def ISR(self, fixCRs = True):
"""Run the ISR stage, removing CRs and patching bad columns"""
mi = self.exposure.getMaskedImage()
mi.getMask().set(0) # XXX
#
# Fix defects
#
# Mask known bad pixels
#
badPixels = measAlg.defects.policyToBadRegionList(os.path.join(eups.productDir("meas_algorithms"),
"examples", "BadPixels.paf"))
# did someone lie about the origin of the maskedImage? If so, adjust bad pixel list
if self.XY0.getX() != mi.getX0() or self.XY0.getY() != mi.getY0():
dx = self.XY0.getX() - mi.getX0()
dy = self.XY0.getY() - mi.getY0()
for bp in badPixels:
bp.shift(-dx, -dy)
measAlg.interpolateOverDefects(mi, self.psf, badPixels)
#
# Subtract background
#
bctrl = afwMath.BackgroundControl("LINEAR");
bctrl.setNxSample(int(mi.getWidth()/256) + 1);
bctrl.setNySample(int(mi.getHeight()/256) + 1);
backobj = afwMath.makeBackground(mi.getImage(), bctrl)
img = mi.getImage(); img -= backobj.getImageF(); del img
#
# Remove CRs
#
if fixCRs:
crConfig = measAlg.FindCosmicRaysConfig()
crs = measAlg.findCosmicRays(mi, self.psf, 0, pexConfig.makePolicy(crConfig))
if self.display:
ds9.mtv(mi, frame = 0, lowOrderBits = True)
def testDetection(self):
"""Test CR detection."""
#
# Subtract background
#
bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE)
bctrl.setNxSample(int(self.mi.getWidth() / 256) + 1)
bctrl.setNySample(int(self.mi.getHeight() / 256) + 1)
bctrl.getStatisticsControl().setNumSigmaClip(3.0)
bctrl.getStatisticsControl().setNumIter(2)
im = self.mi.getImage()
try:
backobj = afwMath.makeBackground(im, bctrl)
except Exception as e:
print(e, file=sys.stderr)
bctrl.setInterpStyle(afwMath.Interpolate.CONSTANT)
backobj = afwMath.makeBackground(im, bctrl)
im -= backobj.getImageF()
if display:
frame = 0
disp = afwDisplay.Display(frame=frame)
disp.mtv(self.mi,
title=self._testMethodName + ": Raw") # raw frame
if self.mi.getWidth() > 256:
disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0())
#
# Mask known bad pixels
#
measAlgorithmsDir = lsst.utils.getPackageDir('meas_algorithms')
badPixels = defects.policyToBadRegionList(
os.path.join(measAlgorithmsDir, "policy", "BadPixels.paf"))
# did someone lie about the origin of the maskedImage? If so, adjust bad pixel list
if self.XY0.getX() != self.mi.getX0() or self.XY0.getY(
) != self.mi.getY0():
dx = self.XY0.getX() - self.mi.getX0()
dy = self.XY0.getY() - self.mi.getY0()
for bp in badPixels:
bp.shift(-dx, -dy)
algorithms.interpolateOverDefects(self.mi, self.psf, badPixels)
stats = afwMath.makeStatistics(self.mi.getImage(),
afwMath.MEANCLIP | afwMath.STDEVCLIP)
background = stats.getValue(afwMath.MEANCLIP)
crConfig = algorithms.FindCosmicRaysConfig()
crs = algorithms.findCosmicRays(self.mi, self.psf, background,
pexConfig.makePolicy(crConfig))
if display:
frame += 1
disp = afwDisplay.Display(frame=frame)
disp.mtv(self.mi, title=self._testMethodName + ": CRs removed")
if self.mi.getWidth() > 256:
disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0())
print("Detected %d CRs" % len(crs))
if display and False:
for cr in crs:
bbox = cr.getBBox()
bbox.shift(
lsst.geom.ExtentI(-self.mi.getX0(), -self.mi.getY0()))
disp.line([(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5),
(bbox.getMaxX() + 0.5, bbox.getMinY() - 0.5),
(bbox.getMaxX() + 0.5, bbox.getMaxY() + 0.5),
(bbox.getMinX() - 0.5, bbox.getMaxY() + 0.5),
(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5)])
if self.nCR is not None:
self.assertEqual(len(crs), self.nCR)
def testDetection(self):
crConfig = algorithms.FindCosmicRaysConfig()
crs = algorithms.findCosmicRays(self.mi, self.psf, 0.0,
pexConfig.makePolicy(crConfig))
self.assertEqual(len(crs), 0, "Found %d CRs in empty image" % len(crs))
def testDetection(self):
"""Test CR detection."""
#
# Subtract background
#
bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE)
bctrl.setNxSample(int(self.mi.getWidth() / 256) + 1)
bctrl.setNySample(int(self.mi.getHeight() / 256) + 1)
bctrl.getStatisticsControl().setNumSigmaClip(3.0)
bctrl.getStatisticsControl().setNumIter(2)
im = self.mi.getImage()
try:
backobj = afwMath.makeBackground(im, bctrl)
except Exception as e:
print(e, file=sys.stderr)
bctrl.setInterpStyle(afwMath.Interpolate.CONSTANT)
backobj = afwMath.makeBackground(im, bctrl)
im -= backobj.getImageF()
if display:
frame = 0
disp = afwDisplay.Display(frame=frame)
disp.mtv(self.mi,
title=self._testMethodName + ": Raw") # raw frame
if self.mi.getWidth() > 256:
disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0())
#
# Mask known bad pixels
#
badPixels = testUtils.makeDefectList()
algorithms.interpolateOverDefects(self.mi, self.psf, badPixels)
stats = afwMath.makeStatistics(self.mi.getImage(),
afwMath.MEANCLIP | afwMath.STDEVCLIP)
background = stats.getValue(afwMath.MEANCLIP)
crConfig = algorithms.FindCosmicRaysConfig()
crs = algorithms.findCosmicRays(self.mi, self.psf, background,
pexConfig.makePropertySet(crConfig))
if display:
frame += 1
disp = afwDisplay.Display(frame=frame)
disp.mtv(self.mi, title=self._testMethodName + ": CRs removed")
if self.mi.getWidth() > 256:
disp.pan(944 - self.mi.getX0(), 260 - self.mi.getY0())
print("Detected %d CRs" % len(crs))
if display and False:
for cr in crs:
bbox = cr.getBBox()
bbox.shift(
lsst.geom.ExtentI(-self.mi.getX0(), -self.mi.getY0()))
disp.line([(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5),
(bbox.getMaxX() + 0.5, bbox.getMinY() - 0.5),
(bbox.getMaxX() + 0.5, bbox.getMaxY() + 0.5),
(bbox.getMinX() - 0.5, bbox.getMaxY() + 0.5),
(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5)])
if self.nCR is not None:
self.assertEqual(len(crs), self.nCR)
def testDetection(self):
"""Test object detection"""
#
# Fix defects
#
# Mask known bad pixels
#
measAlgorithmsDir = lsst.utils.getPackageDir('meas_algorithms')
badPixels = defects.policyToBadRegionList(os.path.join(measAlgorithmsDir,
"policy/BadPixels.paf"))
# did someone lie about the origin of the maskedImage? If so, adjust bad pixel list
if self.XY0.getX() != self.mi.getX0() or self.XY0.getY() != self.mi.getY0():
dx = self.XY0.getX() - self.mi.getX0()
dy = self.XY0.getY() - self.mi.getY0()
for bp in badPixels:
bp.shift(-dx, -dy)
algorithms.interpolateOverDefects(self.mi, self.psf, badPixels)
#
# Subtract background
#
bgGridSize = 64 # was 256 ... but that gives only one region and the spline breaks
bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE)
bctrl.setNxSample(int(self.mi.getWidth()/bgGridSize) + 1)
bctrl.setNySample(int(self.mi.getHeight()/bgGridSize) + 1)
backobj = afwMath.makeBackground(self.mi.getImage(), bctrl)
self.mi.getImage()[:] -= backobj.getImageF()
#
# Remove CRs
#
crConfig = algorithms.FindCosmicRaysConfig()
algorithms.findCosmicRays(self.mi, self.psf, 0, pexConfig.makePolicy(crConfig))
#
# We do a pretty good job of interpolating, so don't propagagate the convolved CR/INTRP bits
# (we'll keep them for the original CR/INTRP pixels)
#
savedMask = self.mi.getMask().Factory(self.mi.getMask(), True)
saveBits = savedMask.getPlaneBitMask("CR") | \
savedMask.getPlaneBitMask("BAD") | \
savedMask.getPlaneBitMask("INTRP") # Bits to not convolve
savedMask &= saveBits
msk = self.mi.getMask()
msk &= ~saveBits # Clear the saved bits
del msk
#
# Smooth image
#
psf = algorithms.DoubleGaussianPsf(15, 15, self.FWHM/(2*math.sqrt(2*math.log(2))))
cnvImage = self.mi.Factory(self.mi.getBBox())
kernel = psf.getKernel()
afwMath.convolve(cnvImage, self.mi, kernel, afwMath.ConvolutionControl())
msk = cnvImage.getMask()
msk |= savedMask # restore the saved bits
del msk
threshold = afwDetection.Threshold(3, afwDetection.Threshold.STDEV)
#
# Only search the part of the frame that was PSF-smoothed
#
llc = lsst.geom.PointI(psf.getKernel().getWidth()//2, psf.getKernel().getHeight()//2)
urc = lsst.geom.PointI(cnvImage.getWidth() - llc[0] - 1, cnvImage.getHeight() - llc[1] - 1)
middle = cnvImage.Factory(cnvImage, lsst.geom.BoxI(llc, urc), afwImage.LOCAL)
ds = afwDetection.FootprintSet(middle, threshold, "DETECTED")
del middle
#
# Reinstate the saved (e.g. BAD) (and also the DETECTED | EDGE) bits in the unsmoothed image
#
savedMask[:] = cnvImage.getMask()
msk = self.mi.getMask()
msk |= savedMask
del msk
del savedMask
if display:
disp = afwDisplay.Display(frame=2)
disp.mtv(self.mi, title=self._testMethodName + ": image")
afwDisplay.Display(frame=3).mtv(cnvImage, title=self._testMethodName + ": cnvImage")
#
# Time to actually measure
#
schema = afwTable.SourceTable.makeMinimalSchema()
sfm_config = measBase.SingleFrameMeasurementConfig()
sfm_config.plugins = ["base_SdssCentroid", "base_CircularApertureFlux", "base_PsfFlux",
"base_SdssShape", "base_GaussianFlux",
"base_PixelFlags"]
sfm_config.slots.centroid = "base_SdssCentroid"
sfm_config.slots.shape = "base_SdssShape"
sfm_config.slots.psfFlux = "base_PsfFlux"
sfm_config.slots.gaussianFlux = None
sfm_config.slots.apFlux = "base_CircularApertureFlux_3_0"
sfm_config.slots.modelFlux = "base_GaussianFlux"
sfm_config.slots.calibFlux = None
sfm_config.plugins["base_SdssShape"].maxShift = 10.0
sfm_config.plugins["base_CircularApertureFlux"].radii = [3.0]
task = measBase.SingleFrameMeasurementTask(schema, config=sfm_config)
measCat = afwTable.SourceCatalog(schema)
# detect the sources and run with the measurement task
ds.makeSources(measCat)
self.exposure.setPsf(self.psf)
task.run(measCat, self.exposure)
self.assertGreater(len(measCat), 0)
for source in measCat:
if source.get("base_PixelFlags_flag_edge"):
continue
if display:
disp.dot("+", source.getX(), source.getY())
class CosmicRayTestCase(unittest.TestCase):
"""A test case for Cosmic Ray detection"""
def setUp(self):
self.FWHM = 5 # pixels
self.psf = algorithms.DoubleGaussianPsf(
29, 29, self.FWHM / (2 * sqrt(2 * log(2))))
self.mi = afwImage.MaskedImageF(imageFile)
self.XY0 = afwGeom.PointI(0, 0) # origin of the subimage we use
if imageFile == imageFile0:
if True: # use full image, trimmed to data section
self.XY0 = afwGeom.PointI(32, 2)
self.mi = self.mi.Factory(
self.mi, afwGeom.BoxI(self.XY0, afwGeom.PointI(2079,
4609)),
afwImage.LOCAL)
self.mi.setXY0(afwGeom.PointI(0, 0))
self.nCR = 1076 # number of CRs we should detect
else: # use sub-image
if True:
self.XY0 = afwGeom.PointI(824, 140)
self.nCR = 10
else:
self.XY0 = afwGeom.PointI(280, 2750)
self.nCR = 2
self.mi = self.mi.Factory(
self.mi,
afwGeom.BoxI(self.XY0, afwGeom.ExtentI(256, 256),
afwImage.LOCAL))
self.mi.setXY0(afwGeom.PointI(0, 0))
else:
self.nCR = None
self.mi.getMask().addMaskPlane("DETECTED")
def tearDown(self):
del self.mi
del self.psf
def testDetection(self):
"""Test CR detection"""
#
# Subtract background
#
bctrl = afwMath.BackgroundControl(afwMath.Interpolate.NATURAL_SPLINE)
bctrl.setNxSample(int(self.mi.getWidth() / 256) + 1)
bctrl.setNySample(int(self.mi.getHeight() / 256) + 1)
bctrl.getStatisticsControl().setNumSigmaClip(3.0)
bctrl.getStatisticsControl().setNumIter(2)
im = self.mi.getImage()
try:
backobj = afwMath.makeBackground(im, bctrl)
except Exception, e:
print >> sys.stderr, e,
bctrl.setInterpStyle(afwMath.Interpolate.CONSTANT)
backobj = afwMath.makeBackground(im, bctrl)
im -= backobj.getImageF()
if display:
frame = 0
ds9.mtv(self.mi, frame=frame, title="Raw") # raw frame
if self.mi.getWidth() > 256:
ds9.pan(944 - self.mi.getX0(), 260 - self.mi.getY0())
#
# Mask known bad pixels
#
badPixels = defects.policyToBadRegionList(
os.path.join(os.environ["MEAS_ALGORITHMS_DIR"], "policy",
"BadPixels.paf"))
# did someone lie about the origin of the maskedImage? If so, adjust bad pixel list
if self.XY0.getX() != self.mi.getX0() or self.XY0.getY(
) != self.mi.getY0():
dx = self.XY0.getX() - self.mi.getX0()
dy = self.XY0.getY() - self.mi.getY0()
for bp in badPixels:
bp.shift(-dx, -dy)
algorithms.interpolateOverDefects(self.mi, self.psf, badPixels)
stats = afwMath.makeStatistics(self.mi.getImage(),
afwMath.MEANCLIP | afwMath.STDEVCLIP)
background = stats.getValue(afwMath.MEANCLIP)
crConfig = algorithms.FindCosmicRaysConfig()
crs = algorithms.findCosmicRays(self.mi, self.psf, background,
pexConfig.makePolicy(crConfig))
if display:
ds9.mtv(self.mi, frame=frame + 1, title="CRs removed")
if self.mi.getWidth() > 256:
ds9.pan(944 - self.mi.getX0(), 260 - self.mi.getY0())
print "Detected %d CRs" % len(crs)
if display and False:
for cr in crs:
bbox = cr.getBBox()
bbox.shift(afwGeom.ExtentI(-self.mi.getX0(), -self.mi.getY0()))
ds9.line([(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5),
(bbox.getMaxX() + 0.5, bbox.getMinY() - 0.5),
(bbox.getMaxX() + 0.5, bbox.getMaxY() + 0.5),
(bbox.getMinX() - 0.5, bbox.getMaxY() + 0.5),
(bbox.getMinX() - 0.5, bbox.getMinY() - 0.5)],
frame=frame + 1)
if self.nCR is not None:
self.assertEqual(len(crs), self.nCR)
