def test_sticks_and_ball():
d = 0.0015
S, sticks = sticks_and_ball(gtab, d=d, S0=1, angles=[(0, 0), ],
fractions=[100], snr=None)
assert_array_equal(sticks, [[0, 0, 1]])
S_st = SingleTensor(gtab, 1, evals=[d, 0, 0], evecs=[[0, 0, 0],
[0, 0, 0],
[1, 0, 0]])
assert_array_almost_equal(S, S_st)
def test_single_tensor():
evals = np.array([1.4, .35, .35]) * 10**(-3)
evecs = np.eye(3)
S = SingleTensor(gtab, 100, evals, evecs, snr=None)
assert_array_almost_equal(S[gtab.b0s_mask], 100)
assert_(np.mean(S[~gtab.b0s_mask]) < 100)
from dipy.reconst.dti import TensorModel
m = TensorModel(gtab)
t = m.fit(S)
assert_array_almost_equal(t.fa, 0.707, decimal=3)
def test_single_tensor():
fimg, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
#bvals=np.loadtxt(fbvals)
#bvecs=np.loadtxt(fbvecs).T
img = nib.load(fimg)
data = img.get_data()
evals = np.array([1.4, .35, .35]) * 10**(-3)
evecs = np.eye(3)
S = SingleTensor(bvals, bvecs, 100, evals, evecs, snr=None)
"""
def orbital_phantom(gtab=None,
evals=diffusion_evals,
func=None,
t=np.linspace(0, 2 * np.pi, 1000),
datashape=(64, 64, 64, 65),
origin=(32, 32, 32),
scale=(25, 25, 25),
angles=np.linspace(0, 2 * np.pi, 32),
radii=np.linspace(0.2, 2, 6),
S0=100.,
snr=None):
"""Create a phantom based on a 3-D orbit ``f(t) -> (x,y,z)``.
Parameters
-----------
gtab : GradientTable
Gradient table of measurement directions.
evals : array, shape (3,)
Tensor eigenvalues.
func : user defined function f(t)->(x,y,z)
It could be desirable for ``-1=<x,y,z <=1``.
If None creates a circular orbit.
t : array, shape (K,)
Represents time for the orbit. Default is
``np.linspace(0, 2 * np.pi, 1000)``.
datashape : array, shape (X,Y,Z,W)
Size of the output simulated data
origin : tuple, shape (3,)
Define the center for the volume
scale : tuple, shape (3,)
Scale the function before applying to the grid
angles : array, shape (L,)
Density angle points, always perpendicular to the first eigen vector
Default np.linspace(0, 2 * np.pi, 32).
radii : array, shape (M,)
Thickness radii. Default ``np.linspace(0.2, 2, 6)``.
angles and radii define the total thickness options
S0 : double, optional
Maximum simulated signal. Default 100.
snr : float, optional
The signal to noise ratio set to apply Rician noise to the data.
Default is to not add noise at all.
Returns
-------
data : array, shape (datashape)
See Also
--------
add_noise
Examples
---------
>>> def f(t):
... x = np.sin(t)
... y = np.cos(t)
... z = np.linspace(-1, 1, len(x))
... return x, y, z
>>> data = orbital_phantom(func=f)
"""
if gtab is None:
fimg, fbvals, fbvecs = get_data('small_64D')
gtab = gradient_table(fbvals, fbvecs)
if func is None:
x = np.sin(t)
y = np.cos(t)
z = np.zeros(t.shape)
else:
x, y, z = func(t)
dx = np.diff(x)
dy = np.diff(y)
dz = np.diff(z)
x = scale[0] * x + origin[0]
y = scale[1] * y + origin[1]
z = scale[2] * z + origin[2]
bx = np.zeros(len(angles))
by = np.sin(angles)
bz = np.cos(angles)
# The entire volume is considered to be inside the brain.
# Voxels without a fiber crossing through them are taken
# to be isotropic with signal = S0.
vol = np.zeros(datashape) + S0
for i in range(len(dx)):
evecs, R = diff2eigenvectors(dx[i], dy[i], dz[i])
S = SingleTensor(gtab, S0, evals, evecs, snr=None)
vol[int(x[i]), int(y[i]), int(z[i]), :] += S
for r in radii:
for j in range(len(angles)):
rb = np.dot(R, np.array([bx[j], by[j], bz[j]]))
ix = int(x[i] + r * rb[0])
iy = int(y[i] + r * rb[1])
iz = int(z[i] + r * rb[2])
vol[ix, iy, iz] = vol[ix, iy, iz] + S
vol = vol / np.max(vol, axis=-1)[..., np.newaxis]
vol *= S0
if snr is not None:
vol = add_noise(vol, snr, S0=S0, noise_type='rician')
return vol
def orbital_phantom(bvals=None,
bvecs=None,
evals=np.array([1.4, .35, .35]) * 10**(-3),
func=None,
t=np.linspace(0, 2 * np.pi, 1000),
datashape=(64, 64, 64, 65),
origin=(32, 32, 32),
scale=(25, 25, 25),
angles=np.linspace(0, 2 * np.pi, 32),
radii=np.linspace(0.2, 2, 6),
S0=100.):
""" Create a phantom based on a 3d orbit f(t)->(x,y,z)
Parameters
-----------
bvals : array, shape (N,)
bvecs : array, shape (N,3)
evals : array, shape (3,)
tensor eigenvalues
func : user defined function f(t)->(x,y,z)
It could be desirable for -1=<x,y,z <=1
if None creates a circular orbit
t : array, shape (K,)
represents time for the orbit
Default is np.linspace(0,2*np.pi,1000)
datashape : array, shape (X,Y,Z,W)
size of the output simulated data
origin : tuple, shape (3,)
define the center for the volume
scale : tuple, shape (3,)
scale the function before applying to the grid
angles : array, shape (L,)
density angle points, always perpendicular to the first eigen vector
Default np.linspace(0,2*np.pi,32),
radii : array, shape (M,)
thickness radii
Default np.linspace(0.2,2,6)
angles and radii define the total thickness options
S0 : double, simulated signal without diffusion gradients applied
Default 100.
snr : signal to noise ratio
Used for applying rician noise to the data.
Default 200. Common is 20.
background_noise : boolean, Default False
Returns
---------
data : array, shape (datashape)
Notes
--------
Crossings can be created by adding multiple orbitual_phantom outputs.
Examples
---------
def f(t):
x=np.sin(t)
y=np.cos(t)
z=np.linspace(-1,1,len(x))
return x,y,z
data=orbitual_phantom(func=f)
"""
if bvals == None:
fimg, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
bvecs[np.isnan(bvecs)] = 0
if func == None:
x = np.sin(t)
y = np.cos(t)
z = np.zeros(t.shape)
else:
x, y, z = func(t)
#stop
dx = np.diff(x)
dy = np.diff(y)
dz = np.diff(z)
x = scale[0] * x + origin[0]
y = scale[1] * y + origin[1]
z = scale[2] * z + origin[2]
bx = np.zeros(len(angles))
by = np.sin(angles)
bz = np.cos(angles)
vol = np.zeros(datashape)
for i in range(len(dx)):
evecs, R = diff2eigenvectors(dx[i], dy[i], dz[i])
S = SingleTensor(bvals, bvecs, S0, evals, evecs, snr=None)
#print sigma, S0/snr, S0, snr
vol[x[i], y[i], z[i], :] += S
for r in radii:
for j in range(len(angles)):
rb = np.dot(R, np.array([bx[j], by[j], bz[j]]))
vol[x[i] + r * rb[0], y[i] + r * rb[1], z[i] + r * rb[2]] += S
#ten=Tensor(vol,bvals,bvecs)
#FA=ten.fa()
#FA[np.isnan(FA)]=0
#vol[np.isnan(vol)]=0
return vol