def test_diffusivities():
psphere = get_sphere('symmetric362')
bvecs = np.concatenate(([[0, 0, 0]], psphere.vertices))
bvals = np.zeros(len(bvecs)) + 1000
bvals[0] = 0
gtab = grad.gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0001], [0.0015, 0.0003, 0.0003]))
mevecs = [np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
np.array([[0, 0, 1], [0, 1, 0], [1, 0, 0]])]
S = single_tensor(gtab, 100, mevals[0], mevecs[0], snr=None)
dm = dti.TensorModel(gtab, 'LS')
dmfit = dm.fit(S)
md = mean_diffusivity(dmfit.evals)
Trace = trace(dmfit.evals)
rd = radial_diffusivity(dmfit.evals)
ad = axial_diffusivity(dmfit.evals)
lin = linearity(dmfit.evals)
plan = planarity(dmfit.evals)
spher = sphericity(dmfit.evals)
assert_almost_equal(md, (0.0015 + 0.0003 + 0.0001) / 3)
assert_almost_equal(Trace, (0.0015 + 0.0003 + 0.0001))
assert_almost_equal(ad, 0.0015)
assert_almost_equal(rd, (0.0003 + 0.0001) / 2)
assert_almost_equal(lin, (0.0015 - 0.0003)/Trace)
assert_almost_equal(plan, 2 * (0.0003 - 0.0001)/Trace)
assert_almost_equal(spher, (3 * 0.0001)/Trace)
def test_diffusivities():
psphere = get_sphere('symmetric362')
bvecs = np.concatenate(([[0, 0, 0]], psphere.vertices))
bvals = np.zeros(len(bvecs)) + 1000
bvals[0] = 0
gtab = grad.gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0001], [0.0015, 0.0003, 0.0003]))
mevecs = [np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
np.array([[0, 0, 1], [0, 1, 0], [1, 0, 0]])]
S = single_tensor(gtab, 100, mevals[0], mevecs[0], snr=None)
dm = dti.TensorModel(gtab, 'LS')
dmfit = dm.fit(S)
md = mean_diffusivity(dmfit.evals)
Trace = trace(dmfit.evals)
rd = radial_diffusivity(dmfit.evals)
ad = axial_diffusivity(dmfit.evals)
lin = linearity(dmfit.evals)
plan = planarity(dmfit.evals)
spher = sphericity(dmfit.evals)
assert_almost_equal(md, (0.0015 + 0.0003 + 0.0001) / 3)
assert_almost_equal(Trace, (0.0015 + 0.0003 + 0.0001))
assert_almost_equal(ad, 0.0015)
assert_almost_equal(rd, (0.0003 + 0.0001) / 2)
assert_almost_equal(lin, (0.0015 - 0.0003)/Trace)
assert_almost_equal(plan, 2 * (0.0003 - 0.0001)/Trace)
assert_almost_equal(spher, (3 * 0.0001)/Trace)
def test_wls_and_ls_fit():
"""
Tests the WLS and LS fitting functions to see if they returns the correct
eigenvalues and eigenvectors.
Uses data/55dir_grad.bvec as the gradient table and 3by3by56.nii
as the data.
"""
# Defining Test Voxel (avoid nibabel dependency) ###
# Recall: D = [Dxx,Dyy,Dzz,Dxy,Dxz,Dyz,log(S_0)] and D ~ 10^-4 mm^2 /s
b0 = 1000.
bvec, bval = read_bvec_file(get_data('55dir_grad.bvec'))
B = bval[1]
# Scale the eigenvalues and tensor by the B value so the units match
D = np.array([1., 1., 1., 0., 0., 1., -np.log(b0) * B]) / B
evals = np.array([2., 1., 0.]) / B
md = evals.mean()
tensor = from_lower_triangular(D)
# Design Matrix
gtab = grad.gradient_table(bval, bvec)
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
# Testing WLS Fit on Single Voxel
# If you do something wonky (passing min_signal<0), you should get an
# error:
npt.assert_raises(ValueError, TensorModel, gtab, fit_method='WLS',
min_signal=-1)
# Estimate tensor from test signals
model = TensorModel(gtab, fit_method='WLS', return_S0_hat=True)
tensor_est = model.fit(Y)
assert_equal(tensor_est.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_est.evals[0], evals)
assert_array_almost_equal(tensor_est.quadratic_form[0], tensor,
err_msg="Calculation of tensor from Y does not "
"compare to analytical solution")
assert_almost_equal(tensor_est.md[0], md)
assert_array_almost_equal(tensor_est.S0_hat[0], b0, decimal=3)
# Test that we can fit a single voxel's worth of data (a 1d array)
y = Y[0]
tensor_est = model.fit(y)
assert_equal(tensor_est.shape, tuple())
assert_array_almost_equal(tensor_est.evals, evals)
assert_array_almost_equal(tensor_est.quadratic_form, tensor)
assert_almost_equal(tensor_est.md, md)
assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
# Test using fit_method='LS'
model = TensorModel(gtab, fit_method='LS')
tensor_est = model.fit(y)
assert_equal(tensor_est.shape, tuple())
assert_array_almost_equal(tensor_est.evals, evals)
assert_array_almost_equal(tensor_est.quadratic_form, tensor)
assert_almost_equal(tensor_est.md, md)
assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
assert_array_almost_equal(tensor_est.linearity, linearity(evals))
assert_array_almost_equal(tensor_est.planarity, planarity(evals))
assert_array_almost_equal(tensor_est.sphericity, sphericity(evals))
def test_wls_and_ls_fit():
"""
Tests the WLS and LS fitting functions to see if they returns the correct
eigenvalues and eigenvectors.
Uses data/55dir_grad.bvec as the gradient table and 3by3by56.nii
as the data.
"""
# Defining Test Voxel (avoid nibabel dependency) ###
# Recall: D = [Dxx,Dyy,Dzz,Dxy,Dxz,Dyz,log(S_0)] and D ~ 10^-4 mm^2 /s
b0 = 1000.
bvec, bval = read_bvec_file(get_data('55dir_grad.bvec'))
B = bval[1]
# Scale the eigenvalues and tensor by the B value so the units match
D = np.array([1., 1., 1., 0., 0., 1., -np.log(b0) * B]) / B
evals = np.array([2., 1., 0.]) / B
md = evals.mean()
tensor = from_lower_triangular(D)
# Design Matrix
gtab = grad.gradient_table(bval, bvec)
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
# Testing WLS Fit on Single Voxel
# If you do something wonky (passing min_signal<0), you should get an
# error:
npt.assert_raises(ValueError, TensorModel, gtab, fit_method='WLS',
min_signal=-1)
# Estimate tensor from test signals
model = TensorModel(gtab, fit_method='WLS', return_S0_hat=True)
tensor_est = model.fit(Y)
assert_equal(tensor_est.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_est.evals[0], evals)
assert_array_almost_equal(tensor_est.quadratic_form[0], tensor,
err_msg="Calculation of tensor from Y does not "
"compare to analytical solution")
assert_almost_equal(tensor_est.md[0], md)
assert_array_almost_equal(tensor_est.S0_hat[0], b0, decimal=3)
# Test that we can fit a single voxel's worth of data (a 1d array)
y = Y[0]
tensor_est = model.fit(y)
assert_equal(tensor_est.shape, tuple())
assert_array_almost_equal(tensor_est.evals, evals)
assert_array_almost_equal(tensor_est.quadratic_form, tensor)
assert_almost_equal(tensor_est.md, md)
assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
# Test using fit_method='LS'
model = TensorModel(gtab, fit_method='LS')
tensor_est = model.fit(y)
assert_equal(tensor_est.shape, tuple())
assert_array_almost_equal(tensor_est.evals, evals)
assert_array_almost_equal(tensor_est.quadratic_form, tensor)
assert_almost_equal(tensor_est.md, md)
assert_array_almost_equal(tensor_est.lower_triangular(b0), D)
assert_array_almost_equal(tensor_est.linearity, linearity(evals))
assert_array_almost_equal(tensor_est.planarity, planarity(evals))
assert_array_almost_equal(tensor_est.sphericity, sphericity(evals))
def fit(self, data, mask=None):
tenfit = self.tenmodel.fit(data, mask)
evals = tenfit.evals
tensor_linearity = dti.linearity(evals)
if tensor_linearity > self.tensor_linearity_threshold:
R = tenfit.evecs
else:
R = None
# improves robustness of the fitting to include a
# lower bound on eigenvalues.
evals = np.clip(evals, self.tensor_scale_lower_bound, evals.max())
mu = np.sqrt(evals.mean() * 2 * self.tau)
qvals = np.sqrt(self.gtab.bvals / self.tau) / (2 * np.pi)
Q_mu_dependent = shore_Q_mu_dependent(self.radial_order, mu, qvals)
M = Q_mu_dependent * self.Q_mu_independent
if not self.positive_constraint and not self.constraint_e0 and not\
self.laplacian_regularization and not\
self.separated_regularization:
coef = np.dot(np.dot(np.linalg.pinv((np.dot(M.T, M))), M.T), data)
if self.laplacian_regularization:
laplacian_matrix = self.laplacian_matrix * mu
if self.laplacian_weighting == 'GCV':
lopt = generalized_crossvalidation(data, M, laplacian_matrix)
else:
lopt = self.laplacian_weighting
if self.constraint_e0 or self.positive_constraint:
Q = matrix(np.dot(M.T, M) + lopt * laplacian_matrix)
else:
Mreg = np.dot(M.T, M) + lopt * laplacian_matrix
zeros = np.zeros(Mreg.shape[0])
coef = zeros
if (data == 0).all():
coef = zeros
else:
try:
MregInv = np.linalg.pinv(Mreg)
coef = np.dot(np.dot(MregInv, M.T), data)
except np.linalg.linalg.LinAlgError as err:
if 'SVD did not converge' in err.message:
warnings.warn('SVD did not converge')
coef = zeros
else:
raise
else:
lopt = 0
if self.separated_regularization:
N_mat = self.N_mat
L_mat = self.L_mat
if self.separated_weighting == 'GCV':
loptN, loptL = generalized_crossvalidation2D(
data, M, N_mat, L_mat)
else:
loptN = loptL = self.separated_weighting
if self.constraint_e0 or self.positive_constraint:
Q = matrix(np.dot(M.T, M) + loptN * N_mat + loptL * L_mat)
else:
Mreg = np.dot(M.T, M) + loptN * N_mat + loptL * L_mat
zeros = np.zeros(Mreg.shape[0])
coef = zeros
if (data == 0).all():
coef = zeros
else:
try:
MregInv = np.linalg.pinv(Mreg)
coef = np.dot(np.dot(MregInv, M.T), data)
except np.linalg.linalg.LinAlgError as err:
if 'SVD did not converge' in err.message:
warnings.warn('SVD did not converge')
coef = zeros
else:
raise
else:
loptN = loptL = 0
if self.constraint_e0 or self.positive_constraint:
Q = matrix(np.dot(M.T, M))
if self.positive_constraint:
constraint_grid = self.constraint_grid
K_independent = self.pos_K_independent
K_dependent = shore_K_mu_dependent(self.radial_order, mu,
constraint_grid)
K = K_independent * K_dependent
G = matrix(-1 * K)
h = matrix(np.zeros((K.shape[0])), (K.shape[0], 1))
else:
G = None
h = None
if self.constraint_e0:
data = data / data[self.gtab.b0s_mask].mean()
p = matrix(-1 * np.dot(M.T, data))
A = matrix(M[0], (1, M.shape[1]))
b = matrix(1.0)
else:
p = matrix(-1 * np.dot(M.T, data))
A = None
b = None
solvers.options['show_progress'] = False
try:
sol = solvers.qp(Q, p, G, h, A, b)
coef = np.array(sol['x'])[:, 0]
except ValueError:
coef = np.zeros(self.ind_mat.shape[0])
if not (self.constraint_e0):
coef = coef / sum(coef * self.B_mat)
# Apply the mask to the coefficients
if mask is not None:
mask = np.asarray(mask, dtype=bool)
coef *= mask[..., None]
return ShoreOzarslanFit(self, coef, mu, R, lopt, loptN, loptL)