan data to use.
The output types may be different when fitType != MEDIAN_PER_ROW.
"""
self.config.overscan.fitType = 'MEDIAN_PER_ROW'
statBefore = computeImageMedianAndStd(
self.inputExp.image[self.amp.getRawDataBBox()])
oscanResults = self.task.overscanCorrection(self.inputExp, self.amp)
self.assertIsInstance(oscanResults, Struct)
self.assertIsInstance(oscanResults.imageFit, afwImage.ImageF)
self.assertIsInstance(oscanResults.overscanFit, afwImage.ImageF)
self.assertIsInstance(oscanResults.overscanImage,
afwImage.MaskedImageF)
statAfter = computeImageMedianAndStd(
self.inputExp.image[self.amp.getRawDataBBox()])
self.assertLess(statAfter[0], statBefore[0])
def test_runDataRef(self):
"""Expect a dataRef to be handled correctly.
"""
self.config.doLinearize = False
self.config.doWrite = False
self.task = IsrTask(config=self.config)
results = self.task.runDataRef(self.dataRef)
self.assertIsInstance(results, Struct)
self.assertIsInstance(results.exposure, afwImage.Exposure)
def test_run_allTrue(self):
"""Expect successful run with expected outputs when all non-exclusive
configuration options are on.
Output results should be tested more precisely by the
individual function tests.
"""
self.batchSetConfiguration(True)
self.validateIsrResults()
def test_run_allFalse(self):
"""Expect successful run with expected outputs when all non-exclusive
configuration options are off.
Output results should be tested more precisely by the
individual function tests.
"""
self.batchSetConfiguration(False)
self.validateIsrResults()
def test_failCases(self):
"""Expect failure with crosstalk enabled.
Output results should be tested more precisely by the
individual function tests.
"""
self.batchSetConfiguration(True)
# This breaks it
self.config.doCrosstalk = True
with self.assertRaises(RuntimeError):
self.validateIsrResults()
def test_maskingCase_negativeVariance(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.doSaturation = False
self.config.doWidenSaturationTrails = False
self.config.doSaturationInterpolation = False
self.config.doSuspect = False
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = True
self.config.doInterpolate = False
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 40800)
def test_maskingCase_noMasking(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.doSaturation = False
self.config.doWidenSaturationTrails = False
self.config.doSaturationInterpolation = False
self.config.doSuspect = False
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False
self.config.doInterpolate = False
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0)
def test_maskingCase_satMasking(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = False
self.config.doSuspect = False
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0)
def test_maskingCase_satMaskingAndInterp(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.doSuspect = False
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0)
def test_maskingCase_throughEdge(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.numEdgeSuspect = 5
self.config.doSuspect = True
self.config.doSetBadRegions = False
self.config.doDefect = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 0)
def test_maskingCase_throughDefects(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.numEdgeSuspect = 5
self.config.doSuspect = True
self.config.doDefect = True
self.config.doSetBadRegions = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 3940)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000)
def test_maskingCase_throughDefectsAmpEdges(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.numEdgeSuspect = 5
self.config.doSuspect = True
self.config.doDefect = True
self.config.edgeMaskLevel = 'AMP'
self.config.doSetBadRegions = False
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 11280)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000)
def test_maskingCase_throughBad(self):
"""Test masking cases of configuration parameters.
"""
self.batchSetConfiguration(True)
self.config.overscanFitType = "POLY"
self.config.overscanOrder = 1
self.config.saturation = 20000.0
self.config.doSaturation = True
self.config.doWidenSaturationTrails = True
self.config.doSaturationInterpolation = True
self.config.doSuspect = True
self.config.doDefect = True
self.config.doSetBadRegions = True
self.config.doBrighterFatter = False
self.config.maskNegativeVariance = False # These are mock images.
results = self.validateIsrResults()
self.assertEqual(countMaskedPixels(results.exposure, "SAT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "INTRP"), 2000)
self.assertEqual(countMaskedPixels(results.exposure, "SUSPECT"), 0)
self.assertEqual(countMaskedPixels(results.exposure, "BAD"), 2000)
class EmpiricalVarianceTestCast(lsst.utils.tests.TestCase):
def setUp(self):
"""Constructs a CCD with two amplifiers and prepares for ISR"""
np.random.seed(12345)
baseValue = 100.0
gain = 1.0
readNoise = 123456789.0
saturation = 987654321.0
height = 234
imageSize = Extent2I(123, height)
overscanSize = Extent2I(16, height)
self.sigma = 1.234
# Set up the various regions
overscan1 = Box2I(Point2I(0, 0), overscanSize)
image1 = Box2I(Point2I(overscanSize[0], 0), imageSize)
image2 = Box2I(Point2I(overscanSize[0] + imageSize[0], 0), imageSize)
overscan2 = Box2I(Point2I(overscanSize[0] + 2 * imageSize[0], 0),
overscanSize)
leftBox = Box2I(
overscan1.getMin(),
Extent2I(overscan1.getWidth() + image1.getWidth(), height))
rightBox = Box2I(
image2.getMin(),
Extent2I(image2.getWidth() + overscan2.getWidth(), height))
target1 = Box2I(Point2I(0, 0), imageSize)
target2 = Box2I(Point2I(image1.getWidth(), 0), imageSize)
# Set the pixels
exposure = ExposureF(
Box2I(Point2I(0, 0),
Extent2I(imageSize[0] * 2 + overscanSize[0] * 2, height)))
yy = np.arange(0, height, 1, dtype=np.float32)
leftImage = ExposureF(exposure, leftBox)
leftImage.image.array[:] = baseValue + yy[:, np.newaxis]
rightImage = ExposureF(exposure, rightBox)
rightImage.image.array[:] = baseValue - yy[:, np.newaxis]
leftOverscan = ExposureF(exposure, overscan1)
leftOverscan.image.array += np.random.normal(
0.0, self.sigma, leftOverscan.image.array.shape)
rightOverscan = ExposureF(exposure, overscan2)
rightOverscan.image.array += np.random.normal(
0.0, self.sigma, leftOverscan.image.array.shape)
exposure.mask.array[:] = 0.0
exposure.variance.array[:] = np.nan
# Construct the detectors
amp1 = makeAmplifier("left", target1, image1, overscan1, gain,
readNoise, saturation)
amp2 = makeAmplifier("right", target2, image2, overscan2, gain,
readNoise, saturation)
ccdBox = Box2I(Point2I(0, 0),
Extent2I(image1.getWidth() + image2.getWidth(), height))
camBuilder = cameraGeom.Camera.Builder("fakeCam")
detBuilder = camBuilder.add("detector", 1)
detBuilder.setSerial("det1")
detBuilder.setBBox(ccdBox)
detBuilder.setPixelSize(Extent2D(1.0, 1.0))
detBuilder.setOrientation(cameraGeom.Orientation())
detBuilder.append(amp1)
detBuilder.append(amp2)
cam = camBuilder.finish()
exposure.setDetector(cam.get('detector'))
header = PropertyList()
header.add("EXPTIME", 0.0)
exposure.getInfo().setVisitInfo(VisitInfo(header))
self.exposure = exposure
self.config = IsrTask.ConfigClass()
# Disable everything we don't care about
self.config.doBias = False
self.config.doDark = False
self.config.doFlat = False
self.config.doFringe = False
self.config.doDefect = False
self.config.doWrite = False
self.config.expectWcs = False
self.config.doLinearize = False
self.config.doCrosstalk = False
self.config.doBrighterFatter = False
self.config.doAttachTransmissionCurve = False
self.config.doAssembleCcd = False
self.config.doNanMasking = False
self.config.doInterpolate = False
self.config.maskNegativeVariance = False # This runs on mocks.
# Set the things that match our test setup
self.config.overscan.fitType = "CHEB"
self.config.overscan.order = 1
self.config.doEmpiricalReadNoise = True
self.task = IsrTask(config=self.config)
def tearDown(self):
del self.exposure
def testEmpiricalVariance(self):
results = self.task.run(self.exposure)
postIsr = results.exposure
self.assertFloatsEqual(postIsr.mask.array, 0)
# Image is not exactly zero because the noise in the overscan (required
# to be able to set the empirical variance) leads to a slight
# misestimate in the polynomial fit.
self.assertFloatsAlmostEqual(np.median(postIsr.image.array),
0.0,
atol=5.0e-2)
self.assertFloatsAlmostEqual(np.nanmedian(postIsr.variance.array),
self.sigma**2,
rtol=5.0e-2)
print("finished ingesting spots images")
spots_butler = Butler(SPOTS_REPO_DIR)
visits = []
my_metaData = spots_butler.queryMetadata('raw', ['visit', 'dateObs'])
for item in my_metaData:
visits.append(item[0])
byamp_results = []
byamp_corrected_results = []
for visit in visits:
print("Getting exposure # %d"%visit)
sys.stdout.flush()
exposure = spots_butler.get('raw', dataId={'visit': visit, 'detector': DETECTOR})
# Perform the instrument signature removal (mainly assembling the CCD)
isrTask = IsrTask(config=isrConfig)
exposure_isr = isrTask.run(exposure).exposure
# For now, we're applying the gain manually
ccd = exposure_isr.getDetector()
for do_bf_corr in [False, True]:
exposure_copy=exposure_isr.clone()
for amp in ccd:
if spots_bbox.overlaps(amp.getBBox()):
gain = gain_data[amp.getName()]
img = exposure_copy.image
sim = img.Factory(img, amp.getBBox())
sim *= gain
print(amp.getName(), gain, amp.getBBox())
sys.stdout.flush()
if do_bf_corr:
brighterFatterCorrection(exposure_copy[amp.getBBox()],bf_kernel.kernel[amp.getName()],20,10,False)
else:
