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"""Tool to provide Shepp-Logan phantoms."""
__authors__ = ["N. Vigano"]
__license__ = "MIT"
__date__ = "01/09/2014"
import sys
import numpy
[docs]class PhantomGenerator(object):
'''
Class for generating different Phantoms
'''
class Ellipsoid:
def __init__(self, a, b, c, x0, y0, z0, alpha, mu):
self.a = a; self.b = b; self.c = c
self.x0 = x0; self.y0 = y0; self.z0 = z0
self.alpha = alpha * numpy.pi / 180.0; self.mu = mu
self.cosAlpha = numpy.cos(self.alpha)
self.sinAlpha = numpy.sin(self.alpha)
sheppLogan = [
# a b c x0 y0 z0 alpha mu
Ellipsoid(0.69, 0.92, 0.90, 0.0, 0.0, 0.0, 0.0, 0.10),
Ellipsoid(0.6624, 0.874, 0.88, 0.0, -0.02, 0.0, 0.0, -0.08),
Ellipsoid(0.11, 0.31, 0.21, 0.22, -0.0, 0.0, -18.0, -0.02),
Ellipsoid(0.16, 0.41, 0.22, -0.22, 0.0, -0.25, 18.0, -0.02),
Ellipsoid(0.21, 0.25, 0.35, 0.0, 0.35, -0.25, 0.0, 0.03),
Ellipsoid(0.046, 0.046, 0.046, 0.0, 0.10, -0.25, 0.0, 0.01),
Ellipsoid(0.046, 0.046, 0.02, 0.0, -0.10, -0.25, 0.0, 0.01),
Ellipsoid(0.046, 0.023, 0.02, -0.08, -0.605, -0.25, 0.0, 0.01),
Ellipsoid(0.023, 0.023, 0.10, 0.0, -0.605, -0.25, 0.0, 0.01),
Ellipsoid(0.023, 0.046, 0.10, 0.06, -0.605, -0.25, 0.0, 0.01)
]
metalPhantom = [
# a b c x0 y0 z0 alpha mu
Ellipsoid(0.95, 0.95, 0.95, 0.0, 0.0, 0.0, 0.0, 0.02),
Ellipsoid(0.15, 0.15, 0.15, 0.0, 0.6, 0.0, 0.0, 0.08),
Ellipsoid(0.10, 0.10, 0.10, 0.4242, 0.4242, 0.0, 0.0, 0.08),
Ellipsoid(0.05, 0.05, 0.05, 0.6, 0.0, 0.0, 0.0, 0.08),
Ellipsoid(0.02, 0.02, 0.02, 0.4242, -0.4242, 0.0, 0.0, 0.08),
Ellipsoid(0.15, 0.15, 0.15, 0.0, -0.6, 0.0, 0.0, 0.88),
Ellipsoid(0.10, 0.10, 0.10, -0.4242, -0.4242, 0.0, 0.0, 0.88),
Ellipsoid(0.05, 0.05, 0.05, -0.6, 0.0, 0.0, 0.0, 0.88),
Ellipsoid(0.02, 0.02, 0.02, -0.4242, 0.4242, 0.0, 0.0, 0.88)
]
def __init__(self):
pass
[docs] def get3DPhantomSheppLogan(self, n):
"""
:param n: The width (and height) of the phantom to generate
:return: A numpy array of dimension n*n fit with the sheppLogan phantom
"""
volume = numpy.ndarray(shape=(n, n, n))
volume.fill(0.)
count = 0
for ell in PhantomGenerator.sheppLogan:
count = count+1
# print("Ellisse n: %d con mu: %f" % (count, ell.mu))
squareZ = self._getSquareZ(n, ell)
squareZ.shape = (1,n)
for x in range(n):
sumSquareXandY = self._getSquareXandYsum(n, x, ell)
sumSquareXandY.shape = (n,1)
sumSquareXYZ = numpy.add(squareZ, sumSquareXandY)
indices = sumSquareXYZ <= 1
volume[x,indices] = ell.mu
indices = numpy.abs(volume) > 0
volume[indices] = numpy.multiply(volume[indices] + 0.1, 5)
return volume
[docs] def get2DPhantomSheppLogan(self, n, ellipsoidID=None):
"""
:param n: The width (and height) of the phantom to generate
:param ellipsoidID: The Id of the ellipsoid to pick. If None will produce all the ellipsoid
"""
assert(ellipsoidID is None or (ellipsoidID >=0 and ellipsoidID < len(PhantomGenerator.sheppLogan)))
if ellipsoidID is None :
area = self._get2DPhantom(n, PhantomGenerator.sheppLogan)
else :
area = self._get2DPhantom(n, [PhantomGenerator.sheppLogan[ellipsoidID]])
indices = numpy.abs(area) > 0
area[indices] = numpy.multiply(area[indices] + 0.1, 5)
return area / 100.0
def _get2DPhantom(self, n, phantomSpec):
area = numpy.ndarray(shape=(n, n))
area.fill(0.)
count = 0
for ell in phantomSpec:
count = count+1
for x in range(n):
sumSquareXandY = self._getSquareXandYsum(n, x, ell)
indices = sumSquareXandY <= 1
area[indices, x] = ell.mu
return area
def _getSquareXandYsum(self, n, x, ell):
div = lambda x, y: numpy.divide(x, y)
mul = lambda x, y: numpy.multiply(x, y)
sub = lambda x, y: numpy.subtract(x, y)
add = lambda x, y: numpy.add(x, y)
pow2 = lambda x: numpy.power(x, 2)
supportX1 = numpy.ndarray(shape=(n, ))
supportX2 = numpy.ndarray(shape=(n, ))
support_consts = numpy.ndarray(shape=(n, ))
xScaled = float(2*x-n)/float(n)
xCos = xScaled*ell.cosAlpha
xSin = -xScaled*ell.sinAlpha
supportX1.fill(xCos)
supportX2.fill(xSin)
supportY1 = numpy.arange(n)
support_consts.fill(2.)
supportY1 = mul(support_consts, supportY1)
support_consts.fill(n)
supportY1 = sub(supportY1, support_consts)
support_consts.fill(n)
supportY1 = div(supportY1, support_consts)
supportY2 = numpy.array(supportY1)
support_consts.fill(ell.sinAlpha)
supportY1 = add(supportX1, mul(supportY1, support_consts))
support_consts.fill(ell.cosAlpha)
supportY2 = add(supportX2, mul(supportY2, support_consts))
support_consts.fill(ell.x0)
supportY1 = sub(supportY1, support_consts)
support_consts.fill(ell.y0)
supportY2 = sub(supportY2, support_consts)
support_consts.fill(ell.a)
supportY1 = pow2(div(supportY1, support_consts))
support_consts.fill(ell.b)
supportY2 = pow2(div(supportY2, support_consts))
return add(supportY1, supportY2)
def _getSquareZ(self, n, ell):
div = lambda x, y: numpy.divide(x, y)
mul = lambda x, y: numpy.multiply(x, y)
sub = lambda x, y: numpy.subtract(x, y)
pow2 = lambda x: numpy.power(x, 2)
supportZ1 = numpy.arange(n)
support_consts = numpy.ndarray(shape=(n, ))
support_consts.fill(2.)
supportZ1 = mul(support_consts, supportZ1)
support_consts.fill(n)
supportZ1 = sub(supportZ1, support_consts)
support_consts.fill(n)
supportZ1 = div(supportZ1, support_consts)
support_consts.fill(ell.z0)
supportZ1 = sub(supportZ1, ell.z0)
support_consts.fill(ell.c)
return pow2(div(supportZ1, support_consts))
def print2DPhantomToPlainTxt(self, ph, file="output.txt"):
f = open(file,"w")
shp = ph.shape
f.write("%d\n" % shp[0])
f.write("%d\n" % shp[1])
f.write("1\n")
for y in range(shp[1] - 1,0,-1):
for x in range(shp[0]):
f.write("%1.7e " % ph[y,x])
if (x >= (shp[0]-1)):
f.write("\n")
f.close()
if __name__ == "__main__":
if len(sys.argv) != 2:
print("genph usage: genph <Phantom file name>")
sys.exit(-1)
phgen = PhantomGenerator()
phantom = phgen.get2DPhantomSheppLogan(256)
phgen.print2DPhantomToPlainTxt(phantom,sys.argv[1])