def makeTest1(doAddNoise):
gaussian1 = afwMath.GaussianFunction2D(1.*gScale, 1.*gScale, 0.)
kernel1 = afwMath.AnalyticKernel(imSize, imSize, gaussian1)
image1 = afwImage.ImageD(kernel1.getDimensions())
kernel1.computeImage(image1, doNorm)
image1 *= scaling # total counts = scaling
image1 = image1.convertF()
mask1 = afwImage.Mask(kernel1.getDimensions())
var1 = afwImage.ImageF(image1, True)
mi1 = afwImage.MaskedImageF(image1, mask1, var1)
if doAddNoise:
addNoise(mi1)
gaussian2 = afwMath.GaussianFunction2D(2.*gScale, 1.5*gScale, 0.5*np.pi)
kernel2 = afwMath.AnalyticKernel(imSize, imSize, gaussian2)
image2 = afwImage.ImageD(kernel2.getDimensions())
kernel2.computeImage(image2, doNorm)
image2 *= scaling # total counts = scaling
image2 = image2.convertF()
mask2 = afwImage.Mask(kernel2.getDimensions())
var2 = afwImage.ImageF(image2, True)
mi2 = afwImage.MaskedImageF(image2, mask2, var2)
if doAddNoise:
addNoise(mi2)
return mi1, mi2
def makeTest1(doAddNoise):
gaussian1 = afwMath.GaussianFunction2D(1., 1., 0.)
kernel1 = afwMath.AnalyticKernel(imSize, imSize, gaussian1)
image1 = afwImage.ImageD(kernel1.getDimensions())
kernel1.computeImage(image1, False)
image1 *= 10000
image1 = image1.convertF()
mask1 = afwImage.Mask(kernel1.getDimensions())
var1 = afwImage.ImageF(image1, True)
mi1 = afwImage.MaskedImageF(image1, mask1, var1)
if doAddNoise:
addNoise(mi1)
gaussian2 = afwMath.GaussianFunction2D(2., 1.5, 0.5 * num.pi)
kernel2 = afwMath.AnalyticKernel(imSize, imSize, gaussian2)
image2 = afwImage.ImageD(kernel2.getDimensions())
kernel2.computeImage(image2, False)
image2 *= 10000
image2 = image2.convertF()
mask2 = afwImage.Mask(kernel2.getDimensions())
var2 = afwImage.ImageF(image2, True)
mi2 = afwImage.MaskedImageF(image2, mask2, var2)
if doAddNoise:
addNoise(mi2)
return mi1, mi2
def main():
butils = measDeblend.BaselineUtilsF
foot = buildExample2()
fbb = foot.getBBox()
mask1 = afwImg.Mask(fbb.getWidth(), fbb.getHeight())
mask1.setXY0(fbb.getMinX(), fbb.getMinY())
afwDet.setMaskFromFootprint(mask1, foot, 1)
if plt:
plt.clf()
plt.imshow(mask1.getArray(), origin='lower', interpolation='nearest',
extent=(fbb.getMinX(), fbb.getMaxX(), fbb.getMinY(), fbb.getMaxY()))
plt.gray()
plt.savefig('foot2.png')
sfoot = butils.symmetrizeFootprint(foot, 355, 227)
mask2 = afwImg.Mask(fbb.getWidth(), fbb.getHeight())
mask2.setXY0(fbb.getMinX(), fbb.getMinY())
afwDet.setMaskFromFootprint(mask2, sfoot, 1)
plt.clf()
plt.imshow(mask2.getArray(), origin='lower', interpolation='nearest',
extent=(fbb.getMinX(), fbb.getMaxX(), fbb.getMinY(), fbb.getMaxY()))
plt.gray()
plt.savefig('sfoot3.png')
def setUp(self):
np.random.seed(1)
self.Mask = afwImage.Mask[afwImage.MaskPixel]
# Store the default mask planes for later use
maskPlaneDict = self.Mask().getMaskPlaneDict()
self.defaultMaskPlanes = sorted(maskPlaneDict,
key=maskPlaneDict.__getitem__)
# reset so tests will be deterministic
self.Mask.clearMaskPlaneDict()
for p in ("BAD", "SAT", "INTRP", "CR", "EDGE"):
self.Mask.addMaskPlane(p)
self.BAD = self.Mask.getPlaneBitMask("BAD")
self.CR = self.Mask.getPlaneBitMask("CR")
self.EDGE = self.Mask.getPlaneBitMask("EDGE")
self.val1 = self.BAD | self.CR
self.val2 = self.val1 | self.EDGE
self.mask1 = afwImage.Mask(100, 200)
self.mask1.set(self.val1)
self.mask2 = afwImage.Mask(self.mask1.getDimensions())
self.mask2.set(self.val2)
if afwdataDir is not None:
self.maskFile = os.path.join(afwdataDir, "data", "small_MI.fits")
# Below: what to expect from the mask plane in the above data.
# For some tests, it is left-shifted by some number of mask planes.
self.expect = np.zeros((256, 256), dtype='i8')
self.expect[:, 0] = 1
def testNoMask(self):
mask = afwImage.Mask(afwGeom.Extent2I(20, 20))
mask.set(0)
fsb = ipDiffim.FindSetBitsU()
bbox = afwGeom.Box2I(afwGeom.Point2I(0, 10), afwGeom.Point2I(9, 12))
fsb.apply(afwImage.Mask(mask, bbox, afwImage.LOCAL))
self.assertEqual(fsb.getBits(), 0)
def testCopyConstructors(self):
dmask = afwImage.Mask(self.mask1, True) # deep copy
smask = afwImage.Mask(self.mask1) # shallow copy
self.mask1 |= 32767 # should only change smask
temp = np.zeros_like(self.mask1.getArray()) | self.val1
self.assertMasksEqual(dmask, temp)
self.assertMasksEqual(smask, self.mask1)
self.assertMasksEqual(smask, temp | 32767)
def testString(self):
mask = afwImage.Mask(100, 100)
self.assertIn(str(np.zeros((100, 100), dtype=mask.dtype)), str(mask))
self.assertIn("bbox=%s"%str(mask.getBBox()), str(mask))
self.assertIn("maskPlaneDict=%s"%str(mask.getMaskPlaneDict()), str(mask))
smallMask = afwImage.Mask(2, 2)
self.assertIn(str(np.zeros((2, 2), dtype=mask.dtype)), str(smallMask))
self.assertIn("MaskX=", repr(mask))
def testInclude(self):
"""Test that we can expand a Footprint to include the union of itself and all others provided."""
region = lsst.geom.Box2I(lsst.geom.Point2I(-6, -6),
lsst.geom.Point2I(6, 6))
parentSpanSet = afwGeom.SpanSet(
lsst.geom.Box2I(lsst.geom.Point2I(-2, -2), lsst.geom.Point2I(2,
2)))
parent = afwDetect.Footprint(parentSpanSet, region)
parent.addPeak(0, 0, float("NaN"))
child1SpanSet = afwGeom.SpanSet(
lsst.geom.Box2I(lsst.geom.Point2I(-3, 0), lsst.geom.Point2I(0, 3)))
child1 = afwDetect.Footprint(child1SpanSet, region)
child1.addPeak(-1, 1, float("NaN"))
child2SpanSet = afwGeom.SpanSet(
lsst.geom.Box2I(lsst.geom.Point2I(-4, -3),
lsst.geom.Point2I(-1, 0)))
child2 = afwDetect.Footprint(child2SpanSet, region)
child3SpanSet = afwGeom.SpanSet(
lsst.geom.Box2I(lsst.geom.Point2I(4, -1), lsst.geom.Point2I(6, 1)))
child3 = afwDetect.Footprint(child3SpanSet)
merge123 = afwDetect.Footprint(parent)
merge123.spans = merge123.spans.union(child1.spans).union(
child2.spans).union(child3.spans)
self.assertTrue(merge123.getBBox().contains(parent.getBBox()))
self.assertTrue(merge123.getBBox().contains(child1.getBBox()))
self.assertTrue(merge123.getBBox().contains(child2.getBBox()))
self.assertTrue(merge123.getBBox().contains(child3.getBBox()))
mask123a = afwImage.Mask(region)
mask123b = afwImage.Mask(region)
parent.spans.setMask(mask123a, 1)
child1.spans.setMask(mask123a, 1)
child2.spans.setMask(mask123a, 1)
child3.spans.setMask(mask123a, 1)
merge123.spans.setMask(mask123b, 1)
self.assertEqual(mask123a.getArray().sum(), merge123.getArea())
self.assertFloatsAlmostEqual(mask123a.getArray(),
mask123b.getArray(),
rtol=0,
atol=0)
# Test that ignoreSelf=True works for include
childOnly = afwDetect.Footprint()
childOnly.spans = childOnly.spans.union(child1.spans).union(
child2.spans).union(child3.spans)
merge123 = afwDetect.Footprint(parent)
merge123.spans = child1.spans.union(child2.spans).union(child3.spans)
maskChildren = afwImage.Mask(region)
mask123 = afwImage.Mask(region)
childOnly.spans.setMask(maskChildren, 1)
merge123.spans.setMask(mask123, 1)
self.assertTrue(np.all(maskChildren.getArray() == mask123.getArray()))
def preMeasureImage(self, source, ref, exp, setFlags=True):
if self.config.calculateVariance:
# Calculate the noise around each object, maybe I should get this from the variance plane?
image = exp.getMaskedImage().getImage()
maskPlanes = [
"BAD", "CR", "DETECTED", "DETECTED_NEGATIVE", "NO_DATA", "SAT",
"EDGE", "SUSPECT", "INTRP"
]
badBit = afwImage.Mask().getPlaneBitMask(maskPlanes)
failed = True
meanSrc = -1
varSrc = -1
# try multiples of the noiseGrow parameter until there are a sufficient number of pixels
for scale in (1, 2, 4, 8):
fp = afwDet.Footprint(source.getFootprint())
fp.dilate(scale * self.config.noiseGrow,
afwGeom.Stencil.MANHATTAN)
if fp.getArea() == 0:
continue
fp.clipTo(exp.getBBox(lsst.afw.image.PARENT))
box = fp.getBBox()
span = fp.spans.intersectNot(
exp.getMaskedImage().getMask()[box], badBit)
maskImage = afwImage.Mask(box, 0)
span.setMask(maskImage, 0x1)
mask = maskImage.array == 0
if span.getArea() < self.config.minVariancePixels:
continue
varSrc = numpy.nanvar(image[box].getArray()[mask])
meanSrc = numpy.nanmean(image[box].getArray()[mask])
failed = False
break
if setFlags and failed:
source.set('bfd.flags.variance', True)
source.set('bfd.flags', True)
return False
source.set('noise_variance', float(varSrc))
source.set('noise_mean', float(meanSrc))
return True
def testOneMask(self):
mask = afwImage.Mask(afwGeom.Extent2I(20, 20))
mask.set(0)
bitmaskBad = mask.getPlaneBitMask('BAD')
fsb = ipDiffim.FindSetBitsU()
bbox = afwGeom.Box2I(afwGeom.Point2I(9, 10), afwGeom.Point2I(11, 12))
submask = afwImage.Mask(mask, bbox, afwImage.LOCAL)
submask |= bitmaskBad
bbox2 = afwGeom.Box2I(afwGeom.Point2I(8, 8), afwGeom.Point2I(19, 19))
fsb.apply(afwImage.Mask(mask, bbox2, afwImage.LOCAL))
self.assertEqual(fsb.getBits(), bitmaskBad)
def testLogicalMasksMismatch(self):
"Test logical operations on Masks of different sizes"
i1 = afwImage.Mask(lsst.geom.ExtentI(100, 100))
i1.set(100)
i2 = afwImage.Mask(lsst.geom.ExtentI(10, 10))
i2.set(10)
with self.assertRaises(lsst.pex.exceptions.LengthError):
i1 |= i2
with self.assertRaises(lsst.pex.exceptions.LengthError):
i1 &= i2
with self.assertRaises(lsst.pex.exceptions.LengthError):
i1 ^= i2
def testFitsReadNoConform2(self):
"""Check that reading a mask doesn't invalidate the plane dictionary"""
testMask = afwImage.Mask(self.fileName, hdu=2)
mask = self.mi.getMask()
mask |= testMask
def setUp(self):
self.imgVal1, self.varVal1 = 100.0, 10.0
self.imgVal2, self.varVal2 = 200.0, 15.0
self.mimage = afwImage.MaskedImageF(100, 200)
self.mimage.image.set(self.imgVal1)
#
# Set center of mask to 0, with 2 pixel border set to EDGE
#
self.BAD = afwImage.Mask.getPlaneBitMask("BAD")
self.EDGE = afwImage.Mask.getPlaneBitMask("EDGE")
self.mimage.mask.set(self.EDGE)
centre = afwImage.Mask(
self.mimage.mask,
lsst.geom.Box2I(lsst.geom.Point2I(2, 2),
self.mimage.getDimensions() - lsst.geom.Extent2I(4)),
afwImage.LOCAL)
centre.set(0x0)
#
self.mimage.variance.set(self.varVal1)
#
# Second MaskedImage
#
self.mimage2 = afwImage.MaskedImageF(self.mimage.getDimensions())
self.mimage2.image.set(self.imgVal2)
self.mimage2.variance.set(self.varVal2)
#
# a Function2
#
self.function = afwMath.PolynomialFunction2D(2)
self.function.setParameters(
list(range(self.function.getNParameters())))
def makeTestImage(xsize=200, ysize=100, nCR=15):
randArr = numpy.random.poisson(1000., xsize * ysize)
randArr = numpy.array(randArr.reshape(ysize, xsize),
dtype=numpy.float32) # force to ImageF
factory = measAlg.GaussianPsfFactory()
factory.addWing = False
psf = factory.apply(4) # FWHM in pixels
img = afwImage.makeImageFromArray(randArr)
var = afwImage.ImageF(img, True) # copy constructor
mask = afwImage.Mask(xsize, ysize)
xind = numpy.random.randint(0, xsize, nCR)
yind = numpy.random.randint(0, ysize, nCR)
# set some CRs
for xi, yi in zip(xind, yind):
xi, yi = int(xi), int(yi)
img.set(xi, yi, 1e6)
mi = afwImage.makeMaskedImage(img, mask, var)
exp = afwImage.makeExposure(mi)
exp.setPsf(psf)
return exp
def testCtorWithPlaneDefs(self):
"""Test that we can create a Mask with a given MaskPlaneDict"""
FOO, val = "FOO", 2
mask = afwImage.Mask(100, 200, {FOO: val})
mpd = mask.getMaskPlaneDict()
self.assertIn(FOO, mpd.keys())
self.assertEqual(mpd[FOO], val)
def makeExposure(self, im, mask=None, variance=None):
"""Method for constructing an exposure object from an image and the
information contained in this class to construct the Detector.
Parameters
----------
im : `lsst.afw.image.Image`
Image used to construct the exposure.
mask : `lsst.afw.image.MaskU`
Optional mask plane.
variance : `lsst.afw.image.Image`
Optional variance plance as an image of the same type as im.
Returns
-------
exposure : `lsst.afw.image.Exposure`
Constructed exposure (specific type will match that of ``im``).
"""
if mask is None:
mask = afwImage.Mask(im.getDimensions())
if variance is None:
variance = im
mi = afwImage.makeMaskedImage(im, mask, variance)
detector = self.buildDetector()
exp = afwImage.makeExposure(mi)
exp.setDetector(detector)
return exp
def getSkySourceFootprints(self, mergedList, skyInfo, seed):
"""!
@brief Return a list of Footprints of sky objects which don't overlap with anything in mergedList
@param mergedList The merged Footprints from all the input bands
@param skyInfo A description of the patch
@param seed Seed for the random number generator
"""
mask = afwImage.Mask(skyInfo.patchInfo.getOuterBBox())
detected = mask.getPlaneBitMask("DETECTED")
for s in mergedList:
s.getFootprint().spans.setMask(mask, detected)
footprints = self.skyObjects.run(mask, seed)
if not footprints:
return footprints
# Need to convert the peak catalog's schema so we can set the "merge_peak_<skyFilterName>" flags
schema = self.merged.getPeakSchema()
mergeKey = schema.find("merge_peak_%s" % self.config.skyFilterName).key
converted = []
for oldFoot in footprints:
assert len(oldFoot.getPeaks()) == 1, "Should be a single peak only"
peak = oldFoot.getPeaks()[0]
newFoot = afwDetect.Footprint(oldFoot.spans, schema)
newFoot.addPeak(peak.getFx(), peak.getFy(), peak.getPeakValue())
newFoot.getPeaks()[0].set(mergeKey, True)
converted.append(newFoot)
return converted
def testFromMask(self):
xy0 = afwGeom.Point2I(12345, 67890) # xy0 for image
dims = afwGeom.Extent2I(123, 45) # Dimensions of image
box = afwGeom.Box2I(xy0, dims) # Bounding box of image
value = 32
other = 16
assert value & other == 0 # Setting 'other' unsets 'value'
point = afwGeom.Point2I(3 + xy0.getX(),
3 + xy0.getY()) # Point in the image
mask = afwImage.Mask(box)
mask.set(value)
# We can create a SpanSet from bit planes
spans = afwGeom.SpanSet.fromMask(mask, value)
self.assertEqual(spans.getArea(), box.getArea())
self.assertEqual(spans.getBBox(), box)
self.assertTrue(point in spans)
# Pixels not matching the desired bit plane are ignored as they should be
mask.set(point.getX() - xy0.getX(),
point.getY() - xy0.getY(), other) # unset one pixel
spans = afwGeom.SpanSet.fromMask(mask, value)
self.assertEqual(spans.getArea(), box.getArea() - 1)
self.assertEqual(spans.getBBox(), box)
self.assertFalse(point in spans)
def testClipped(self):
"""Test that we set mask bits when pixels are clipped"""
box = lsst.geom.Box2I(lsst.geom.Point2I(12345, 67890), lsst.geom.Extent2I(3, 3))
num = 10
maskVal = 0xAD
value = 0.0
images = [afwImage.MaskedImageF(box) for _ in range(num)]
statsCtrl = afwMath.StatisticsControl()
statsCtrl.setAndMask(maskVal)
clipped = 1 << afwImage.Mask().addMaskPlane("CLIPPED")
# No clipping: check that vanilla is working
for img in images:
img.getImage().set(value)
img.getMask().set(0)
stack = afwMath.statisticsStack(images, afwMath.MEANCLIP, clipped=clipped)
self.assertFloatsAlmostEqual(stack.getImage().getArray(), 0.0, atol=0.0)
self.assertFloatsAlmostEqual(stack.getMask().getArray(), 0, atol=0.0) # Not floats, but that's OK
# Clip a pixel; the CLIPPED bit should be set
images[0].getImage()[1, 1, afwImage.LOCAL] = value + 1.0
stack = afwMath.statisticsStack(images, afwMath.MEANCLIP, clipped=clipped)
self.assertFloatsAlmostEqual(stack.getImage().getArray(), 0.0, atol=0.0)
self.assertEqual(stack.mask[1, 1, afwImage.LOCAL], clipped)
# Mask a pixel; the CLIPPED bit should be set
images[0].getMask()[1, 1, afwImage.LOCAL] = maskVal
stack = afwMath.statisticsStack(images, afwMath.MEAN, statsCtrl, clipped=clipped)
self.assertFloatsAlmostEqual(stack.getImage().getArray(), 0.0, atol=0.0)
self.assertEqual(stack.mask[1, 1, afwImage.LOCAL], clipped)
# Excuse that mask; the CLIPPED bit should not be set
stack = afwMath.statisticsStack(images, afwMath.MEAN, statsCtrl, clipped=clipped, excuse=maskVal)
self.assertFloatsAlmostEqual(stack.getImage().getArray(), 0.0, atol=0.0)
self.assertEqual(stack.mask[1, 1, afwImage.LOCAL], 0)
# Map that mask value to a different one.
rejected = 1 << afwImage.Mask().addMaskPlane("REJECTED")
maskMap = [(maskVal, rejected)]
images[0].mask[1, 1, afwImage.LOCAL] = 0 # only want to clip, not mask, this one
images[1].mask[1, 2, afwImage.LOCAL] = maskVal # only want to mask, not clip, this one
stack = afwMath.statisticsStack(images, afwMath.MEANCLIP, statsCtrl, wvector=[], clipped=clipped,
maskMap=maskMap)
self.assertFloatsAlmostEqual(stack.getImage().getArray(), 0.0, atol=0.0)
self.assertEqual(stack.mask[1, 1, afwImage.LOCAL], clipped)
self.assertEqual(stack.mask[1, 2, afwImage.LOCAL], rejected)
def getExposure(self):
"""Construct a test exposure.
The test exposure has a simple WCS set, as well as a list of
unlikely header keywords that can be removed during ISR
processing to exercise that code.
Returns
-------
exposure : `lsst.afw.exposure.Exposure`
Construct exposure containing masked image of the
appropriate size.
"""
camera = self.getCamera()
detector = camera[self.config.detectorIndex]
image = afwUtils.makeImageFromCcd(detector,
isTrimmed=self.config.isTrimmed,
showAmpGain=False,
rcMarkSize=0,
binSize=1,
imageFactory=afwImage.ImageF)
var = afwImage.ImageF(image.getDimensions())
mask = afwImage.Mask(image.getDimensions())
image.assign(0.0)
maskedImage = afwImage.makeMaskedImage(image, mask, var)
exposure = afwImage.makeExposure(maskedImage)
exposure.setDetector(detector)
exposure.setWcs(self.getWcs())
visitInfo = afwImage.VisitInfo(exposureTime=self.config.expTime, darkTime=self.config.darkTime)
exposure.getInfo().setVisitInfo(visitInfo)
metadata = exposure.getMetadata()
metadata.add("SHEEP", 7.3, "number of sheep on farm")
metadata.add("MONKEYS", 155, "monkeys per tree")
metadata.add("VAMPIRES", 4, "How scary are vampires.")
ccd = exposure.getDetector()
newCcd = ccd.rebuild()
newCcd.clear()
for amp in ccd:
newAmp = amp.rebuild()
newAmp.setLinearityCoeffs((0., 1., 0., 0.))
newAmp.setLinearityType("Polynomial")
newAmp.setGain(self.config.gain)
newAmp.setSuspectLevel(25000.0)
newAmp.setSaturation(32000.0)
newCcd.append(newAmp)
exposure.setDetector(newCcd.finish())
exposure.image.array[:] = np.zeros(exposure.getImage().getDimensions()).transpose()
exposure.mask.array[:] = np.zeros(exposure.getMask().getDimensions()).transpose()
exposure.variance.array[:] = np.zeros(exposure.getVariance().getDimensions()).transpose()
return exposure
def testRandomMap(self):
"""Test setCoaddEdgeBits using a random depth map
"""
imDim = geom.Extent2I(50, 55)
coaddMask = afwImage.Mask(imDim)
np.random.seed(12345)
depthMapArray = np.random.randint(0, 3, list(
(imDim[1], imDim[0]))).astype(np.uint16)
depthMap = afwImage.makeImageFromArray(depthMapArray)
refCoaddMask = afwImage.Mask(imDim)
refCoaddMaskArray = refCoaddMask.getArray()
edgeMask = afwImage.Mask.getPlaneBitMask("NO_DATA")
refCoaddMaskArray |= np.array(np.where(depthMapArray > 0, 0, edgeMask),
dtype=refCoaddMaskArray.dtype)
coaddUtils.setCoaddEdgeBits(coaddMask, depthMap)
self.assertMasksEqual(coaddMask, refCoaddMask)
def testSubmasks(self):
smask = afwImage.Mask(
self.mask1,
afwGeom.Box2I(afwGeom.Point2I(1, 1), afwGeom.ExtentI(3, 2)),
afwImage.LOCAL)
mask2 = afwImage.Mask(smask.getDimensions())
mask2.set(666)
smask[:] = mask2
del smask
del mask2
self.assertEqual(self.mask1.get(0, 0), self.val1)
self.assertEqual(self.mask1.get(1, 1), 666)
self.assertEqual(self.mask1.get(4, 1), self.val1)
self.assertEqual(self.mask1.get(1, 2), 666)
self.assertEqual(self.mask1.get(4, 2), self.val1)
self.assertEqual(self.mask1.get(1, 3), self.val1)
def testSubmasks(self):
smask = afwImage.Mask(
self.mask1,
lsst.geom.Box2I(lsst.geom.Point2I(1, 1), lsst.geom.ExtentI(3, 2)),
afwImage.LOCAL)
mask2 = afwImage.Mask(smask.getDimensions())
mask2.set(666)
smask[:] = mask2
del smask
del mask2
self.assertEqual(self.mask1[0, 0, afwImage.LOCAL], self.val1)
self.assertEqual(self.mask1[1, 1, afwImage.LOCAL], 666)
self.assertEqual(self.mask1[4, 1, afwImage.LOCAL], self.val1)
self.assertEqual(self.mask1[1, 2, afwImage.LOCAL], 666)
self.assertEqual(self.mask1[4, 2, afwImage.LOCAL], self.val1)
self.assertEqual(self.mask1[1, 3, afwImage.LOCAL], self.val1)
def testManyMask(self):
mask = afwImage.Mask(geom.Extent2I(20, 20))
mask.set(0)
bitmaskBad = mask.getPlaneBitMask('BAD')
bitmaskSat = mask.getPlaneBitMask('SAT')
fsb = ipDiffim.FindSetBitsU()
bbox = geom.Box2I(geom.Point2I(9, 10), geom.Point2I(11, 12))
submask = afwImage.Mask(mask, bbox, afwImage.LOCAL)
submask |= bitmaskBad
bbox2 = geom.Box2I(geom.Point2I(8, 8), geom.Point2I(19, 19))
submask2 = afwImage.Mask(mask, bbox2, afwImage.LOCAL)
submask2 |= bitmaskSat
bbox3 = geom.Box2I(geom.Point2I(0, 0), geom.Point2I(19, 19))
fsb.apply(afwImage.Mask(mask, bbox3, afwImage.LOCAL))
self.assertEqual(fsb.getBits(), bitmaskBad | bitmaskSat)
def convertfpM(infile, allPlanes=False):
hdr = pyfits.open(infile)
run = hdr[0].header['RUN']
camcol = hdr[0].header['CAMCOL']
field = hdr[0].header['FIELD']
nRows = hdr[0].header['MASKROWS']
nCols = hdr[0].header['MASKCOLS']
nPlane = hdr[0].header['NPLANE']
names = hdr[-1].data.names
if (not "attributeName" in names) or (not "Value" in names):
raise LookupError("Missing data in fpM header")
planes = hdr[-1].data.field("attributeName").tolist()
values = hdr[-1].data.field("Value").tolist()
mask = afwImage.Mask(afwGeom.ExtentI(nCols, nRows))
# Minimal sets of mask planes needed for LSST
interpPlane = planes.index("S_MASK_INTERP") + 1
satPlane = planes.index("S_MASK_SATUR") + 1
crPlane = planes.index("S_MASK_CR") + 1
interpBitMask = afwImage.Mask.getPlaneBitMask("INTRP")
satBitMask = afwImage.Mask.getPlaneBitMask("SAT")
crBitMask = afwImage.Mask.getPlaneBitMask("CR")
listToSet = [(interpPlane, interpBitMask), (satPlane, satBitMask),
(crPlane, crBitMask)]
# Add the rest of the SDSS planes
if allPlanes:
for plane in [
'S_MASK_NOTCHECKED', 'S_MASK_OBJECT', 'S_MASK_BRIGHTOBJECT',
'S_MASK_BINOBJECT', 'S_MASK_CATOBJECT', 'S_MASK_SUBTRACTED',
'S_MASK_GHOST'
]:
idx = planes.index(plane) + 1
planeName = re.sub("S_MASK_", "", plane)
planeId = mask.addMaskPlane(planeName)
planeBitMask = afwImage.Mask.getPlaneBitMask(planeName)
listToSet.append((idx, planeBitMask))
for plane, bitmask in listToSet:
if len(hdr) < plane:
continue
if hdr[plane].data is None:
continue
nmask = len(hdr[plane].data)
for i in range(nmask):
frow = hdr[plane].data[i]
Objmask(frow, bitmask).setMask(mask)
return mask
def runMeasurement(self, algorithmName, imageid, x, y, v):
"""Run the measurement algorithm on an image"""
# load the test image
imgFile = os.path.join(self.dataDir, "image.%d.fits" % imageid)
img = afwImage.ImageF(imgFile)
img -= self.bkgd
nx, ny = img.getWidth(), img.getHeight()
msk = afwImage.Mask(geom.Extent2I(nx, ny), 0x0)
var = afwImage.ImageF(geom.Extent2I(nx, ny), v)
mimg = afwImage.MaskedImageF(img, msk, var)
msk.getArray()[:] = np.where(np.fabs(img.getArray()) < 1.0e-8, msk.getPlaneBitMask("BAD"), 0)
# Put it in a bigger image, in case it matters
big = afwImage.MaskedImageF(self.offset + mimg.getDimensions())
big.getImage().set(0)
big.getMask().set(0)
big.getVariance().set(v)
subBig = afwImage.MaskedImageF(big, geom.Box2I(big.getXY0() + self.offset, mimg.getDimensions()))
subBig <<= mimg
mimg = big
mimg.setXY0(self.xy0)
exposure = afwImage.makeExposure(mimg)
cdMatrix = np.array([1.0/(2.53*3600.0), 0.0, 0.0, 1.0/(2.53*3600.0)])
cdMatrix.shape = (2, 2)
exposure.setWcs(afwGeom.makeSkyWcs(crpix=geom.Point2D(1.0, 1.0),
crval=geom.SpherePoint(0, 0, geom.degrees),
cdMatrix=cdMatrix))
# load the corresponding test psf
psfFile = os.path.join(self.dataDir, "psf.%d.fits" % imageid)
psfImg = afwImage.ImageD(psfFile)
psfImg -= self.bkgd
kernel = afwMath.FixedKernel(psfImg)
kernelPsf = algorithms.KernelPsf(kernel)
exposure.setPsf(kernelPsf)
# perform the shape measurement
msConfig = base.SingleFrameMeasurementConfig()
alg = base.SingleFramePlugin.registry[algorithmName].PluginClass.AlgClass
control = base.SingleFramePlugin.registry[algorithmName].PluginClass.ConfigClass().makeControl()
msConfig.algorithms.names = [algorithmName]
# Note: It is essential to remove the floating point part of the position for the
# Algorithm._apply. Otherwise, when the PSF is realised it will have been warped
# to account for the sub-pixel offset and we won't get *exactly* this PSF.
plugin, table = makePluginAndCat(alg, algorithmName, control, centroid="centroid")
center = geom.Point2D(int(x), int(y)) + geom.Extent2D(self.offset + geom.Extent2I(self.xy0))
source = table.makeRecord()
source.set("centroid_x", center.getX())
source.set("centroid_y", center.getY())
source.setFootprint(afwDetection.Footprint(afwGeom.SpanSet(exposure.getBBox(afwImage.PARENT))))
plugin.measure(source, exposure)
return source
def plantSources(bbox, kwid, sky, coordList, addPoissonNoise=True):
"""Make an exposure with stars (modelled as Gaussians)
@param bbox: parent bbox of exposure
@param kwid: kernel width (and height; kernel is square)
@param sky: amount of sky background (counts)
@param coordList: a list of [x, y, counts, sigma], where:
* x,y are relative to exposure origin
* counts is the integrated counts for the star
* sigma is the Gaussian sigma in pixels
@param addPoissonNoise: add Poisson noise to the exposure?
"""
# make an image with sources
img = afwImage.ImageD(bbox)
meanSigma = 0.0
for coord in coordList:
x, y, counts, sigma = coord
meanSigma += sigma
# make a single gaussian psf
psf = SingleGaussianPsf(kwid, kwid, sigma)
# make an image of it and scale to the desired number of counts
thisPsfImg = psf.computeImage(afwGeom.PointD(x, y))
thisPsfImg *= counts
# bbox a window in our image and add the fake star image
psfBox = thisPsfImg.getBBox()
psfBox.clip(bbox)
if psfBox != thisPsfImg.getBBox():
thisPsfImg = thisPsfImg[psfBox, afwImage.PARENT]
imgSeg = img[psfBox, afwImage.PARENT]
imgSeg += thisPsfImg
meanSigma /= len(coordList)
img += sky
# add Poisson noise
if (addPoissonNoise):
np.random.seed(seed=1) # make results reproducible
imgArr = img.getArray()
imgArr[:] = np.random.poisson(imgArr)
# bundle into a maskedimage and an exposure
mask = afwImage.Mask(bbox)
var = img.convertFloat()
img -= sky
mimg = afwImage.MaskedImageF(img.convertFloat(), mask, var)
exposure = afwImage.makeExposure(mimg)
# insert an approximate psf
psf = SingleGaussianPsf(kwid, kwid, meanSigma)
exposure.setPsf(psf)
return exposure
def im_to_array(imfile, hdu):
image = afw_image.ImageF(imfile, hdu)
mask = afw_image.Mask(image.getDimensions())
masked_image = afw_image.MaskedImageF(image, mask)
md = afw_image.readMetadata(imfile, hdu)
imsec = masked_image.Factory(masked_image, get_bbox(md.get('DATASEC')))
values, mask, var = imsec.getArrays()
values = values.flatten()
values = values.astype(int)
return values
def testMismatch(self):
"""Test that we get an exception when there's a size mismatch"""
scale = 5
dims = self.image.getDimensions()
mask = afwImage.Mask(dims * scale)
mask.set(0xFF)
ctrl = afwMath.StatisticsControl()
ctrl.setAndMask(0xFF)
# If it didn't raise, this would result in a NaN (the image data is
# completely masked).
self.assertRaises(lsst.pex.exceptions.InvalidParameterError,
afwMath.makeStatistics, self.image, mask,
afwMath.MEDIAN, ctrl)
subMask = afwImage.Mask(
mask, afwGeom.Box2I(afwGeom.Point2I(dims * (scale - 1)), dims))
subMask.set(0)
# Using subMask is successful.
self.assertEqual(
afwMath.makeStatistics(self.image, subMask, afwMath.MEDIAN,
ctrl).getValue(), self.val)
def makeMaskAndSpanSetForOperationTest(self):
firstMaskPart = afwGeom.SpanSet.fromShape(2, afwGeom.Stencil.BOX).shiftedBy(3, 2)
secondMaskPart = afwGeom.SpanSet.fromShape(2, afwGeom.Stencil.BOX).shiftedBy(3, 8)
spanSetMaskOperation = afwGeom.SpanSet.fromShape(2, afwGeom.Stencil.BOX).shiftedBy(3, 5)
mask = afwImage.Mask(20, 20)
firstMaskPart.setMask(mask, 3)
secondMaskPart.setMask(mask, 3)
spanSetMaskOperation.setMask(mask, 4)
return mask, spanSetMaskOperation
