def test_coordinate_transformation():
# test for a vector of size 3
cartesian_vector = np.random.rand(3)
spherical_vector = utils.cart2sphere(cartesian_vector)
recovered_cartesian_vector = utils.sphere2cart(spherical_vector)
assert_almost_equal(cartesian_vector, recovered_cartesian_vector)
# test for a vector of size N x 3
cartesian_vector = np.random.rand(10, 3)
spherical_vector = utils.cart2sphere(cartesian_vector)
recovered_cartesian_vector = utils.sphere2cart(spherical_vector)
assert_almost_equal(cartesian_vector, recovered_cartesian_vector)
def test_rotation_on_bingham_tensor():
# test 5: does combined rotation rotate Bingham well?
kappa_ = np.random.rand()
beta_ = kappa_ / 2. # beta<kappa
Bdiag_ = np.diag(np.r_[kappa_, beta_, 0])
theta_ = np.random.rand() * np.pi
phi_ = (np.random.rand() - .5) * np.pi
psi_ = np.random.rand() * np.pi * 0
R_ = rotation_matrix_100_to_theta_phi_psi(theta_, phi_, psi_)
B_ = R_.dot(Bdiag_).dot(R_.T)
eigvals, eigvecs = np.linalg.eigh(B_)
main_evec = eigvecs[:, np.argmax(eigvals)]
_, theta_rec0, phi_rec0 = utils.cart2sphere(main_evec)
# checking if the angles are antipodal to each other
if abs(theta_ - theta_rec0) > 1e-5:
theta_rec = np.pi - theta_rec0
if phi_rec0 > 0:
phi_rec = phi_rec0 - np.pi
elif phi_rec0 < 0:
phi_rec = phi_rec0 + np.pi
else:
theta_rec = theta_rec0
phi_rec = phi_rec0
assert_almost_equal(theta_, theta_rec)
assert_almost_equal(phi_, phi_rec)
assert_almost_equal(np.diag(Bdiag_), np.sort(eigvals)[::-1])
def test_rotation_100_to_theta_phi():
# test 1: does R100_to_theta_phi rotate a vector theta_phi?
theta_ = np.random.rand() * np.pi
phi_ = (np.random.rand() - .5) * np.pi
R100_to_theta_pi = rotation_matrix_100_to_theta_phi(theta_, phi_)
xyz = np.dot(R100_to_theta_pi, np.r_[1, 0, 0])
_, theta_rec, phi_rec = utils.cart2sphere(xyz)
assert_almost_equal(theta_, theta_rec)
assert_almost_equal(phi_, phi_rec)
def test_psi_insensitivity_when_doing_psi_theta_phi_rotation():
# test 3: does psi still have no influence on main eigenvector when doing
# both rotations?
theta_ = np.random.rand() * np.pi
phi_ = (np.random.rand() - .5) * np.pi
psi_ = np.random.rand() * np.pi
R_ = rotation_matrix_100_to_theta_phi_psi(theta_, phi_, psi_)
xyz = np.dot(R_, np.r_[1, 0, 0])
_, theta_rec, phi_rec = utils.cart2sphere(xyz)
assert_almost_equal(theta_, theta_rec)
assert_almost_equal(phi_, phi_rec)
def test_watson_orienting():
# test for orienting the axis of the Watson distribution mu for k>0
# first test to see if Wn is highest along mu
sphere = get_sphere('repulsion724')
n = sphere.vertices
indices = np.array(range(n.shape[0]))
np.random.shuffle(indices)
mu_index = indices[0]
mu_cart = n[mu_index]
mu_sphere = utils.cart2sphere(mu_cart)[1:]
odi = np.random.rand()
watson = distributions.SD1Watson(mu=mu_sphere, odi=odi)
Wn_vector = watson(n=n)
assert_almost_equal(Wn_vector[mu_index], max(Wn_vector))
# second test to see if Wn is lowest prependicular to mu
mu_perp = utils.perpendicular_vector(mu_cart)
Wn_perp = watson(n=mu_perp)
assert_equal(np.all(Wn_perp < Wn_vector), True)
def test_spherical_convolution_watson_sh(sh_order=4):
sphere = get_sphere('symmetric724')
n = sphere.vertices
bval = np.tile(1e9, len(n))
scheme = acquisition_scheme_from_bvalues(bval, n, delta, Delta)
indices_sphere_orientations = np.arange(sphere.vertices.shape[0])
np.random.shuffle(indices_sphere_orientations)
mu_index = indices_sphere_orientations[0]
mu_watson = sphere.vertices[mu_index]
mu_watson_sphere = utils.cart2sphere(mu_watson)[1:]
watson = distributions.SD1Watson(mu=mu_watson_sphere, odi=.3)
f_sf = watson(n=sphere.vertices)
f_sh = sf_to_sh(f_sf, sphere, sh_order)
lambda_par = 2e-9
stick = cylinder_models.C1Stick(mu=[0, 0], lambda_par=lambda_par)
k_sf = stick(scheme)
sh_matrix, m, n = real_sym_sh_mrtrix(sh_order, sphere.theta, sphere.phi)
sh_matrix_inv = np.linalg.pinv(sh_matrix)
k_sh = np.dot(sh_matrix_inv, k_sf)
k_rh = k_sh[m == 0]
fk_convolved_sh = sh_convolution(f_sh, k_rh)
fk_convolved_sf = sh_to_sf(fk_convolved_sh, sphere, sh_order)
# assert if spherical mean is the same between kernel and convolved kernel
assert_almost_equal(abs(np.mean(k_sf) - np.mean(fk_convolved_sf)), 0., 2)
# assert if the lowest signal attenuation (E(b,n)) is orientation along
# the orientation of the watson distribution.
min_position = np.argmin(fk_convolved_sf)
if min_position == mu_index:
assert_equal(min_position, mu_index)
else: # then it's the opposite direction
sphere_positions = np.arange(sphere.vertices.shape[0])
opposite_index = np.all(
np.round(sphere.vertices - mu_watson, 2) == 0, axis=1
)
min_position_opposite = sphere_positions[opposite_index]
assert_equal(min_position_opposite, mu_index)
def __call__(self, n, **kwargs):
r"""Returns the sphere function at cartesian orientations n given
spherical harmonic coefficients.
Parameters
----------
n : array of shape(N x 3),
sampled orientations of the Watson distribution.
Returns
-------
SHn: array of shape(N),
Probability density at orientations n, given sh coeffs.
"""
# calculate SHT matrix
_, theta, phi = utils.cart2sphere(n).T
SHT = real_sym_sh_mrtrix(self.sh_order, theta, phi)[0]
# transform coefficients to sphere values
sh_coeff = kwargs.get('sh_coeff', self.sh_coeff)
SHn = SHT.dot(sh_coeff)
return SHn
from scipy import interpolate
from dmipy.core.modeling_framework import ModelProperties
from dipy.utils.optpkg import optional_package
from dipy.data import get_sphere, HemiSphere
sphere = get_sphere('symmetric724')
hemisphere = HemiSphere(phi=sphere.phi, theta=sphere.theta)
numba, have_numba, _ = optional_package("numba")
GRADIENT_TABLES_PATH = pkg_resources.resource_filename('dmipy',
'data/gradient_tables')
SIGNAL_MODELS_PATH = pkg_resources.resource_filename('dmipy', 'signal_models')
DATA_PATH = pkg_resources.resource_filename('dmipy', 'data')
SPHERE_CARTESIAN = np.loadtxt(join(GRADIENT_TABLES_PATH,
'sphere_with_cap.txt'))
SPHERE_SPHERICAL = utils.cart2sphere(SPHERE_CARTESIAN)
log_bingham_normalization_splinefit = np.load(join(
DATA_PATH, "bingham_normalization_splinefit.npz"),
encoding='bytes')['arr_0']
inverse_sh_matrix_kernel = {
sh_order: np.linalg.pinv(
real_sym_sh_mrtrix(sh_order, hemisphere.theta, hemisphere.phi)[0])
for sh_order in np.arange(0, 15, 2)
}
BETA_SCALING = 1e-6
__all__ = [
'get_sh_order_from_odi', 'SD1Watson', 'SD2Bingham', 'DD1Gamma',
'odi2kappa', 'kappa2odi'
]