def TimepixToExposure(filename, xmin, xmax, ymin, ymax):
data = np.loadtxt(filename)
my_array = np.zeros((256,256), dtype = np.int32)
if data.shape == (0,):
my_image = makeImageFromArray(my_array)
elif data.shape == (3,):
x = data[0]
y = data[1]
t = data[2]
if x >= xmin and x <= xmax and y >= ymin and y <= ymax:
my_array[y,x] = t
my_image = makeImageFromArray(my_array)
else:
x = data[:, 0]
y = data[:, 1]
t = data[:, 2]
for pointnum in range(len(x)):
if x[pointnum] >= xmin and x[pointnum] <= xmax and y[pointnum] >= ymin and y[pointnum] <= ymax:
my_array[y[pointnum],x[pointnum]] = t[pointnum]
my_image = makeImageFromArray(my_array)
return my_image
def TimepixToExposure(filename, xmin, xmax, ymin, ymax):
import numpy as np
from lsst.afw.image import makeImageFromArray
data = np.loadtxt(filename)
my_array = np.zeros((256, 256), dtype=np.int32)
if data.shape == (0, ):
my_image = makeImageFromArray(my_array)
elif data.shape == (3, ):
x = data[0]
y = data[1]
t = data[2]
if x >= xmin and x <= xmax and y >= ymin and y <= ymax:
my_array[y, x] = t
my_image = makeImageFromArray(my_array)
else:
x = data[:, 0]
y = data[:, 1]
t = data[:, 2]
for pointnum in range(len(x)):
if x[pointnum] >= xmin and x[pointnum] <= xmax and y[
pointnum] >= ymin and y[pointnum] <= ymax:
my_array[y[pointnum], x[pointnum]] = t[pointnum]
my_image = makeImageFromArray(my_array)
return my_image
def testTicket873(self):
"""Demonstrate ticket 873: convolution of a MaskedImage with a spatially varying
LinearCombinationKernel of basis kernels with low covariance gives incorrect variance.
"""
# create spatial model
sFunc = 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, -0.5/self.width, -0.5/self.height),
(0.0, 1.0/self.width, 0.0/self.height),
(0.0, 0.0/self.width, 1.0/self.height),
)
# create three kernels with some non-overlapping pixels
# (non-zero pixels in one kernel vs. zero pixels in other kernels);
# note: the extreme example of this is delta function kernels, but this
# is less extreme
basisKernelList = []
kImArr = numpy.zeros([5, 5], dtype=float)
kImArr[1:4, 1:4] = 0.5
kImArr[2, 2] = 1.0
kImage = afwImage.makeImageFromArray(kImArr)
basisKernelList.append(afwMath.FixedKernel(kImage))
kImArr[:, :] = 0.0
kImArr[0:2, 0:2] = 0.125
kImArr[3:5, 3:5] = 0.125
kImage = afwImage.makeImageFromArray(kImArr)
basisKernelList.append(afwMath.FixedKernel(kImage))
kImArr[:, :] = 0.0
kImArr[0:2, 3:5] = 0.125
kImArr[3:5, 0:2] = 0.125
kImage = afwImage.makeImageFromArray(kImArr)
basisKernelList.append(afwMath.FixedKernel(kImage))
kernel = afwMath.LinearCombinationKernel(basisKernelList, sFunc)
kernel.setSpatialParameters(sParams)
for maxInterpDist, rtol, methodStr in (
(0, 1.0e-5, "brute force"),
(10, 3.0e-3, "interpolation over 10 x 10 pixels"),
):
self.runStdTest(
kernel,
kernelDescr="Spatially varying LinearCombinationKernel of basis "
"kernels with low covariance, using %s" % (
methodStr,),
maxInterpDist=maxInterpDist,
rtol=rtol)
def testTicket873(self):
"""Demonstrate ticket 873: convolution of a MaskedImage with a spatially varying
LinearCombinationKernel of basis kernels with low covariance gives incorrect variance.
"""
# create spatial model
sFunc = 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, -0.5/self.width, -0.5/self.height),
(0.0, 1.0/self.width, 0.0/self.height),
(0.0, 0.0/self.width, 1.0/self.height),
)
# create three kernels with some non-overlapping pixels
# (non-zero pixels in one kernel vs. zero pixels in other kernels);
# note: the extreme example of this is delta function kernels, but this is less extreme
basisKernelList = afwMath.KernelList()
kImArr = numpy.zeros([5, 5], dtype=float)
kImArr[1:4, 1:4] = 0.5
kImArr[2, 2] = 1.0
kImage = afwImage.makeImageFromArray(kImArr)
basisKernelList.append(afwMath.FixedKernel(kImage))
kImArr[:, :] = 0.0
kImArr[0:2, 0:2] = 0.125
kImArr[3:5, 3:5] = 0.125
kImage = afwImage.makeImageFromArray(kImArr)
basisKernelList.append(afwMath.FixedKernel(kImage))
kImArr[:, :] = 0.0
kImArr[0:2, 3:5] = 0.125
kImArr[3:5, 0:2] = 0.125
kImage = afwImage.makeImageFromArray(kImArr)
basisKernelList.append(afwMath.FixedKernel(kImage))
kernel = afwMath.LinearCombinationKernel(basisKernelList, sFunc)
kernel.setSpatialParameters(sParams)
for maxInterpDist, rtol, methodStr in (
(0, 1.0e-5, "brute force"),
(10, 3.0e-3, "interpolation over 10 x 10 pixels"),
):
self.runStdTest(
kernel,
kernelDescr = \
"Spatially varying LinearCombinationKernel of basis kernels with low covariance, using %s" % (methodStr,),
maxInterpDist = maxInterpDist,
rtol = rtol)
def XYT_to_image(xyt_array, display=False):
import numpy as np
from lsst.afw.image import makeImageFromArray
if display:
import lsst.afw.display.ds9 as ds9
try:
ds9.initDS9(False)
except ds9.Ds9Error:
print()
my_array = np.zeros((256, 256), dtype=np.int32)
xs = xyt_array[:, 0]
ys = xyt_array[:, 1]
# for x,y in zip(xs,ys):
# my_array[y,x] += 1
n_counts = 0
for x, y in zip(xs, ys):
if n_counts >= 1000000: break
n_counts += 1
my_array[y, x] += 1
my_image = makeImageFromArray(my_array)
if display: ds9.mtv(my_image)
return my_image
def addNoise(self, inputExposure):
mi = inputExposure.getMaskedImage()
(x, y) = mi.getDimensions()
noiseArr = numpy.random.poisson(self.config.noiseValue, size=x*y).reshape(y, x)
noiseArr = noiseArr.astype(numpy.float32)
noiseImage = afwImage.makeImageFromArray(noiseArr)
mi += noiseImage
def testRandomMap(self):
"""Test setCoaddEdgeBits using a random depth map
"""
imDim = afwGeom.Extent2I(50, 55)
coaddMask = afwImage.MaskU(imDim)
numpy.random.seed(12345)
depthMapArray = numpy.random.randint(0, 3, list((imDim[1], imDim[0]))).astype(numpy.uint16)
depthMap = afwImage.makeImageFromArray(depthMapArray)
refCoaddMaskArray = coaddMask.getArray()
edgeMask = afwImage.MaskU.getPlaneBitMask("NO_DATA")
refCoaddMaskArray |= numpy.array(numpy.where(depthMapArray > 0, 0, edgeMask),
dtype=refCoaddMaskArray.dtype)
coaddUtils.setCoaddEdgeBits(coaddMask, depthMap)
coaddMaskArray = coaddMask.getArray()
if numpy.any(refCoaddMaskArray != coaddMaskArray):
errMsgList = (
"Coadd mask does not match reference:",
"computed= %s" % (coaddMaskArray,),
"reference= %s" % (refCoaddMaskArray,),
)
errMsg = "\n".join(errMsgList)
self.fail(errMsg)
def addNoise(self, inputExposure):
mi = inputExposure.getMaskedImage()
(x, y) = mi.getDimensions()
noiseArr = numpy.random.poisson(self.config.noiseValue, size=x*y).reshape(y, x)
noiseArr = noiseArr.astype(numpy.float32)
noiseImage = afwImage.makeImageFromArray(noiseArr)
mi += noiseImage
def testArrays(self):
for cls in (afwImage.ImageU, afwImage.ImageI, afwImage.ImageF,
afwImage.ImageD):
image1 = cls(lsst.geom.Extent2I(5, 6))
array1 = image1.getArray()
self.assertEqual(array1.shape[0], image1.getHeight())
self.assertEqual(array1.shape[1], image1.getWidth())
image2 = cls(array1, False)
self.assertEqual(array1.shape[0], image2.getHeight())
self.assertEqual(array1.shape[1], image2.getWidth())
image3 = afwImage.makeImageFromArray(array1)
self.assertEqual(array1.shape[0], image2.getHeight())
self.assertEqual(array1.shape[1], image2.getWidth())
self.assertEqual(type(image3), cls)
array2 = image1.array
np.testing.assert_array_equal(array1, array2)
array1[:, :] = np.random.uniform(low=0, high=10, size=array1.shape)
for j in range(image1.getHeight()):
for i in range(image1.getWidth()):
self.assertEqual(image1[i, j, afwImage.LOCAL], array1[j,
i])
self.assertEqual(image2[i, j, afwImage.LOCAL], array1[j,
i])
array3 = np.random.uniform(low=0, high=10,
size=array1.shape).astype(array1.dtype)
image1.array[:] = array3
np.testing.assert_array_equal(array1, array3)
image1.array[2:4, 3:] = 10
np.testing.assert_array_equal(array1[2:4, 3:], 10)
array4 = image1.array.copy()
array4 += 5
image1.array += 5
np.testing.assert_array_equal(image1.array, array4)
def getInterpImage(self, bbox):
"""Return an image interpolated in R.A direction covering supplied bounding box
@param[in] bbox: integer bounding box for image (afwGeom.Box2I)
"""
npoints = len(self._xList)
# sort by X coordinate
if npoints < 1:
raise RuntimeError(
"Cannot create scaling image. Found no fluxMag0s to interpolate"
)
x, z = list(zip(*sorted(zip(self._xList, self._scaleList))))
xvec = np.array(x, dtype=float)
zvec = np.array(z, dtype=float)
height = bbox.getHeight()
width = bbox.getWidth()
x0, y0 = bbox.getMin()
interp = afwMath.makeInterpolate(xvec, zvec, self.interpStyle)
interpValArr = np.zeros(width, dtype=np.float32)
for i, xInd in enumerate(range(x0, x0 + width)):
xPos = afwImage.indexToPosition(xInd)
interpValArr[i] = interp.interpolate(xPos)
# assume the maskedImage being scaled is MaskedImageF (which is usually true); see ticket #3070
interpGrid = np.meshgrid(interpValArr,
range(0, height))[0].astype(np.float32)
image = afwImage.makeImageFromArray(interpGrid)
image.setXY0(x0, y0)
return image
def testArrays(self):
for cls in (afwImage.ImageU, afwImage.ImageI, afwImage.ImageF, afwImage.ImageD):
image1 = cls(lsst.geom.Extent2I(5, 6))
array1 = image1.getArray()
self.assertEqual(array1.shape[0], image1.getHeight())
self.assertEqual(array1.shape[1], image1.getWidth())
image2 = cls(array1, False)
self.assertEqual(array1.shape[0], image2.getHeight())
self.assertEqual(array1.shape[1], image2.getWidth())
image3 = afwImage.makeImageFromArray(array1)
self.assertEqual(array1.shape[0], image2.getHeight())
self.assertEqual(array1.shape[1], image2.getWidth())
self.assertEqual(type(image3), cls)
array2 = image1.array
np.testing.assert_array_equal(array1, array2)
array1[:, :] = np.random.uniform(low=0, high=10, size=array1.shape)
for j in range(image1.getHeight()):
for i in range(image1.getWidth()):
self.assertEqual(image1[i, j, afwImage.LOCAL], array1[j, i])
self.assertEqual(image2[i, j, afwImage.LOCAL], array1[j, i])
array3 = np.random.uniform(low=0, high=10,
size=array1.shape).astype(array1.dtype)
image1.array[:] = array3
np.testing.assert_array_equal(array1, array3)
image1.array[2:4, 3:] = 10
np.testing.assert_array_equal(array1[2:4, 3:], 10)
array4 = image1.array.copy()
array4 += 5
image1.array += 5
np.testing.assert_array_equal(image1.array, array4)
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 getInterpImage(self, bbox):
"""Return an image interpolated in R.A direction covering supplied bounding box
@param[in] bbox: integer bounding box for image (afwGeom.Box2I)
"""
npoints = len(self._xList)
#sort by X coordinate
if npoints < 1:
raise RuntimeError("Cannot create scaling image. Found no fluxMag0s to interpolate")
x, z = zip(*sorted(zip(self._xList, self._scaleList)))
xvec = afwMath.vectorD(x)
zvec = afwMath.vectorD(z)
height = bbox.getHeight()
width = bbox.getWidth()
x0, y0 = bbox.getMin()
interp = afwMath.makeInterpolate(xvec, zvec, self.interpStyle)
interpValArr = numpy.zeros(width, dtype=numpy.float32)
for i, xInd in enumerate(range(x0, x0 + width)):
xPos = afwImage.indexToPosition(xInd)
interpValArr[i] = interp.interpolate(xPos)
# assume the maskedImage being scaled is MaskedImageF (which is usually true); see ticket #3070
interpGrid = numpy.meshgrid(interpValArr, range(0, height))[0].astype(numpy.float32)
image = afwImage.makeImageFromArray(interpGrid)
image.setXY0(x0, y0)
return image
def testSVLinearCombinationKernel(self):
"""Test a spatially varying LinearCombinationKernel
"""
kWidth = 3
kHeight = 2
# create image arrays for the basis kernels
basisImArrList = []
imArr = np.zeros((kWidth, kHeight), dtype=float)
imArr += 0.1
imArr[kWidth//2, :] = 0.9
basisImArrList.append(imArr)
imArr = np.zeros((kWidth, kHeight), dtype=float)
imArr += 0.2
imArr[:, kHeight//2] = 0.8
basisImArrList.append(imArr)
# create a list of basis kernels from the images
kVec = []
for basisImArr in basisImArrList:
basisImage = afwImage.makeImageFromArray(
basisImArr.transpose().copy())
kernel = afwMath.FixedKernel(basisImage)
kVec.append(kernel)
# create spatially varying linear combination kernel
spFunc = afwMath.PolynomialFunction2D(1)
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(0.0, 1.0, 0.0),
(0.0, 0.0, 1.0),
)
k = afwMath.LinearCombinationKernel(kVec, spFunc)
k.setSpatialParameters(sParams)
with lsst.utils.tests.getTempFilePath(".fits") as filename:
k.writeFits(filename)
k2 = afwMath.LinearCombinationKernel.readFits(filename)
self.kernelCheck(k, k2)
kImage = afwImage.ImageD(lsst.geom.Extent2I(kWidth, kHeight))
for colPos, rowPos, coeff0, coeff1 in [
(0.0, 0.0, 0.0, 0.0),
(1.0, 0.0, 1.0, 0.0),
(0.0, 1.0, 0.0, 1.0),
(1.0, 1.0, 1.0, 1.0),
(0.5, 0.5, 0.5, 0.5),
]:
k2.computeImage(kImage, False, colPos, rowPos)
kImArr = kImage.getArray().transpose()
refKImArr = (basisImArrList[0] * coeff0) + \
(basisImArrList[1] * coeff1)
if not np.allclose(kImArr, refKImArr):
self.fail("%s = %s != %s at colPos=%s, rowPos=%s" %
(k2.__class__.__name__, kImArr, refKImArr, colPos, rowPos))
def testSVLinearCombinationKernel(self):
"""Test a spatially varying LinearCombinationKernel
"""
kWidth = 3
kHeight = 2
# create image arrays for the basis kernels
basisImArrList = []
imArr = np.zeros((kWidth, kHeight), dtype=float)
imArr += 0.1
imArr[kWidth // 2, :] = 0.9
basisImArrList.append(imArr)
imArr = np.zeros((kWidth, kHeight), dtype=float)
imArr += 0.2
imArr[:, kHeight // 2] = 0.8
basisImArrList.append(imArr)
# create a list of basis kernels from the images
kVec = []
for basisImArr in basisImArrList:
basisImage = afwImage.makeImageFromArray(
basisImArr.transpose().copy())
kernel = afwMath.FixedKernel(basisImage)
kVec.append(kernel)
# create spatially varying linear combination kernel
spFunc = afwMath.PolynomialFunction2D(1)
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(0.0, 1.0, 0.0),
(0.0, 0.0, 1.0),
)
k = afwMath.LinearCombinationKernel(kVec, spFunc)
k.setSpatialParameters(sParams)
with lsst.utils.tests.getTempFilePath(".fits") as filename:
k.writeFits(filename)
k2 = afwMath.LinearCombinationKernel.readFits(filename)
self.kernelCheck(k, k2)
kImage = afwImage.ImageD(lsst.geom.Extent2I(kWidth, kHeight))
for colPos, rowPos, coeff0, coeff1 in [
(0.0, 0.0, 0.0, 0.0),
(1.0, 0.0, 1.0, 0.0),
(0.0, 1.0, 0.0, 1.0),
(1.0, 1.0, 1.0, 1.0),
(0.5, 0.5, 0.5, 0.5),
]:
k2.computeImage(kImage, False, colPos, rowPos)
kImArr = kImage.getArray().transpose()
refKImArr = (basisImArrList[0] * coeff0) + \
(basisImArrList[1] * coeff1)
if not np.allclose(kImArr, refKImArr):
self.fail(f"{k2.__class__.__name__} = {kImArr} != {refKImArr} "
f"at colPos={colPos}, rowPos={rowPos}")
def ViewIntensityArrayInDs9(intensity_array, savefile=None):
import lsst.afw.display.ds9 as ds9
ds9.mtv(
makeImageFromArray(100 * intensity_array /
float(intensity_array.max())))
if savefile is not None:
arg = 'saveimage jpeg ' + str(savefile) + ' 100'
ds9.ds9Cmd(arg)
def MakeCompositeImage_PImMS(path,
winow_xmin=0,
winow_xmax=999,
winow_ymin=0,
winow_ymax=999,
offset_us=0,
maxfiles=None,
t_min=-9999,
t_max=9999,
return_raw_array=False):
from lsst.afw.image import makeImageFromArray
import string, os
import numpy as np
import pylab as pl
my_array = np.zeros((72, 72), dtype=np.int32)
files = []
for filename in os.listdir(path):
files.append(path + filename)
for filenum, filename in enumerate(files):
if filenum % 500 == 0: print("Compiled %s files" % filenum)
xs, ys, ts = GetXYTarray_SingleFile(filename, winow_xmin, winow_xmax,
winow_ymin, winow_ymax)
# if len(xs) > 5000: continue # skip glitch files
for i in range(len(xs)):
x = xs[i]
y = ys[i]
t = ts[i]
if x >= winow_xmin and x <= winow_xmax and y >= winow_ymin and y <= winow_ymax:
if t >= t_min and t <= t_max:
my_array[x, y] += 1
if maxfiles != None and filenum >= maxfiles:
if return_raw_array: return my_array
my_image = makeImageFromArray(my_array)
return my_image
my_image = makeImageFromArray(my_array)
if return_raw_array: return my_array
return my_image
def XYI_array_to_exposure(xs, ys, i_s):
from lsst.afw.image import makeImageFromArray
import numpy as np
my_array = np.zeros((256, 256), dtype=np.int32)
for pointnum in range(len(xs)):
my_array[xs[pointnum], ys[pointnum]] = i_s[pointnum]
my_image = makeImageFromArray(my_array)
return my_image
def TimepixToExposure_binary(filename,
xmin,
xmax,
ymin,
ymax,
mask_pixels=np.ones((1), dtype=np.float64)):
from lsst.afw.image import makeImageFromArray
data = np.loadtxt(filename)
my_array = np.zeros((256, 256), dtype=np.int32)
if data.shape == (0, ):
my_image = makeImageFromArray(my_array)
elif data.shape == (3, ):
x = data[0]
y = data[1]
t = data[2]
if x >= xmin and x <= xmax and y >= ymin and y <= ymax:
my_array[y, x] = 1
my_image = makeImageFromArray(my_array * mask_pixels.transpose())
return_npix = (
my_array *
mask_pixels.transpose()).sum() #apply the mask, *then* sum!
else:
x = data[:, 0]
y = data[:, 1]
t = data[:, 2]
for pointnum in range(len(x)):
if x[pointnum] >= xmin and x[pointnum] <= xmax and y[
pointnum] >= ymin and y[pointnum] <= ymax:
my_array[y[pointnum], x[pointnum]] = 1
my_image = makeImageFromArray(my_array * mask_pixels.transpose())
return_npix = (
my_array *
mask_pixels.transpose()).sum() #apply the mask, *then* sum!
return my_image, return_npix
def MakeCompositeImage_Medipix(path,
winow_xmin=0,
winow_xmax=999,
winow_ymin=0,
winow_ymax=999,
offset_us=0,
maxfiles=None):
from lsst.afw.image import makeImageFromArray
import string, os
import numpy as np
import pylab as pl
my_array = np.zeros((256, 256), dtype=np.int32)
files = []
for filename in os.listdir(path):
files.append(path + filename)
num = 0
for filename in files:
data = pl.loadtxt(filename, usecols=(0, 1, 2))
num += 1
if (num % 10 == 0): print('loaded %s files' % num)
for i in range(len(data)):
x = int(data[i, 0])
y = int(data[i, 1])
intensity = int(data[i, 2])
if x >= winow_xmin and x <= winow_xmax and y >= winow_ymin and y <= winow_ymax:
my_array[x, y] += intensity
if maxfiles != None and num == maxfiles:
my_image = makeImageFromArray(my_array)
return my_image
my_image = makeImageFromArray(my_array)
return my_image
def testRandomMap(self):
"""Test setCoaddEdgeBits using a random depth map
"""
imDim = afwGeom.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 testArrays(self):
for cls in (afwImage.ImageU, afwImage.ImageI, afwImage.ImageF, afwImage.ImageD):
image1 = cls(afwGeom.Extent2I(5,6))
array1 = image1.getArray()
self.assertEqual(array1.shape[0], image1.getHeight())
self.assertEqual(array1.shape[1], image1.getWidth())
image2 = cls(array1, False)
self.assertEqual(array1.shape[0], image2.getHeight())
self.assertEqual(array1.shape[1], image2.getWidth())
image3 = afwImage.makeImageFromArray(array1)
self.assertEqual(array1.shape[0], image2.getHeight())
self.assertEqual(array1.shape[1], image2.getWidth())
self.assertEqual(type(image3), cls)
array1[:,:] = numpy.random.uniform(low=0, high=10, size=array1.shape)
for j in range(image1.getHeight()):
for i in range(image1.getWidth()):
self.assertEqual(image1.get(i, j), array1[j, i])
self.assertEqual(image2.get(i, j), array1[j, i])
def testArrays(self):
for cls in (afwImage.ImageU, afwImage.ImageI, afwImage.ImageF, afwImage.ImageD):
image1 = cls(afwGeom.Extent2I(5,6))
array1 = image1.getArray()
self.assertEqual(array1.shape[0], image1.getHeight())
self.assertEqual(array1.shape[1], image1.getWidth())
image2 = cls(array1, False)
self.assertEqual(array1.shape[0], image2.getHeight())
self.assertEqual(array1.shape[1], image2.getWidth())
image3 = afwImage.makeImageFromArray(array1)
self.assertEqual(array1.shape[0], image2.getHeight())
self.assertEqual(array1.shape[1], image2.getWidth())
self.assertEqual(type(image3), cls)
array1[:,:] = numpy.random.uniform(low=0, high=10, size=array1.shape)
for j in range(image1.getHeight()):
for i in range(image1.getWidth()):
self.assertEqual(image1.get(i, j), array1[j, i])
self.assertEqual(image2.get(i, j), array1[j, i])
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 TimepixToExposure(filename):
from lsst.afw.image import makeImageFromArray
import numpy as np
data = np.loadtxt(filename)
x = data[:, 0]
y = data[:, 1]
t = data[:, 2]
my_array = np.zeros((256,256), dtype = np.int32)
for pointnum in range(len(x)):
my_array[x[pointnum],y[pointnum]] = t[pointnum]
my_image = makeImageFromArray(my_array)
return my_image
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.MaskU(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 testSVLinearCombinationKernel(self):
"""Test a spatially varying LinearCombinationKernel
"""
kWidth = 3
kHeight = 2
pol = pexPolicy.Policy()
additionalData = dafBase.PropertySet()
loc = dafPersist.LogicalLocation(
os.path.join(testPath, "data", "kernel6.boost"))
persistence = dafPersist.Persistence.getPersistence(pol)
# create image arrays for the basis kernels
basisImArrList = []
imArr = np.zeros((kWidth, kHeight), dtype=float)
imArr += 0.1
imArr[kWidth // 2, :] = 0.9
basisImArrList.append(imArr)
imArr = np.zeros((kWidth, kHeight), dtype=float)
imArr += 0.2
imArr[:, kHeight // 2] = 0.8
basisImArrList.append(imArr)
# create a list of basis kernels from the images
kVec = []
for basisImArr in basisImArrList:
basisImage = afwImage.makeImageFromArray(
basisImArr.transpose().copy())
kernel = afwMath.FixedKernel(basisImage)
kVec.append(kernel)
# create spatially varying linear combination kernel
spFunc = afwMath.PolynomialFunction2D(1)
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(0.0, 1.0, 0.0),
(0.0, 0.0, 1.0),
)
k = afwMath.LinearCombinationKernel(kVec, spFunc)
k.setSpatialParameters(sParams)
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)
k2 = persistence.unsafeRetrieve("LinearCombinationKernel",
storageList2, additionalData)
self.kernelCheck(k, k2)
kImage = afwImage.ImageD(afwGeom.Extent2I(kWidth, kHeight))
for colPos, rowPos, coeff0, coeff1 in [
(0.0, 0.0, 0.0, 0.0),
(1.0, 0.0, 1.0, 0.0),
(0.0, 1.0, 0.0, 1.0),
(1.0, 1.0, 1.0, 1.0),
(0.5, 0.5, 0.5, 0.5),
]:
k2.computeImage(kImage, False, colPos, rowPos)
kImArr = kImage.getArray().transpose()
refKImArr = (basisImArrList[0] * coeff0) + \
(basisImArrList[1] * coeff1)
if not np.allclose(kImArr, refKImArr):
self.fail(
"%s = %s != %s at colPos=%s, rowPos=%s" %
(k2.__class__.__name__, kImArr, refKImArr, colPos, rowPos))
def testSVLinearCombinationKernelFixed(self):
"""Test a spatially varying LinearCombinationKernel
"""
kWidth = 3
kHeight = 2
# create image arrays for the basis kernels
basisImArrList = []
imArr = numpy.zeros((kWidth, kHeight), dtype=float)
imArr += 0.1
imArr[kWidth//2, :] = 0.9
basisImArrList.append(imArr)
imArr = numpy.zeros((kWidth, kHeight), dtype=float)
imArr += 0.2
imArr[:, kHeight//2] = 0.8
basisImArrList.append(imArr)
# create a list of basis kernels from the images
basisKernelList = afwMath.KernelList()
for basisImArr in basisImArrList:
basisImage = afwImage.makeImageFromArray(basisImArr.transpose().copy())
kernel = afwMath.FixedKernel(basisImage)
basisKernelList.append(kernel)
# create spatially varying linear combination kernel
spFunc = afwMath.PolynomialFunction2D(1)
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(0.0, 1.0, 0.0),
(0.0, 0.0, 1.0),
)
kernel = afwMath.LinearCombinationKernel(basisKernelList, spFunc)
self.assert_(not kernel.isDeltaFunctionBasis())
self.basicTests(kernel, 2, 3)
kernel.setSpatialParameters(sParams)
kImage = afwImage.ImageD(afwGeom.Extent2I(kWidth, kHeight))
for colPos, rowPos, coeff0, coeff1 in [
(0.0, 0.0, 0.0, 0.0),
(1.0, 0.0, 1.0, 0.0),
(0.0, 1.0, 0.0, 1.0),
(1.0, 1.0, 1.0, 1.0),
(0.5, 0.5, 0.5, 0.5),
]:
kernel.computeImage(kImage, False, colPos, rowPos)
kImArr = kImage.getArray().transpose()
refKImArr = (basisImArrList[0] * coeff0) + (basisImArrList[1] * coeff1)
if not numpy.allclose(kImArr, refKImArr):
self.fail("%s = %s != %s at colPos=%s, rowPos=%s" % \
(kernel.__class__.__name__, kImArr, refKImArr, colPos, rowPos))
sParams = (
(0.1, 1.0, 0.0),
(0.1, 0.0, 1.0),
)
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),
)
kernel.setSpatialParameters(newSParams)
errStr = self.compareKernels(kernel, kernelClone)
if not errStr:
self.fail("Clone was modified by changing original's spatial parameters")
def testSVLinearCombinationKernel(self):
"""Test a spatially varying LinearCombinationKernel
"""
kWidth = 3
kHeight = 2
pol = pexPolicy.Policy()
additionalData = dafBase.PropertySet()
loc = dafPersist.LogicalLocation("tests/data/kernel6.boost")
persistence = dafPersist.Persistence.getPersistence(pol)
# create image arrays for the basis kernels
basisImArrList = []
imArr = numpy.zeros((kWidth, kHeight), dtype=float)
imArr += 0.1
imArr[kWidth//2, :] = 0.9
basisImArrList.append(imArr)
imArr = numpy.zeros((kWidth, kHeight), dtype=float)
imArr += 0.2
imArr[:, kHeight//2] = 0.8
basisImArrList.append(imArr)
# create a list of basis kernels from the images
kVec = afwMath.KernelList()
for basisImArr in basisImArrList:
basisImage = afwImage.makeImageFromArray(basisImArr.transpose().copy())
kernel = afwMath.FixedKernel(basisImage)
kVec.append(kernel)
# create spatially varying linear combination kernel
spFunc = afwMath.PolynomialFunction2D(1)
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(0.0, 1.0, 0.0),
(0.0, 0.0, 1.0),
)
k = afwMath.LinearCombinationKernel(kVec, spFunc)
k.setSpatialParameters(sParams)
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("LinearCombinationKernel",
storageList2, additionalData)
k2 = afwMath.LinearCombinationKernel.swigConvert(x)
self.kernelCheck(k, k2)
kImage = afwImage.ImageD(afwGeom.Extent2I(kWidth, kHeight))
for colPos, rowPos, coeff0, coeff1 in [
(0.0, 0.0, 0.0, 0.0),
(1.0, 0.0, 1.0, 0.0),
(0.0, 1.0, 0.0, 1.0),
(1.0, 1.0, 1.0, 1.0),
(0.5, 0.5, 0.5, 0.5),
]:
k2.computeImage(kImage, False, colPos, rowPos)
kImArr = kImage.getArray().transpose()
refKImArr = (basisImArrList[0] * coeff0) + (basisImArrList[1] * coeff1)
if not numpy.allclose(kImArr, refKImArr):
self.fail("%s = %s != %s at colPos=%s, rowPos=%s" % \
(k2.__class__.__name__, kImArr, refKImArr, colPos, rowPos))
if __name__ == '__main__':
try:
ds9.initDS9(False)
except ds9.Ds9Error:
print 'DS9 launch bug error thrown away (probably)'
t_total = 0
t0 = time.time()
data = np.loadtxt(filename, dtype=np.int32, delimiter=',')#, converters, skiprows, usecols, unpack, ndmin)
dt = time.time() - t0
print "Load time = %.2f us" %(dt*1e6)
t0 = time.time()
t_start = time.time()
image = makeImageFromArray(data)
dt = time.time() - t0
print "DM image made in = %.2f us" %(dt*1e6)
t_total += dt
t0 = time.time()
sigma = 0.75
# kWidth = (int(sigma * 7 + 0.5) // 2) * 2 + 1 # make sure it is odd
kWidth = 5
####### discrete method
gaussFunc = math.GaussianFunction1D(sigma)
gaussKernel = math.SeparableKernel(kWidth, kWidth, gaussFunc, gaussFunc)
math.convolve(image, image, gaussKernel, math.ConvolutionControl())
if ha is None:
mi = ai.MaskedImageF("QE_R%i%i_S%i%i.fits.gz"%(rx, ry, sx, sy))
elif ha == 'A':
mi = ai.MaskedImageF("QE_R%i%i_S%i%i_C0.fits.gz"%(rx, ry, sx, sy))
elif ha == 'B':
mi = ai.MaskedImageF("QE_R%i%i_S%i%i_C1.fits.gz"%(rx, ry, sx, sy))
else:
raise ValueError("passed an invalid value for ha")
im = mi.getImage()
arr = im.getArray()
deadidx = numpy.where(arr == 0.)
hotidx = numpy.where(arr > 1.1)
arr[deadidx] = 2.
arr[hotidx] = 3.
im2 = ai.makeImageFromArray(arr)
thresh = afwDetection.Threshold(1.1)
fs = afwDetection.FootprintSet(im2, thresh)
x0 = []
y0 = []
width = []
height = []
for f in fs.getFootprints():
for bbox in afwDetection.footprintToBBoxList(f):
bbox = cameraGeom.rotateBBoxBy90(bbox, 3, im.getBBox().getDimensions())
x0.append(bbox.getMinX())
y0.append(bbox.getMinY())
width.append(bbox.getWidth())
height.append(bbox.getHeight())
head = fits.Header()
def ViewMaskInDs9(mask_array):
import lsst.afw.display.ds9 as ds9
ds9.mtv(makeImageFromArray(mask_array))
def testSVLinearCombinationKernelFixed(self):
"""Test a spatially varying LinearCombinationKernel whose bases are FixedKernels"""
kWidth = 3
kHeight = 2
# create image arrays for the basis kernels
basisImArrList = []
imArr = np.zeros((kWidth, kHeight), dtype=float)
imArr += 0.1
imArr[kWidth//2, :] = 0.9
basisImArrList.append(imArr)
imArr = np.zeros((kWidth, kHeight), dtype=float)
imArr += 0.2
imArr[:, kHeight//2] = 0.8
basisImArrList.append(imArr)
# create a list of basis kernels from the images
basisKernelList = []
for basisImArr in basisImArrList:
basisImage = afwImage.makeImageFromArray(
basisImArr.transpose().copy())
kernel = afwMath.FixedKernel(basisImage)
basisKernelList.append(kernel)
# create spatially varying linear combination kernel
spFunc = afwMath.PolynomialFunction2D(1)
# spatial parameters are a list of entries, one per kernel parameter;
# each entry is a list of spatial parameters
sParams = (
(0.0, 1.0, 0.0),
(0.0, 0.0, 1.0),
)
kernel = afwMath.LinearCombinationKernel(basisKernelList, spFunc)
self.assertFalse(kernel.isDeltaFunctionBasis())
self.basicTests(kernel, 2, nSpatialParams=3)
kernel.setSpatialParameters(sParams)
kImage = afwImage.ImageD(lsst.geom.Extent2I(kWidth, kHeight))
for colPos, rowPos, coeff0, coeff1 in [
(0.0, 0.0, 0.0, 0.0),
(1.0, 0.0, 1.0, 0.0),
(0.0, 1.0, 0.0, 1.0),
(1.0, 1.0, 1.0, 1.0),
(0.5, 0.5, 0.5, 0.5),
]:
kernel.computeImage(kImage, False, colPos, rowPos)
kImArr = kImage.getArray().transpose()
refKImArr = (basisImArrList[0] * coeff0) + \
(basisImArrList[1] * coeff1)
if not np.allclose(kImArr, refKImArr):
self.fail(f"{kernel.__class__.__name__} = {kImArr} != "
f"{refKImArr} at colPos={colPos}, rowPos={rowPos}")
sParams = (
(0.1, 1.0, 0.0),
(0.1, 0.0, 1.0),
)
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),
)
kernel.setSpatialParameters(newSParams)
errStr = self.compareKernels(kernel, kernelClone)
if not errStr:
self.fail(
"Clone was modified by changing original's spatial parameters")
if ha is None:
mi = ai.MaskedImageF("QE_R%i%i_S%i%i.fits.gz" % (rx, ry, sx, sy))
elif ha == 'A':
mi = ai.MaskedImageF("QE_R%i%i_S%i%i_C0.fits.gz" % (rx, ry, sx, sy))
elif ha == 'B':
mi = ai.MaskedImageF("QE_R%i%i_S%i%i_C1.fits.gz" % (rx, ry, sx, sy))
else:
raise ValueError("passed an invalid value for ha")
im = mi.getImage()
arr = im.getArray()
deadidx = numpy.where(arr == 0.)
hotidx = numpy.where(arr > 1.1)
arr[deadidx] = 2.
arr[hotidx] = 3.
im2 = ai.makeImageFromArray(arr)
thresh = afwDetection.Threshold(1.1)
fs = afwDetection.FootprintSet(im2, thresh)
x0 = []
y0 = []
width = []
height = []
for f in fs.getFootprints():
for bbox in afwDetection.footprintToBBoxList(f):
bbox = cameraGeom.rotateBBoxBy90(bbox, 3, im.getBBox().getDimensions())
x0.append(bbox.getMinX())
y0.append(bbox.getMinY())
width.append(bbox.getWidth())
height.append(bbox.getHeight())
head = pyfits.Header()