def testSetCtr(self):
"""Test setCtrCol/Row"""
kWidth = 3
kHeight = 4
pol = pexPolicy.Policy()
additionalData = dafBase.PropertySet()
loc = dafPersist.LogicalLocation("tests/data/kernel7.boost")
persistence = dafPersist.Persistence.getPersistence(pol)
gaussFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
k = afwMath.AnalyticKernel(kWidth, kHeight, gaussFunc)
for xCtr in range(kWidth):
k.setCtrX(xCtr)
for yCtr in range(kHeight):
k.setCtrY(yCtr)
storageList = dafPersist.StorageList()
storage = persistence.getPersistStorage("XmlStorage", loc)
storageList.append(storage)
persistence.persist(k, storageList, additionalData)
storageList2 = dafPersist.StorageList()
storage2 = persistence.getRetrieveStorage("XmlStorage", loc)
storageList2.append(storage2)
x = persistence.unsafeRetrieve("AnalyticKernel", storageList2,
additionalData)
k2 = afwMath.AnalyticKernel.swigConvert(x)
self.kernelCheck(k, k2)
self.assertEqual(k2.getCtrX(), xCtr)
self.assertEqual(k2.getCtrY(), yCtr)
def testZeroSizeKernel(self):
"""Creating a kernel with width or height < 1 should raise an exception.
Note: this ignores the default constructors, which produce kernels with height = width = 0.
The default constructors are only intended to support persistence, not to produce useful kernels.
"""
gaussFunc2D = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
gaussFunc1D = afwMath.GaussianFunction1D(1.0)
zeroPoint = lsst.geom.Point2I(0, 0)
for kWidth in (-1, 0, 1):
for kHeight in (-1, 0, 1):
if (kHeight > 0) and (kWidth > 0):
continue
if (kHeight >= 0) and (kWidth >= 0):
# don't try to create an image with negative dimensions
blankImage = afwImage.ImageF(
lsst.geom.Extent2I(kWidth, kHeight))
self.assertRaises(Exception, afwMath.FixedKernel,
blankImage)
self.assertRaises(Exception, afwMath.AnalyticKernel, kWidth,
kHeight, gaussFunc2D)
self.assertRaises(Exception, afwMath.SeparableKernel, kWidth,
kHeight, gaussFunc1D, gaussFunc1D)
self.assertRaises(Exception, afwMath.DeltaFunctionKernel,
kWidth, kHeight, zeroPoint)
def makeKernel(self):
kCols = 7
kRows = 6
# create spatial model
sFunc = afwMath.PolynomialFunction2D(1)
minSigma = 0.1
maxSigma = 3.0
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
xSlope = (maxSigma - minSigma) / self.bbox.getWidth()
ySlope = (maxSigma - minSigma) / self.bbox.getHeight()
xOrigin = minSigma - (self.xy0[0] * xSlope)
yOrigin = minSigma - (self.xy0[1] * ySlope)
sParams = (
(xOrigin, xSlope, 0.0),
(yOrigin, 0.0, ySlope),
(0.0, 0.0, 0.0),
)
kFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
kernel = afwMath.AnalyticKernel(kCols, kRows, kFunc, sFunc)
kernel.setSpatialParameters(sParams)
return kernel
def testSpatiallyVaryingAnalyticConvolve(self):
"""Test in-place convolution with a spatially varying AnalyticKernel
"""
kWidth = 7
kHeight = 6
# create spatial model
sFunc = afwMath.PolynomialFunction2D(1)
minSigma = 1.5
maxSigma = 1.501
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(minSigma, (maxSigma - minSigma) / self.width, 0.0),
(minSigma, 0.0, (maxSigma - minSigma) / self.height),
(0.0, 0.0, 0.0),
)
kFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
kernel = afwMath.AnalyticKernel(kWidth, kHeight, kFunc, sFunc)
kernel.setSpatialParameters(sParams)
for maxInterpDist, rtol, methodStr in (
(0, 1.0e-5, "brute force"),
(10, 1.0e-5, "interpolation over 10 x 10 pixels"),
):
self.runStdTest(
kernel,
kernelDescr="Spatially Varying Gaussian Analytic Kernel using %s" % (methodStr,),
maxInterpDist=maxInterpDist,
rtol=rtol)
def testSpatiallyVaryingSeparableConvolve(self):
"""Test convolution with a spatially varying SeparableKernel
"""
kWidth = 7
kHeight = 6
# create spatial model
sFunc = afwMath.PolynomialFunction2D(1)
minSigma = 0.1
maxSigma = 3.0
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(minSigma, (maxSigma - minSigma) / self.width, 0.0),
(minSigma, 0.0, (maxSigma - minSigma) / self.height),
(0.0, 0.0, 0.0),
)
gaussFunc1 = afwMath.GaussianFunction1D(1.0)
gaussFunc2 = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
separableKernel = afwMath.SeparableKernel(kWidth, kHeight, gaussFunc1, gaussFunc1, sFunc)
analyticKernel = afwMath.AnalyticKernel(kWidth, kHeight, gaussFunc2, sFunc)
separableKernel.setSpatialParameters(sParams[0:2])
analyticKernel.setSpatialParameters(sParams)
self.runStdTest(separableKernel, refKernel=analyticKernel,
kernelDescr="Spatially Varying Gaussian Separable Kernel")
def addStar(image, center, flux, fwhm):
"""Add a perfect single Gaussian star to an image
@warning uses Python to iterate over all pixels (because there is no C++
function that computes a Gaussian offset by a non-integral amount).
@param[in,out] image: Image to which to add star
@param[in] center: position of center of star on image (pair of float)
@param[in] flux: flux of Gaussian star, in counts
@param[in] fwhm: FWHM of Gaussian star, in pixels
"""
sigma = fwhm / FwhmPerSigma
func = afwMath.GaussianFunction2D(sigma, sigma, 0)
starImage = afwImage.ImageF(image.getBBox())
# The flux in the region of the image will not be exactly the desired flux because the Gaussian
# does not extend to infinity, so keep track of the actual flux and correct for it
actFlux = 0
# No function exists that has a fractional x and y offset, so set the image the slow way
for i in range(image.getWidth()):
x = center[0] - i
for j in range(image.getHeight()):
y = center[1] - j
pixVal = flux * func(x, y)
actFlux += pixVal
starImage[i, j] += pixVal
starImage *= flux / actFlux
image += starImage
def _computeVaryingPsf(self):
"""Compute a varying PSF as a linear combination of PCA (== Karhunen-Loeve) basis functions
We simply desire a PSF that is not constant across the image, so the precise choice of
parameters (e.g., sigmas, setSpatialParameters) are not crucial.
"""
kernelSize = 31
sigma1 = 1.75
sigma2 = 2.0 * sigma1
basisKernelList = []
for sigma in (sigma1, sigma2):
basisKernel = afwMath.AnalyticKernel(
kernelSize, kernelSize,
afwMath.GaussianFunction2D(sigma, sigma))
basisImage = afwImage.ImageD(basisKernel.getDimensions())
basisKernel.computeImage(basisImage, True)
basisImage /= np.sum(basisImage.getArray())
if sigma == sigma1:
basisImage0 = basisImage
else:
basisImage -= basisImage0
basisKernelList.append(afwMath.FixedKernel(basisImage))
order = 1
spFunc = afwMath.PolynomialFunction2D(order)
exactKernel = afwMath.LinearCombinationKernel(basisKernelList, spFunc)
exactKernel.setSpatialParameters([[1.0, 0, 0], [0.0, 0.5E-2, 0.2E-2]])
exactPsf = measAlg.PcaPsf(exactKernel)
return exactPsf
def testAnalyticKernel(self):
"""Test AnalyticKernel using a Gaussian function
"""
kWidth = 5
kHeight = 8
gaussFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
k = afwMath.AnalyticKernel(kWidth, kHeight, gaussFunc)
fArr = np.zeros(shape=[k.getWidth(), k.getHeight()], dtype=float)
for xsigma in (0.1, 1.0, 3.0):
for ysigma in (0.1, 1.0, 3.0):
for angle in (0.0, 0.4, 1.1):
gaussFunc.setParameters((xsigma, ysigma, angle))
# compute array of function values and normalize
for row in range(k.getHeight()):
y = row - k.getCtrY()
for col in range(k.getWidth()):
x = col - k.getCtrX()
fArr[col, row] = gaussFunc(x, y)
fArr /= fArr.sum()
k.setKernelParameters((xsigma, ysigma, angle))
with lsst.utils.tests.getTempFilePath(".fits") as filename:
k.writeFits(filename)
k2 = afwMath.AnalyticKernel.readFits(filename)
self.kernelCheck(k, k2)
kImage = afwImage.ImageD(k2.getDimensions())
k2.computeImage(kImage, True)
kArr = kImage.getArray().transpose()
if not np.allclose(fArr, kArr):
self.fail("%s = %s != %s for xsigma=%s, ysigma=%s" %
(k2.__class__.__name__, kArr, fArr, xsigma, ysigma))
def testSVAnalyticKernel(self):
"""Test spatially varying AnalyticKernel using a Gaussian function
Just tests cloning.
"""
kWidth = 5
kHeight = 8
# spatial model
spFunc = afwMath.PolynomialFunction2D(1)
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(1.0, 1.0, 0.0),
(1.0, 0.0, 1.0),
(0.5, 0.5, 0.5),
)
gaussFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
kernel = afwMath.AnalyticKernel(kWidth, kHeight, gaussFunc, spFunc)
kernel.setSpatialParameters(sParams)
kernelClone = kernel.clone()
errStr = self.compareKernels(kernel, kernelClone)
if errStr:
self.fail(errStr)
newSParams = (
(0.1, 0.2, 0.5),
(0.1, 0.5, 0.2),
(0.2, 0.3, 0.3),
)
kernel.setSpatialParameters(newSParams)
errStr = self.compareKernels(kernel, kernelClone)
if not errStr:
self.fail(
"Clone was modified by changing original's spatial parameters")
#
# check that we can construct a FixedKernel from a LinearCombinationKernel
#
x, y = 100, 200
kernel2 = afwMath.FixedKernel(kernel, lsst.geom.PointD(x, y))
self.assertTrue(re.search("AnalyticKernel", kernel.toString()))
self.assertFalse(kernel2.isSpatiallyVarying())
self.assertTrue(re.search("FixedKernel", kernel2.toString()))
self.assertTrue(kernel.isSpatiallyVarying())
kim = afwImage.ImageD(kernel.getDimensions())
kernel.computeImage(kim, True, x, y)
kim2 = afwImage.ImageD(kernel2.getDimensions())
kernel2.computeImage(kim2, True)
assert_allclose(kim.getArray(), kim2.getArray())
def testLinearCombinationKernelAnalytic(self):
"""Test LinearCombinationKernel using analytic basis kernels.
The basis kernels are mutable so that we can verify that the
LinearCombinationKernel has private copies of the basis kernels.
"""
kWidth = 5
kHeight = 8
# create list of kernels
basisImArrList = []
basisKernelList = afwMath.KernelList()
for basisKernelParams in [(1.2, 0.3, 1.570796), (1.0, 0.2, 0.0)]:
basisKernelFunction = afwMath.GaussianFunction2D(
*basisKernelParams)
basisKernel = afwMath.AnalyticKernel(kWidth, kHeight,
basisKernelFunction)
basisImage = afwImage.ImageD(basisKernel.getDimensions())
basisKernel.computeImage(basisImage, True)
basisImArrList.append(basisImage.getArray())
basisKernelList.append(basisKernel)
kParams = [0.0] * len(basisKernelList)
kernel = afwMath.LinearCombinationKernel(basisKernelList, kParams)
self.assertTrue(not kernel.isDeltaFunctionBasis())
self.basicTests(kernel, len(kParams))
# make sure the linear combination kernel has private copies of its basis kernels
# by altering the local basis kernels and making sure the new images do NOT match
modBasisImArrList = []
for basisKernel in basisKernelList:
basisKernel.setKernelParameters((0.4, 0.5, 0.6))
modBasisImage = afwImage.ImageD(basisKernel.getDimensions())
basisKernel.computeImage(modBasisImage, True)
modBasisImArrList.append(modBasisImage.getArray())
for ii in range(len(basisKernelList)):
kParams = [0.0] * len(basisKernelList)
kParams[ii] = 1.0
kernel.setKernelParameters(kParams)
kIm = afwImage.ImageD(kernel.getDimensions())
kernel.computeImage(kIm, True)
kImArr = kIm.getArray()
if not np.allclose(kImArr, basisImArrList[ii]):
self.fail("%s = %s != %s for the %s'th basis kernel" %
(kernel.__class__.__name__, kImArr,
basisImArrList[ii], ii))
if np.allclose(kImArr, modBasisImArrList[ii]):
self.fail("%s = %s == %s for *modified* %s'th basis kernel" %
(kernel.__class__.__name__, kImArr,
modBasisImArrList[ii], ii))
kernelClone = kernel.clone()
errStr = self.compareKernels(kernel, kernelClone)
if errStr:
self.fail(errStr)
self.verifyCache(kernel, hasCache=False)
def testMakeBadKernels(self):
"""Attempt to make various invalid kernels; make sure the constructor shows an exception
"""
kWidth = 4
kHeight = 3
gaussFunc1 = afwMath.GaussianFunction1D(1.0)
gaussFunc2 = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
spFunc = afwMath.PolynomialFunction2D(1)
kernelList = []
kernelList.append(afwMath.FixedKernel(
afwImage.ImageD(lsst.geom.Extent2I(kWidth, kHeight), 0.1)))
kernelList.append(afwMath.FixedKernel(
afwImage.ImageD(lsst.geom.Extent2I(kWidth, kHeight), 0.2)))
for numKernelParams in (2, 4):
spFuncList = []
for ii in range(numKernelParams):
spFuncList.append(spFunc.clone())
try:
afwMath.AnalyticKernel(kWidth, kHeight, gaussFunc2, spFuncList)
self.fail("Should have failed with wrong # of spatial functions")
except pexExcept.Exception:
pass
for numKernelParams in (1, 3):
spFuncList = []
for ii in range(numKernelParams):
spFuncList.append(spFunc.clone())
try:
afwMath.LinearCombinationKernel(kernelList, spFuncList)
self.fail("Should have failed with wrong # of spatial functions")
except pexExcept.Exception:
pass
kParamList = [0.2]*numKernelParams
try:
afwMath.LinearCombinationKernel(kernelList, kParamList)
self.fail("Should have failed with wrong # of kernel parameters")
except pexExcept.Exception:
pass
try:
afwMath.SeparableKernel(
kWidth, kHeight, gaussFunc1, gaussFunc1, spFuncList)
self.fail("Should have failed with wrong # of spatial functions")
except pexExcept.Exception:
pass
for pointX in range(-1, kWidth+2):
for pointY in range(-1, kHeight+2):
if (0 <= pointX < kWidth) and (0 <= pointY < kHeight):
continue
try:
afwMath.DeltaFunctionKernel(
kWidth, kHeight, lsst.geom.Point2I(pointX, pointY))
self.fail("Should have failed with point not on kernel")
except pexExcept.Exception:
pass
def makeSpatialKernel(self, order):
basicGaussian1 = afwMath.GaussianFunction2D(2., 2., 0.)
basicKernel1 = afwMath.AnalyticKernel(self.ksize, self.ksize, basicGaussian1)
basicGaussian2 = afwMath.GaussianFunction2D(5., 3., 0.5 * num.pi)
basicKernel2 = afwMath.AnalyticKernel(self.ksize, self.ksize, basicGaussian2)
basisList = []
basisList.append(basicKernel1)
basisList.append(basicKernel2)
basisList = ipDiffim.renormalizeKernelList(basisList)
spatialKernelFunction = afwMath.PolynomialFunction2D(order)
spatialKernel = afwMath.LinearCombinationKernel(basisList, spatialKernelFunction)
kCoeffs = [[0.0 for x in range(1, spatialKernelFunction.getNParameters()+1)],
[0.01 * x for x in range(1, spatialKernelFunction.getNParameters()+1)]]
kCoeffs[0][0] = 1.0 # it does not vary spatially; constant across image
spatialKernel.setSpatialParameters(kCoeffs)
return spatialKernel
def testSpatiallyInvariantConvolve(self):
"""Test convolution with a spatially invariant Gaussian function
"""
kWidth = 6
kHeight = 7
kFunc = afwMath.GaussianFunction2D(2.5, 1.5, 0.5)
kernel = afwMath.AnalyticKernel(kWidth, kHeight, kFunc)
self.runStdTest(kernel, kernelDescr="Gaussian Analytic Kernel")
def testDoubleGaussianFunction2D(self):
"""Note: Assumes GaussianFunction2D is correct (tested elsewhere)."""
errMsg = "{} = {} != {} for x={}, y={}, sigma1={}, sigma2={}, b={}"
areaMsg = "{} area = {} != 1.0 for sigma1={}, sigma2={}"
f = afwMath.DoubleGaussianFunction2D(1.0, 1.0)
f1 = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
f2 = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
for sigma1 in (1.0,):
for sigma2 in (0.5, 2.0):
for b in (0.0, 0.2, 2.0):
f.setParameters((sigma1, sigma2, b))
g = f.clone()
f1.setParameters((sigma1, sigma1, 0.0))
f2.setParameters((sigma2, sigma2, 0.0))
sigma1Sq = sigma1**2
sigma2Sq = sigma2**2
f1Mult = b * sigma2Sq / sigma1Sq
allMult = sigma1Sq / (sigma1Sq + (b * sigma2Sq))
fSum = 0.0
maxsigma = max(sigma1, sigma2)
minsigma = min(sigma1, sigma2)
delta = minsigma / 5.0
for y in np.arange(-maxsigma * 5, maxsigma * 5.01, delta):
for x in np.arange(-maxsigma * 5.0, maxsigma * 5.01, delta):
predVal = (
f1(x, y) + (f1Mult * f2(x, y))) * allMult
fSum += predVal
msg = errMsg.format(
type(f).__name__,
f(x, y), predVal, x, y, sigma1, sigma2, b)
self.assertFloatsAlmostEqual(
f(x, y), predVal, msg=msg, atol=self.atol, rtol=None)
msg = errMsg.format(type(g).__name__, g(x, y), predVal,
x, y, sigma1, sigma2, b) + "; clone"
self.assertFloatsAlmostEqual(
g(x, y), predVal, msg=msg, atol=self.atol, rtol=None)
approxArea = fSum * delta**2
msg = areaMsg.format(
type(f).__name__, approxArea, sigma1, sigma2)
# approxArea is very approximate, so we need a high
# tolerance threshold.
self.assertFloatsAlmostEqual(
approxArea, 1.0, msg=msg, atol=1e-6, rtol=None)
def testGaussian(self, imsize=50):
# Convolve a delta function with a known gaussian; try to
# recover using delta-function basis
gsize = self.ps["kernelSize"]
tsize = imsize + gsize
gaussFunction = afwMath.GaussianFunction2D(2, 3)
gaussKernel = afwMath.AnalyticKernel(gsize, gsize, gaussFunction)
kImageIn = afwImage.ImageD(geom.Extent2I(gsize, gsize))
gaussKernel.computeImage(kImageIn, False)
# template image with a single hot pixel in the exact center
tmi = afwImage.MaskedImageF(geom.Extent2I(tsize, tsize))
tmi.set(0, 0x0, 1e-4)
cpix = tsize // 2
tmi[cpix, cpix, afwImage.LOCAL] = (1, 0x0, 1)
# science image
smi = afwImage.MaskedImageF(tmi.getDimensions())
convolutionControl = afwMath.ConvolutionControl()
convolutionControl.setDoNormalize(False)
afwMath.convolve(smi, tmi, gaussKernel, convolutionControl)
# get the actual kernel sum (since the image is not infinite)
gscaling = afwMath.makeStatistics(smi,
afwMath.SUM).getValue(afwMath.SUM)
# grab only the non-masked subregion
bbox = gaussKernel.shrinkBBox(smi.getBBox(afwImage.LOCAL))
tmi2 = afwImage.MaskedImageF(tmi, bbox, origin=afwImage.LOCAL)
smi2 = afwImage.MaskedImageF(smi, bbox, origin=afwImage.LOCAL)
# make sure its a valid subregion!
for j in range(tmi2.getHeight()):
for i in range(tmi2.getWidth()):
self.assertEqual(tmi2.mask[i, j, afwImage.LOCAL], 0)
self.assertEqual(smi2.mask[i, j, afwImage.LOCAL], 0)
kc = ipDiffim.KernelCandidateF(0.0, 0.0, tmi2, smi2, self.ps)
kList = ipDiffim.makeKernelBasisList(self.subconfig)
kc.build(kList)
self.assertEqual(kc.isInitialized(), True)
kImageOut = kc.getImage()
soln = kc.getKernelSolution(ipDiffim.KernelCandidateF.RECENT)
self.assertAlmostEqual(soln.getKsum(), gscaling)
self.assertAlmostEqual(soln.getBackground(), 0.0)
for j in range(kImageOut.getHeight()):
for i in range(kImageOut.getWidth()):
self.assertAlmostEqual(
kImageOut[i, j, afwImage.LOCAL] /
kImageIn[i, j, afwImage.LOCAL], 1.0, 5)
def testSetCtr(self):
"""Test setCtrCol/Row"""
kWidth = 3
kHeight = 4
gaussFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
kernel = afwMath.AnalyticKernel(kWidth, kHeight, gaussFunc)
for xCtr in range(kWidth):
for yCtr in range(kHeight):
center = lsst.geom.Point2I(xCtr, yCtr)
kernel.setCtr(center)
self.assertEqual(kernel.getCtr(), center)
def makeTest3(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.MaskU(kernel1.getDimensions())
var1 = afwImage.ImageF(image1, True)
mi1 = afwImage.MaskedImageF(image1, mask1, var1)
gaussian2 = afwMath.GaussianFunction2D(2. * gScale, 1.5 * gScale,
0.5 * num.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.MaskU(kernel2.getDimensions())
var2 = afwImage.ImageF(image2, True)
mi2 = afwImage.MaskedImageF(image2, mask2, var2)
image3 = afwImage.ImageF(image1, True)
for y in range(imSize):
for x in range(imSize // 2):
image3.set(x, y, image2.get(x, y))
counts = afwMath.makeStatistics(image3, afwMath.SUM).getValue()
image3 /= counts
image3 *= scaling
mask3 = afwImage.MaskU(image3.getDimensions())
var3 = afwImage.ImageF(image3, True)
mi3 = afwImage.MaskedImageF(image3, mask3, var3)
if doAddNoise:
addNoise(mi1)
addNoise(mi2)
addNoise(mi3)
return mi1, mi2, mi3
def testSeparableKernel(self):
"""Test SeparableKernel using a Gaussian function
"""
kWidth = 5
kHeight = 8
pol = pexPolicy.Policy()
additionalData = dafBase.PropertySet()
loc = dafPersist.LogicalLocation(
os.path.join(testPath, "data", "kernel4.boost"))
persistence = dafPersist.Persistence.getPersistence(pol)
gaussFunc1 = afwMath.GaussianFunction1D(1.0)
k = afwMath.SeparableKernel(kWidth, kHeight, gaussFunc1, gaussFunc1)
fArr = np.zeros(shape=[k.getWidth(), k.getHeight()], dtype=float)
np.zeros(shape=[k.getWidth(), k.getHeight()], dtype=float)
gaussFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
for xsigma in (0.1, 1.0, 3.0):
gaussFunc1.setParameters((xsigma, ))
for ysigma in (0.1, 1.0, 3.0):
gaussFunc.setParameters((xsigma, ysigma, 0.0))
# compute array of function values and normalize
for row in range(k.getHeight()):
y = row - k.getCtrY()
for col in range(k.getWidth()):
x = col - k.getCtrX()
fArr[col, row] = gaussFunc(x, y)
fArr /= fArr.sum()
k.setKernelParameters((xsigma, ysigma))
storageList = dafPersist.StorageList()
storage = persistence.getPersistStorage("XmlStorage", loc)
storageList.append(storage)
persistence.persist(k, storageList, additionalData)
storageList2 = dafPersist.StorageList()
storage2 = persistence.getRetrieveStorage("XmlStorage", loc)
storageList2.append(storage2)
x = persistence.unsafeRetrieve("SeparableKernel", storageList2,
additionalData)
k2 = afwMath.SeparableKernel.swigConvert(x)
self.kernelCheck(k, k2)
kImage = afwImage.ImageD(k2.getDimensions())
k2.computeImage(kImage, True)
kArr = kImage.getArray().transpose()
if not np.allclose(fArr, kArr):
self.fail(
"%s = %s != %s for xsigma=%s, ysigma=%s" %
(k2.__class__.__name__, kArr, fArr, xsigma, ysigma))
def testGaussianFunction2D(self):
"""Note: Assumes GaussianFunction1D is correct (tested elsewhere)."""
errMsg = "{} = {} != {} for pos1={}, pos2={}, x={}, y={}, sigma1={}, sigma2={}, angle={}"
areaMsg = "%s area = %s != 1.0 for sigma1=%s, sigma2=%s"
f = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
f1 = afwMath.GaussianFunction1D(1.0)
f2 = afwMath.GaussianFunction1D(1.0)
for sigma1 in (0.1, 1.0, 3.0):
for sigma2 in (0.1, 1.0, 3.0):
for angle in (0.0, 0.4, 1.1):
sinNegAngle = math.sin(-angle)
cosNegAngle = math.cos(-angle)
f.setParameters((sigma1, sigma2, angle))
g = f.clone()
f1.setParameters((sigma1, ))
f2.setParameters((sigma2, ))
fSum = 0.0
delta1 = sigma1 / 5.0
delta2 = sigma2 / 5.0
for pos1 in np.arange(-sigma1 * 5, sigma1 * 5.01, delta1):
for pos2 in np.arange(-sigma2 * 5.0, sigma2 * 5.01,
delta2):
x = (cosNegAngle * pos1) + (sinNegAngle * pos2)
y = (-sinNegAngle * pos1) + (cosNegAngle * pos2)
predVal = f1(pos1) * f2(pos2)
fSum += predVal
msg = errMsg.format(
type(f).__name__, f(x, y), predVal, pos1, pos2,
x, y, sigma1, sigma2, angle)
self.assertFloatsAlmostEqual(f(x, y),
predVal,
msg=msg,
atol=self.atol,
rtol=None)
msg = errMsg.format(
type(g).__name__, g(x, y), predVal, pos1, pos2,
x, y, sigma1, sigma2, angle) + "; clone"
self.assertFloatsAlmostEqual(g(x, y),
predVal,
msg=msg,
atol=self.atol,
rtol=None)
approxArea = fSum * delta1 * delta2
msg = areaMsg % (type(f).__name__, approxArea, sigma1,
sigma2)
# approxArea is very approximate, so we need a high
# tolerance threshold.
self.assertFloatsAlmostEqual(approxArea,
1.0,
msg=msg,
atol=1e-6,
rtol=None)
def makeTest2(doAddNoise, shiftX=int(2.0 * gScale), shiftY=int(1.0 * gScale)):
gaussian1 = afwMath.GaussianFunction2D(1. * gScale, 1. * gScale, 0.)
kernel1 = afwMath.AnalyticKernel(imSize, imSize, gaussian1)
image1 = afwImage.ImageD(kernel1.getDimensions())
kernel1.computeImage(image1, doNorm)
image1 = image1.convertF()
####
boxA = afwGeom.Box2I(afwGeom.PointI(0, 0),
afwGeom.ExtentI(imSize - shiftX, imSize - shiftY))
boxB = afwGeom.Box2I(afwGeom.PointI(shiftX, shiftY),
afwGeom.ExtentI(imSize - shiftX, imSize - shiftY))
subregA = afwImage.ImageF(image1, boxA, afwImage.LOCAL)
subregB = afwImage.ImageF(image1, boxB, afwImage.LOCAL, True)
subregA += subregB
# this messes up the total counts so rescale
counts = afwMath.makeStatistics(image1, afwMath.SUM).getValue()
image1 /= counts
image1 *= scaling
###
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 testFixedKernelConvolve(self):
"""Test convolve with a fixed kernel
"""
kWidth = 6
kHeight = 7
kFunc = afwMath.GaussianFunction2D(2.5, 1.5, 0.5)
analyticKernel = afwMath.AnalyticKernel(kWidth, kHeight, kFunc)
kernelImage = afwImage.ImageD(afwGeom.Extent2I(kWidth, kHeight))
analyticKernel.computeImage(kernelImage, False)
fixedKernel = afwMath.FixedKernel(kernelImage)
self.runStdTest(fixedKernel, kernelDescr="Gaussian FixedKernel")
def testSetCtr(self):
"""Test setCtrCol/Row"""
kWidth = 3
kHeight = 4
gaussFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
kernel = afwMath.AnalyticKernel(kWidth, kHeight, gaussFunc)
for xCtr in range(kWidth):
kernel.setCtrX(xCtr)
for yCtr in range(kHeight):
kernel.setCtrY(yCtr)
self.assertEqual(kernel.getCtrX(), xCtr)
self.assertEqual(kernel.getCtrY(), yCtr)
def testRenormalize(self):
# inputs
gauss1 = afwMath.GaussianFunction2D(2, 2)
gauss2 = afwMath.GaussianFunction2D(3, 4)
gauss3 = afwMath.GaussianFunction2D(0.2, 0.25)
gaussKernel1 = afwMath.AnalyticKernel(self.kSize, self.kSize, gauss1)
gaussKernel2 = afwMath.AnalyticKernel(self.kSize, self.kSize, gauss2)
gaussKernel3 = afwMath.AnalyticKernel(self.kSize, self.kSize, gauss3)
kimage1 = afwImage.ImageD(gaussKernel1.getDimensions())
ksum1 = gaussKernel1.computeImage(kimage1, False)
kimage2 = afwImage.ImageD(gaussKernel2.getDimensions())
ksum2 = gaussKernel2.computeImage(kimage2, False)
kimage3 = afwImage.ImageD(gaussKernel3.getDimensions())
ksum3 = gaussKernel3.computeImage(kimage3, False)
self.assertNotEqual(ksum1, 1.)
self.assertNotEqual(ksum2, 1.)
self.assertNotEqual(ksum3, 1.)
# no constraints on first kernels norm
self.assertNotEqual(num.sum(num.ravel(kimage2.getArray())**2), 1.)
self.assertNotEqual(num.sum(num.ravel(kimage3.getArray())**2), 1.)
basisListIn = []
basisListIn.append(gaussKernel1)
basisListIn.append(gaussKernel2)
basisListIn.append(gaussKernel3)
# outputs
basisListOut = ipDiffim.renormalizeKernelList(basisListIn)
gaussKernel1 = basisListOut[0]
gaussKernel2 = basisListOut[1]
gaussKernel3 = basisListOut[2]
ksum1 = gaussKernel1.computeImage(kimage1, False)
ksum2 = gaussKernel2.computeImage(kimage2, False)
ksum3 = gaussKernel3.computeImage(kimage3, False)
self.assertAlmostEqual(ksum1, 1.)
self.assertAlmostEqual(ksum2, 0.)
self.assertAlmostEqual(ksum3, 0.)
# no constraints on first kernels norm
self.assertAlmostEqual(num.sum(num.ravel(kimage2.getArray())**2), 1.)
self.assertAlmostEqual(num.sum(num.ravel(kimage3.getArray())**2), 1.)
def testDoubleGaussianFunction2D(self):
"""A test for DoubleGaussianFunction2D
Assumes GaussianFunction2D is correct (tested elsewhere)
"""
f = afwMath.DoubleGaussianFunction2D(1.0, 1.0)
f1 = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
f2 = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
for sigma1 in (1.0, ):
for sigma2 in (0.5, 2.0):
for b in (0.0, 0.2, 2.0):
f.setParameters((sigma1, sigma2, b))
g = f.clone()
f1.setParameters((sigma1, sigma1, 0.0))
f2.setParameters((sigma2, sigma2, 0.0))
sigma1Sq = sigma1**2
sigma2Sq = sigma2**2
f1Mult = b * sigma2Sq / sigma1Sq
allMult = sigma1Sq / (sigma1Sq + (b * sigma2Sq))
fSum = 0.0
maxsigma = max(sigma1, sigma2)
minsigma = min(sigma1, sigma2)
delta = minsigma / 5.0
for y in numpy.arange(-maxsigma * 5, maxsigma * 5.01,
delta):
for x in numpy.arange(-maxsigma * 5.0, maxsigma * 5.01,
delta):
predVal = (f1(x, y) +
(f1Mult * f2(x, y))) * allMult
fSum += predVal
if not numpy.allclose(predVal, f(x, y)):
self.fail("%s = %s != %s for x=%s, y=%s, sigma1=%s, sigma2=%s, b=%s" % \
(type(f).__name__, f(x, y), predVal, x, y, sigma1, sigma2, b))
if not numpy.allclose(predVal, g(x, y)):
self.fail("%s = %s != %s for x=%s, y=%s, sigma1=%s, sigma2=%s, b=%s; clone" %\
(type(g).__name__, g(x, y), predVal, x, y, sigma1, sigma2, b))
approxArea = fSum * delta**2
if not numpy.allclose(approxArea, 1.0):
self.fail("%s area = %s != 1.0 for sigma1=%s, sigma2=%s" % \
(type(f).__name__, approxArea, sigma1, sigma2))
def createImageAndKernel(sigma, psfSize, image):
function = afwMath.GaussianFunction2D(sigma, sigma)
kernel = afwMath.AnalyticKernel(psfSize, psfSize, function)
psf = measAlg.KernelPsf(kernel)
cim = afwImage.ImageF(image.getDimensions())
afwMath.convolve(cim, image, kernel, True)
# Trim off the border pixels
bbox = kernel.shrinkBBox(cim.getBBox(afwImage.LOCAL))
cim = afwImage.ImageF(cim, bbox, afwImage.LOCAL)
cim.setXY0(0, 0)
return cim, psf
def testAnalyticKernel(self):
"""Test AnalyticKernel using a Gaussian function
"""
kWidth = 5
kHeight = 8
gaussFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
kernel = afwMath.AnalyticKernel(kWidth, kHeight, gaussFunc)
self.basicTests(kernel, 3, dimMustMatch=False)
kernelResized = self.verifyResized(kernel)
self.basicTests(kernelResized, 3, dimMustMatch=False)
fArr = np.zeros(shape=[kernel.getWidth(),
kernel.getHeight()],
dtype=float)
for xsigma in (0.1, 1.0, 3.0):
for ysigma in (0.1, 1.0, 3.0):
gaussFunc.setParameters((xsigma, ysigma, 0.0))
# compute array of function values and normalize
for row in range(kernel.getHeight()):
y = row - kernel.getCtrY()
for col in range(kernel.getWidth()):
x = col - kernel.getCtrX()
fArr[col, row] = gaussFunc(x, y)
fArr /= fArr.sum()
kernel.setKernelParameters((xsigma, ysigma, 0.0))
kImage = afwImage.ImageD(kernel.getDimensions())
kernel.computeImage(kImage, True)
kArr = kImage.getArray().transpose()
if not np.allclose(fArr, kArr):
self.fail("%s = %s != %s for xsigma=%s, ysigma=%s" %
(kernel.__class__.__name__, kArr, fArr, xsigma,
ysigma))
kernel.setKernelParameters((0.5, 1.1, 0.3))
kernelClone = kernel.clone()
errStr = self.compareKernels(kernel, kernelClone)
if errStr:
self.fail(errStr)
kernel.setKernelParameters((1.5, 0.2, 0.7))
errStr = self.compareKernels(kernel, kernelClone)
if not errStr:
self.fail(
"Clone was modified by changing original's kernel parameters")
self.verifyCache(kernel, hasCache=False)
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.MaskU(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.MaskU(kernel2.getDimensions())
var2 = afwImage.ImageF(image2, True)
mi2 = afwImage.MaskedImageF(image2, mask2, var2)
if doAddNoise: addNoise(mi2)
return mi1, mi2
def makeGaussianKernelList(kWidth, kHeight, gaussParamsList):
"""Create a list of gaussian kernels.
This is useful for constructing a LinearCombinationKernel.
Inputs:
- kWidth, kHeight: width and height of kernel
- gaussParamsList: a list of parameters for GaussianFunction2D (each a 3-tuple of floats)
"""
kVec = []
for majorSigma, minorSigma, angle in gaussParamsList:
kFunc = afwMath.GaussianFunction2D(majorSigma, minorSigma, angle)
kVec.append(afwMath.AnalyticKernel(kWidth, kHeight, kFunc))
return kVec
def testSeparableKernel(self):
"""Test SeparableKernel using a Gaussian function
"""
kWidth = 5
kHeight = 8
gaussFunc1 = afwMath.GaussianFunction1D(1.0)
kernel = afwMath.SeparableKernel(
kWidth, kHeight, gaussFunc1, gaussFunc1)
center = kernel.getCtr()
self.basicTests(kernel, 2)
kernelResized = self.verifyResized(kernel)
self.basicTests(kernelResized, 2)
fArr = np.zeros(
shape=[kernel.getWidth(), kernel.getHeight()], dtype=float)
gaussFunc = afwMath.GaussianFunction2D(1.0, 1.0, 0.0)
for xsigma in (0.1, 1.0, 3.0):
gaussFunc1.setParameters((xsigma,))
for ysigma in (0.1, 1.0, 3.0):
gaussFunc.setParameters((xsigma, ysigma, 0.0))
# compute array of function values and normalize
for row in range(kernel.getHeight()):
y = row - center.getY()
for col in range(kernel.getWidth()):
x = col - center.getX()
fArr[col, row] = gaussFunc(x, y)
fArr /= fArr.sum()
kernel.setKernelParameters((xsigma, ysigma))
kImage = afwImage.ImageD(kernel.getDimensions())
kernel.computeImage(kImage, True)
kArr = kImage.getArray().transpose()
if not np.allclose(fArr, kArr):
self.fail(f"{kernel.__class__.__name__} = {kArr} != "
f"{fArr} for xsigma={xsigma}, ysigma={ysigma}")
kernelClone = kernel.clone()
errStr = self.compareKernels(kernel, kernelClone)
if errStr:
self.fail(errStr)
kernel.setKernelParameters((1.2, 0.6))
errStr = self.compareKernels(kernel, kernelClone)
if not errStr:
self.fail(
"Clone was modified by changing original's kernel parameters")
self.verifyCache(kernel, hasCache=True)
def makeTest2(doAddNoise, shiftX=5, shiftY=3):
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()
####
boxA = afwGeom.Box2I(afwGeom.PointI(imSize // 2, imSize // 2),
afwGeom.ExtentI(imSize // 2, imSize // 2))
boxB = afwGeom.Box2I(
afwGeom.PointI(imSize // 2 - shiftX, imSize // 2 - shiftY),
afwGeom.ExtentI(imSize // 2, imSize // 2))
subregA = afwImage.ImageF(image1, boxA, afwImage.PARENT)
subregB = afwImage.ImageF(image1, boxB, afwImage.PARENT, True)
subregA += subregB
###
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