def test_predict():
"""
Test model prediction API
"""
psphere = get_sphere('symmetric362')
bvecs = np.concatenate(([[1, 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)
assert_array_almost_equal(dmfit.predict(gtab, S0=100), S)
assert_array_almost_equal(dm.predict(dmfit.model_params, S0=100), S)
data, gtab = dsi_voxels()
dtim = dti.TensorModel(gtab)
dtif = dtim.fit(data)
S0 = np.mean(data[..., gtab.b0s_mask], -1)
p = dtif.predict(gtab, S0)
def test_adc():
"""
Test the implementation of the calculation of apparent diffusion coefficient
"""
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
mask = np.zeros(data.shape[:-1], dtype=bool)
mask[0, 0, 0] = True
dtifit = dm.fit(data)
sphere = create_unit_sphere(4)
# The ADC in the principal diffusion direction should be equal to the AD in
# each voxel:
pdd0 = dtifit.evecs[0,0,0,0]
sphere_pdd0 = dps.Sphere(x=pdd0[0], y=pdd0[1], z=pdd0[2])
assert_array_almost_equal(dtifit.adc(sphere_pdd0)[0,0,0],
dtifit.ad[0,0,0], decimal=5)
# Test that it works for cases in which the data is 1D
dtifit = dm.fit(data[0,0,0])
sphere_pdd0 = dps.Sphere(x=pdd0[0], y=pdd0[1], z=pdd0[2])
assert_array_almost_equal(dtifit.adc(sphere_pdd0),
dtifit.ad, decimal=5)
def test_adc():
"""
Test the implementation of the calculation of apparent diffusion
coefficient
"""
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
mask = np.zeros(data.shape[:-1], dtype=bool)
mask[0, 0, 0] = True
dtifit = dm.fit(data)
# The ADC in the principal diffusion direction should be equal to the AD in
# each voxel:
pdd0 = dtifit.evecs[0, 0, 0, 0]
sphere_pdd0 = dps.Sphere(x=pdd0[0], y=pdd0[1], z=pdd0[2])
npt.assert_array_almost_equal(dtifit.adc(sphere_pdd0)[0, 0, 0],
dtifit.ad[0, 0, 0],
decimal=5)
# Test that it works for cases in which the data is 1D
dtifit = dm.fit(data[0, 0, 0])
sphere_pdd0 = dps.Sphere(x=pdd0[0], y=pdd0[1], z=pdd0[2])
npt.assert_array_almost_equal(dtifit.adc(sphere_pdd0),
dtifit.ad,
decimal=5)
def test_multib0_dsi():
data, gtab = dsi_voxels()
# Create a new data-set with a b0 measurement:
new_data = np.concatenate([data, data[..., 0, None]], -1)
new_bvecs = np.concatenate([gtab.bvecs, np.zeros((1, 3))])
new_bvals = np.concatenate([gtab.bvals, [0]])
new_gtab = gradient_table(new_bvals, new_bvecs)
ds = DiffusionSpectrumModel(new_gtab)
dsfit = ds.fit(new_data)
pdf = dsfit.pdf()
dsfit.odf(default_sphere)
assert_equal(new_data.shape[:-1] + (17, 17, 17), pdf.shape)
assert_equal(np.alltrue(np.isreal(pdf)), True)
# And again, with one more b0 measurement (two in total):
new_data = np.concatenate([data, data[..., 0, None]], -1)
new_bvecs = np.concatenate([gtab.bvecs, np.zeros((1, 3))])
new_bvals = np.concatenate([gtab.bvals, [0]])
new_gtab = gradient_table(new_bvals, new_bvecs)
ds = DiffusionSpectrumModel(new_gtab)
dsfit = ds.fit(new_data)
pdf = dsfit.pdf()
dsfit.odf(default_sphere)
assert_equal(new_data.shape[:-1] + (17, 17, 17), pdf.shape)
assert_equal(np.alltrue(np.isreal(pdf)), True)
def test_mask():
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
mask = np.zeros(data.shape[:-1], dtype=bool)
mask[0, 0, 0] = True
dtifit = dm.fit(data)
dtifit_w_mask = dm.fit(data, mask=mask)
# Without a mask it has some value
assert_(not np.isnan(dtifit.fa[0, 0, 0]))
# Where mask is False, evals, evecs and fa should all be 0
assert_array_equal(dtifit_w_mask.evals[~mask], 0)
assert_array_equal(dtifit_w_mask.evecs[~mask], 0)
assert_array_equal(dtifit_w_mask.fa[~mask], 0)
# Except for the one voxel that was selected by the mask:
assert_almost_equal(dtifit_w_mask.fa[0, 0, 0], dtifit.fa[0, 0, 0])
# Test with returning S0_hat
dm = dti.TensorModel(gtab, 'LS', return_S0_hat=True)
mask = np.zeros(data.shape[:-1], dtype=bool)
mask[0, 0, 0] = True
dtifit = dm.fit(data)
dtifit_w_mask = dm.fit(data, mask=mask)
# Without a mask it has some value
assert_(not np.isnan(dtifit.fa[0, 0, 0]))
# Where mask is False, evals, evecs and fa should all be 0
assert_array_equal(dtifit_w_mask.evals[~mask], 0)
assert_array_equal(dtifit_w_mask.evecs[~mask], 0)
assert_array_equal(dtifit_w_mask.fa[~mask], 0)
assert_array_equal(dtifit_w_mask.S0_hat[~mask], 0)
# Except for the one voxel that was selected by the mask:
assert_almost_equal(dtifit_w_mask.fa[0, 0, 0], dtifit.fa[0, 0, 0])
assert_almost_equal(dtifit_w_mask.S0_hat[0, 0, 0], dtifit.S0_hat[0, 0, 0])
def test_multib0_dsi():
data, gtab = dsi_voxels()
# Create a new data-set with a b0 measurement:
new_data = np.concatenate([data, data[..., 0, None]], -1)
new_bvecs = np.concatenate([gtab.bvecs, np.zeros((1, 3))])
new_bvals = np.concatenate([gtab.bvals, [0]])
new_gtab = gradient_table(new_bvals, new_bvecs)
ds = DiffusionSpectrumModel(new_gtab)
sphere = get_sphere('repulsion724')
dsfit = ds.fit(new_data)
pdf = dsfit.pdf()
dsfit.odf(sphere)
assert_equal(new_data.shape[:-1] + (17, 17, 17), pdf.shape)
assert_equal(np.alltrue(np.isreal(pdf)), True)
# And again, with one more b0 measurement (two in total):
new_data = np.concatenate([data, data[..., 0, None]], -1)
new_bvecs = np.concatenate([gtab.bvecs, np.zeros((1, 3))])
new_bvals = np.concatenate([gtab.bvals, [0]])
new_gtab = gradient_table(new_bvals, new_bvecs)
ds = DiffusionSpectrumModel(new_gtab)
dsfit = ds.fit(new_data)
pdf = dsfit.pdf()
dsfit.odf(sphere)
assert_equal(new_data.shape[:-1] + (17, 17, 17), pdf.shape)
assert_equal(np.alltrue(np.isreal(pdf)), True)
def test_mask():
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
mask = np.zeros(data.shape[:-1], dtype=bool)
mask[0, 0, 0] = True
dtifit = dm.fit(data)
dtifit_w_mask = dm.fit(data, mask=mask)
# Without a mask it has some value
assert_(not np.isnan(dtifit.fa[0, 0, 0]))
# Where mask is False, evals, evecs and fa should all be 0
assert_array_equal(dtifit_w_mask.evals[~mask], 0)
assert_array_equal(dtifit_w_mask.evecs[~mask], 0)
assert_array_equal(dtifit_w_mask.fa[~mask], 0)
# Except for the one voxel that was selected by the mask:
assert_almost_equal(dtifit_w_mask.fa[0, 0, 0], dtifit.fa[0, 0, 0])
# Test with returning S0_hat
dm = dti.TensorModel(gtab, 'LS', return_S0_hat=True)
mask = np.zeros(data.shape[:-1], dtype=bool)
mask[0, 0, 0] = True
dtifit = dm.fit(data)
dtifit_w_mask = dm.fit(data, mask=mask)
# Without a mask it has some value
assert_(not np.isnan(dtifit.fa[0, 0, 0]))
# Where mask is False, evals, evecs and fa should all be 0
assert_array_equal(dtifit_w_mask.evals[~mask], 0)
assert_array_equal(dtifit_w_mask.evecs[~mask], 0)
assert_array_equal(dtifit_w_mask.fa[~mask], 0)
assert_array_equal(dtifit_w_mask.S0_hat[~mask], 0)
# Except for the one voxel that was selected by the mask:
assert_almost_equal(dtifit_w_mask.fa[0, 0, 0], dtifit.fa[0, 0, 0])
assert_almost_equal(dtifit_w_mask.S0_hat[0, 0, 0], dtifit.S0_hat[0, 0, 0])
def test_design_matrix():
data, gtab = dpd.dsi_voxels()
sphere = dpd.get_sphere()
# Make it with NNLS, so that it gets tested regardless of sklearn
sparse_fascicle_model = sfm.SparseFascicleModel(gtab, sphere,
solver='NNLS')
npt.assert_equal(sparse_fascicle_model.design_matrix.shape,
(np.sum(~gtab.b0s_mask), sphere.vertices.shape[0]))
def test_design_matrix():
data, gtab = dpd.dsi_voxels()
sphere = dpd.get_sphere()
# Make it with NNLS, so that it gets tested regardless of sklearn
sparse_fascicle_model = sfm.SparseFascicleModel(gtab, sphere,
solver='NNLS')
npt.assert_equal(sparse_fascicle_model.design_matrix.shape,
(np.sum(~gtab.b0s_mask), sphere.vertices.shape[0]))
def test_multivox_dsi():
data, gtab = dsi_voxels()
DS = DiffusionSpectrumModel(gtab)
DSfit = DS.fit(data)
PDF = DSfit.pdf()
assert_equal(data.shape[:-1] + (17, 17, 17), PDF.shape)
assert_equal(np.alltrue(np.isreal(PDF)), True)
def test_TensorModel():
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.5, True)
dm = dti.TensorModel(gtab, 'WLS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.5, True)
sphere = create_unit_sphere(4)
assert_equal(len(dtifit.odf(sphere)), len(sphere.vertices))
assert_almost_equal(dtifit.fa, gfa(dtifit.odf(sphere)), 1)
# Check that the multivoxel case works:
dtifit = dm.fit(data)
assert_equal(dtifit.fa.shape, data.shape[:3])
# Make some synthetic data
b0 = 1000.
bvecs, bvals = read_bvec_file(get_data('55dir_grad.bvec'))
gtab = grad.gradient_table_from_bvals_bvecs(bvals, bvecs.T)
# The first b value is 0., so we take the second one:
B = bvals[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)
evecs = np.linalg.eigh(tensor)[1]
#Design Matrix
X = dti.design_matrix(bvecs, bvals)
#Signals
Y = np.exp(np.dot(X,D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
# Test fitting with different methods: #XXX Add NNLS methods!
for fit_method in ['OLS', 'WLS']:
tensor_model = dti.TensorModel(gtab,
fit_method=fit_method)
tensor_fit = tensor_model.fit(Y)
assert_true(tensor_fit.model is tensor_model)
assert_equal(tensor_fit.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_fit.evals[0], evals)
assert_array_almost_equal(tensor_fit.quadratic_form[0], tensor,
err_msg =\
"Calculation of tensor from Y does not compare to analytical solution")
assert_almost_equal(tensor_fit.md[0], md)
assert_equal(tensor_fit.directions.shape[-2], 1)
assert_equal(tensor_fit.directions.shape[-1], 3)
# Test error-handling:
assert_raises(ValueError,
dti.TensorModel,
gtab,
fit_method='crazy_method')
def test_multivox_dsi():
data, gtab = dsi_voxels()
DS = DiffusionSpectrumModel(gtab)
get_sphere('symmetric724')
DSfit = DS.fit(data)
PDF = DSfit.pdf()
assert_equal(data.shape[:-1] + (17, 17, 17), PDF.shape)
assert_equal(np.alltrue(np.isreal(PDF)), True)
def test_multivox_dsi():
data, gtab = dsi_voxels()
DS = DiffusionSpectrumModel(gtab, "standard")
sphere = get_sphere("symmetric724")
DS.direction_finder.config(sphere=sphere, min_separation_angle=25, relative_peak_threshold=0.35)
DSfit = DS.fit(data)
PDF = DSfit.pdf()
assert_equal(data.shape[:-1] + (16, 16, 16), PDF.shape)
assert_equal(np.alltrue(np.isreal(PDF)), True)
def test_mvoxel_gqi():
data, gtab = dsi_voxels()
gq = GeneralizedQSamplingModel(gtab, 'standard')
sphere = get_sphere('symmetric724')
gq.direction_finder.config(sphere=sphere,
min_separation_angle=25,
relative_peak_threshold=.35)
gqfit = gq.fit(data)
directions = gqfit.directions
assert_equal(directions[0, 0, 0].shape[0], 2)
assert_equal(directions[-1, -1, -1].shape[0], 2)
def test_mask():
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
mask = np.zeros(data.shape[:-1], dtype=bool)
mask[0, 0, 0] = True
dtifit = dm.fit(data)
dtifit_w_mask = dm.fit(data, mask=mask)
# Without a mask it has some value
assert_(not np.isnan(dtifit.fa[0, 0, 0]))
# But with the mask, it's a nan:
assert_(np.isnan(dtifit_w_mask.fa[0, 0, 1]))
# Except for the one voxel that was selected by the mask:
assert_almost_equal(dtifit_w_mask.fa[0, 0, 0], dtifit.fa[0, 0, 0])
def test_mvoxel_gqi():
data, gtab = dsi_voxels()
sphere = get_sphere('symmetric724')
gq = GeneralizedQSamplingModel(gtab, 'standard')
gqfit = gq.fit(data)
all_odfs = gqfit.odf(sphere)
# Check that the first and last voxels each have 2 peaks
odf = all_odfs[0, 0, 0]
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(directions.shape[0], 2)
odf = all_odfs[-1, -1, -1]
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(directions.shape[0], 2)
def test_mvoxel_gqi():
data, gtab = dsi_voxels()
sphere = get_sphere('symmetric724')
gq = GeneralizedQSamplingModel(gtab, 'standard')
gqfit = gq.fit(data)
all_odfs = gqfit.odf(sphere)
# Check that the first and last voxels each have 2 peaks
odf = all_odfs[0, 0, 0]
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(directions.shape[0], 2)
odf = all_odfs[-1, -1, -1]
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(directions.shape[0], 2)
def test_color_fa():
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
dmfit = dm.fit(data)
fa = fractional_anisotropy(dmfit.evals)
cfa = color_fa(fa, dmfit.evecs)
fa = np.ones((3, 3, 3))
# evecs should be of shape (fa, 3, 3)
evecs = np.zeros(fa.shape + (3, 2))
npt.assert_raises(ValueError, color_fa, fa, evecs)
evecs = np.zeros(fa.shape + (3, 3))
evecs[..., :, :] = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
assert_equal(fa.shape, evecs[..., 0, 0].shape)
assert_equal((3, 3), evecs.shape[-2:])
# 3D test case
fa = np.ones((3, 3, 3))
evecs = np.zeros(fa.shape + (3, 3))
evecs[..., :, :] = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
cfa = color_fa(fa, evecs)
cfa_truth = np.array([1, 0, 0])
true_cfa = np.reshape(np.tile(cfa_truth, 27), [3, 3, 3, 3])
assert_array_equal(cfa, true_cfa)
# 2D test case
fa = np.ones((3, 3))
evecs = np.zeros(fa.shape + (3, 3))
evecs[..., :, :] = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
cfa = color_fa(fa, evecs)
cfa_truth = np.array([1, 0, 0])
true_cfa = np.reshape(np.tile(cfa_truth, 9), [3, 3, 3])
assert_array_equal(cfa, true_cfa)
# 1D test case
fa = np.ones((3))
evecs = np.zeros(fa.shape + (3, 3))
evecs[..., :, :] = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
cfa = color_fa(fa, evecs)
cfa_truth = np.array([1, 0, 0])
true_cfa = np.reshape(np.tile(cfa_truth, 3), [3, 3])
assert_array_equal(cfa, true_cfa)
def test_color_fa():
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
dmfit = dm.fit(data)
fa = fractional_anisotropy(dmfit.evals)
cfa = color_fa(fa, dmfit.evecs)
fa = np.ones((3, 3, 3))
# evecs should be of shape (fa, 3, 3)
evecs = np.zeros(fa.shape + (3, 2))
npt.assert_raises(ValueError, color_fa, fa, evecs)
evecs = np.zeros(fa.shape + (3, 3))
evecs[..., :, :] = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
assert_equal(fa.shape, evecs[..., 0, 0].shape)
assert_equal((3, 3), evecs.shape[-2:])
# 3D test case
fa = np.ones((3, 3, 3))
evecs = np.zeros(fa.shape + (3, 3))
evecs[..., :, :] = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
cfa = color_fa(fa, evecs)
cfa_truth = np.array([1, 0, 0])
true_cfa = np.reshape(np.tile(cfa_truth, 27), [3, 3, 3, 3])
assert_array_equal(cfa, true_cfa)
# 2D test case
fa = np.ones((3, 3))
evecs = np.zeros(fa.shape + (3, 3))
evecs[..., :, :] = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
cfa = color_fa(fa, evecs)
cfa_truth = np.array([1, 0, 0])
true_cfa = np.reshape(np.tile(cfa_truth, 9), [3, 3, 3])
assert_array_equal(cfa, true_cfa)
# 1D test case
fa = np.ones((3))
evecs = np.zeros(fa.shape + (3, 3))
evecs[..., :, :] = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
cfa = color_fa(fa, evecs)
cfa_truth = np.array([1, 0, 0])
true_cfa = np.reshape(np.tile(cfa_truth, 3), [3, 3])
assert_array_equal(cfa, true_cfa)
def test_predict():
"""
Test model prediction API
"""
psphere = get_sphere('symmetric362')
bvecs = np.concatenate(([[1, 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)
assert_array_almost_equal(dmfit.predict(gtab, S0=100), S)
assert_array_almost_equal(dm.predict(dmfit.model_params, S0=100), S)
data, gtab = dsi_voxels()
dtim = dti.TensorModel(gtab)
dtif = dtim.fit(data)
S0 = np.mean(data[...,gtab.b0s_mask], -1)
p = dtif.predict(gtab, S0)
def test_tensor_model():
fdata, fbval, fbvec = get_data('small_25')
data1 = nib.load(fdata).get_data()
gtab1 = grad.gradient_table(fbval, fbvec)
data2, gtab2 = dsi_voxels()
for data, gtab in zip([data1, data2], [gtab1, gtab2]):
dm = dti.TensorModel(gtab, 'LS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.9, True)
dm = dti.TensorModel(gtab, 'WLS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.9, True)
assert_equal(dtifit.fa > 0, True)
sphere = create_unit_sphere(4)
assert_equal(len(dtifit.odf(sphere)), len(sphere.vertices))
# Check that the multivoxel case works:
dtifit = dm.fit(data)
# Check that it works on signal that has already been normalized to S0:
dm_to_relative = dti.TensorModel(gtab)
if np.any(gtab.b0s_mask):
relative_data = (data[0, 0, 0]/np.mean(data[0, 0, 0,
gtab.b0s_mask]))
dtifit_to_relative = dm_to_relative.fit(relative_data)
npt.assert_almost_equal(dtifit.fa[0, 0, 0], dtifit_to_relative.fa,
decimal=3)
# And smoke-test that all these operations return sensibly-shaped arrays:
assert_equal(dtifit.fa.shape, data.shape[:3])
assert_equal(dtifit.ad.shape, data.shape[:3])
assert_equal(dtifit.md.shape, data.shape[:3])
assert_equal(dtifit.rd.shape, data.shape[:3])
assert_equal(dtifit.trace.shape, data.shape[:3])
assert_equal(dtifit.mode.shape, data.shape[:3])
assert_equal(dtifit.linearity.shape, data.shape[:3])
assert_equal(dtifit.planarity.shape, data.shape[:3])
assert_equal(dtifit.sphericity.shape, data.shape[:3])
# Test for the shape of the mask
assert_raises(ValueError, dm.fit, np.ones((10, 10, 3)), np.ones((3, 3)))
# Make some synthetic data
b0 = 1000.
bvecs, bvals = read_bvec_file(get_data('55dir_grad.bvec'))
gtab = grad.gradient_table_from_bvals_bvecs(bvals, bvecs.T)
# The first b value is 0., so we take the second one:
B = bvals[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)
A_squiggle = tensor - (1 / 3.0) * np.trace(tensor) * np.eye(3)
mode = (3 * np.sqrt(6) * np.linalg.det(A_squiggle /
np.linalg.norm(A_squiggle)))
evals_eigh, evecs_eigh = np.linalg.eigh(tensor)
# Sort according to eigen-value from large to small:
evecs = evecs_eigh[:, np.argsort(evals_eigh)[::-1]]
# Check that eigenvalues and eigenvectors are properly sorted through
# that previous operation:
for i in range(3):
assert_array_almost_equal(np.dot(tensor, evecs[:, i]),
evals[i] * evecs[:, i])
# Design Matrix
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
# Test fitting with different methods:
for fit_method in ['OLS', 'WLS', 'NLLS']:
tensor_model = dti.TensorModel(gtab,
fit_method=fit_method,
return_S0_hat=True)
tensor_fit = tensor_model.fit(Y)
assert_true(tensor_fit.model is tensor_model)
assert_equal(tensor_fit.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_fit.evals[0], evals)
assert_array_almost_equal(tensor_fit.S0_hat, b0, decimal=3)
# Test that the eigenvectors are correct, one-by-one:
for i in range(3):
# Eigenvectors have intrinsic sign ambiguity
# (see
# http://prod.sandia.gov/techlib/access-control.cgi/2007/076422.pdf)
# so we need to allow for sign flips. One of the following should
# always be true:
assert_(
np.all(np.abs(tensor_fit.evecs[0][:, i] -
evecs[:, i]) < 10e-6) or
np.all(np.abs(-tensor_fit.evecs[0][:, i] -
evecs[:, i]) < 10e-6))
# We set a fixed tolerance of 10e-6, similar to array_almost_equal
err_msg = "Calculation of tensor from Y does not compare to "
err_msg += "analytical solution"
assert_array_almost_equal(tensor_fit.quadratic_form[0], tensor,
err_msg=err_msg)
assert_almost_equal(tensor_fit.md[0], md)
assert_array_almost_equal(tensor_fit.mode, mode, decimal=5)
assert_equal(tensor_fit.directions.shape[-2], 1)
assert_equal(tensor_fit.directions.shape[-1], 3)
# Test error-handling:
assert_raises(ValueError,
dti.TensorModel,
gtab,
fit_method='crazy_method')
# Test custom fit tensor method
try:
model = dti.TensorModel(gtab, fit_method=lambda *args, **kwargs: 42)
fit = model.fit_method()
except Exception as exc:
assert False, "TensorModel should accept custom fit methods: %s" % exc
assert fit == 42, "Custom fit method for TensorModel returned %s." % fit
# Test multi-voxel data
data = np.zeros((3, Y.shape[1]))
# Normal voxel
data[0] = Y
# High diffusion voxel, all diffusing weighted signal equal to zero
data[1, gtab.b0s_mask] = b0
data[1, ~gtab.b0s_mask] = 0
# Masked voxel, all data set to zero
data[2] = 0.
tensor_model = dti.TensorModel(gtab)
fit = tensor_model.fit(data)
assert_array_almost_equal(fit[0].evals, evals)
# Return S0_test
tensor_model = dti.TensorModel(gtab, return_S0_hat=True)
fit = tensor_model.fit(data)
assert_array_almost_equal(fit[0].evals, evals)
assert_array_almost_equal(fit[0].S0_hat, b0)
# Evals should be high for high diffusion voxel
assert_(all(fit[1].evals > evals[0] * .9))
# Evals should be zero where data is masked
assert_array_almost_equal(fit[2].evals, 0.)
def test_tensor_model():
fdata, fbval, fbvec = get_data('small_25')
data1 = nib.load(fdata).get_data()
gtab1 = grad.gradient_table(fbval, fbvec)
data2, gtab2 = dsi_voxels()
for data, gtab in zip([data1, data2], [gtab1, gtab2]):
dm = dti.TensorModel(gtab, 'LS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.9, True)
dm = dti.TensorModel(gtab, 'WLS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.9, True)
assert_equal(dtifit.fa > 0, True)
sphere = create_unit_sphere(4)
assert_equal(len(dtifit.odf(sphere)), len(sphere.vertices))
# Check that the multivoxel case works:
dtifit = dm.fit(data)
# Check that it works on signal that has already been normalized to S0:
dm_to_relative = dti.TensorModel(gtab)
if np.any(gtab.b0s_mask):
relative_data = (data[0, 0, 0]/np.mean(data[0, 0, 0,
gtab.b0s_mask]))
dtifit_to_relative = dm_to_relative.fit(relative_data)
npt.assert_almost_equal(dtifit.fa[0, 0, 0], dtifit_to_relative.fa,
decimal=3)
# And smoke-test that all these operations return sensibly-shaped arrays:
assert_equal(dtifit.fa.shape, data.shape[:3])
assert_equal(dtifit.ad.shape, data.shape[:3])
assert_equal(dtifit.md.shape, data.shape[:3])
assert_equal(dtifit.rd.shape, data.shape[:3])
assert_equal(dtifit.trace.shape, data.shape[:3])
assert_equal(dtifit.mode.shape, data.shape[:3])
assert_equal(dtifit.linearity.shape, data.shape[:3])
assert_equal(dtifit.planarity.shape, data.shape[:3])
assert_equal(dtifit.sphericity.shape, data.shape[:3])
# Test for the shape of the mask
assert_raises(ValueError, dm.fit, np.ones((10, 10, 3)), np.ones((3, 3)))
# Make some synthetic data
b0 = 1000.
bvecs, bvals = read_bvec_file(get_data('55dir_grad.bvec'))
gtab = grad.gradient_table_from_bvals_bvecs(bvals, bvecs.T)
# The first b value is 0., so we take the second one:
B = bvals[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)
A_squiggle = tensor - (1 / 3.0) * np.trace(tensor) * np.eye(3)
mode = (3 * np.sqrt(6) * np.linalg.det(A_squiggle /
np.linalg.norm(A_squiggle)))
evals_eigh, evecs_eigh = np.linalg.eigh(tensor)
# Sort according to eigen-value from large to small:
evecs = evecs_eigh[:, np.argsort(evals_eigh)[::-1]]
# Check that eigenvalues and eigenvectors are properly sorted through
# that previous operation:
for i in range(3):
assert_array_almost_equal(np.dot(tensor, evecs[:, i]),
evals[i] * evecs[:, i])
# Design Matrix
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
# Test fitting with different methods:
for fit_method in ['OLS', 'WLS', 'NLLS']:
tensor_model = dti.TensorModel(gtab,
fit_method=fit_method,
return_S0_hat=True)
tensor_fit = tensor_model.fit(Y)
assert_true(tensor_fit.model is tensor_model)
assert_equal(tensor_fit.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_fit.evals[0], evals)
assert_array_almost_equal(tensor_fit.S0_hat, b0, decimal=3)
# Test that the eigenvectors are correct, one-by-one:
for i in range(3):
# Eigenvectors have intrinsic sign ambiguity
# (see
# http://prod.sandia.gov/techlib/access-control.cgi/2007/076422.pdf)
# so we need to allow for sign flips. One of the following should
# always be true:
assert_(
np.all(np.abs(tensor_fit.evecs[0][:, i] -
evecs[:, i]) < 10e-6) or
np.all(np.abs(-tensor_fit.evecs[0][:, i] -
evecs[:, i]) < 10e-6))
# We set a fixed tolerance of 10e-6, similar to array_almost_equal
err_msg = "Calculation of tensor from Y does not compare to "
err_msg += "analytical solution"
assert_array_almost_equal(tensor_fit.quadratic_form[0], tensor,
err_msg=err_msg)
assert_almost_equal(tensor_fit.md[0], md)
assert_array_almost_equal(tensor_fit.mode, mode, decimal=5)
assert_equal(tensor_fit.directions.shape[-2], 1)
assert_equal(tensor_fit.directions.shape[-1], 3)
# Test error-handling:
assert_raises(ValueError,
dti.TensorModel,
gtab,
fit_method='crazy_method')
# Test custom fit tensor method
try:
model = dti.TensorModel(gtab, fit_method=lambda *args, **kwargs: 42)
fit = model.fit_method()
except Exception as exc:
assert False, "TensorModel should accept custom fit methods: %s" % exc
assert fit == 42, "Custom fit method for TensorModel returned %s." % fit
# Test multi-voxel data
data = np.zeros((3, Y.shape[1]))
# Normal voxel
data[0] = Y
# High diffusion voxel, all diffusing weighted signal equal to zero
data[1, gtab.b0s_mask] = b0
data[1, ~gtab.b0s_mask] = 0
# Masked voxel, all data set to zero
data[2] = 0.
tensor_model = dti.TensorModel(gtab)
fit = tensor_model.fit(data)
assert_array_almost_equal(fit[0].evals, evals)
# Return S0_test
tensor_model = dti.TensorModel(gtab, return_S0_hat=True)
fit = tensor_model.fit(data)
assert_array_almost_equal(fit[0].evals, evals)
assert_array_almost_equal(fit[0].S0_hat, b0)
# Evals should be high for high diffusion voxel
assert_(all(fit[1].evals > evals[0] * .9))
# Evals should be zero where data is masked
assert_array_almost_equal(fit[2].evals, 0.)
def test_tensor_model():
fdata, fbval, fbvec = get_data('small_25')
data1 = nib.load(fdata).get_data()
gtab1 = grad.gradient_table(fbval, fbvec)
data2, gtab2 = dsi_voxels()
for data, gtab in zip([data1, data2], [gtab1, gtab2]):
dm = dti.TensorModel(gtab, 'LS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.9, True)
dm = dti.TensorModel(gtab, 'WLS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.9, True)
assert_equal(dtifit.fa > 0, True)
sphere = create_unit_sphere(4)
assert_equal(len(dtifit.odf(sphere)), len(sphere.vertices))
# Check that the multivoxel case works:
dtifit = dm.fit(data)
# Check that it works on signal that has already been normalized to S0:
dm_to_relative = dti.TensorModel(gtab)
if np.any(gtab.b0s_mask):
relative_data = (data[0, 0, 0] /
np.mean(data[0, 0, 0, gtab.b0s_mask]))
dtifit_to_relative = dm_to_relative.fit(relative_data)
npt.assert_almost_equal(dtifit.fa[0, 0, 0],
dtifit_to_relative.fa,
decimal=3)
# And smoke-test that all these operations return sensibly-shaped arrays:
assert_equal(dtifit.fa.shape, data.shape[:3])
assert_equal(dtifit.ad.shape, data.shape[:3])
assert_equal(dtifit.md.shape, data.shape[:3])
assert_equal(dtifit.rd.shape, data.shape[:3])
assert_equal(dtifit.trace.shape, data.shape[:3])
assert_equal(dtifit.mode.shape, data.shape[:3])
assert_equal(dtifit.linearity.shape, data.shape[:3])
assert_equal(dtifit.planarity.shape, data.shape[:3])
assert_equal(dtifit.sphericity.shape, data.shape[:3])
# Test for the shape of the mask
assert_raises(ValueError, dm.fit, np.ones((10, 10, 3)), np.ones((3, 3)))
# Make some synthetic data
b0 = 1000.
bvecs, bvals = read_bvec_file(get_data('55dir_grad.bvec'))
gtab = grad.gradient_table_from_bvals_bvecs(bvals, bvecs.T)
# The first b value is 0., so we take the second one:
B = bvals[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)
A_squiggle = tensor - (1 / 3.0) * np.trace(tensor) * np.eye(3)
mode = 3 * np.sqrt(6) * np.linalg.det(
A_squiggle / np.linalg.norm(A_squiggle))
evecs = np.linalg.eigh(tensor)[1]
# Design Matrix
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1, ) + Y.shape
# Test fitting with different methods:
for fit_method in ['OLS', 'WLS', 'NLLS']:
tensor_model = dti.TensorModel(gtab, fit_method=fit_method)
tensor_fit = tensor_model.fit(Y)
assert_true(tensor_fit.model is tensor_model)
assert_equal(tensor_fit.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_fit.evals[0], evals)
assert_array_almost_equal(tensor_fit.quadratic_form[0], tensor,
err_msg=\
"Calculation of tensor from Y does not compare to analytical solution")
assert_almost_equal(tensor_fit.md[0], md)
assert_array_almost_equal(tensor_fit.mode, mode, decimal=5)
assert_equal(tensor_fit.directions.shape[-2], 1)
assert_equal(tensor_fit.directions.shape[-1], 3)
# Test error-handling:
assert_raises(ValueError, dti.TensorModel, gtab, fit_method='crazy_method')
# Test multi-voxel data
data = np.zeros((3, Y.shape[1]))
# Normal voxel
data[0] = Y
# High diffusion voxel, all diffusing weighted signal equal to zero
data[1, gtab.b0s_mask] = b0
data[1, ~gtab.b0s_mask] = 0
# Masked voxel, all data set to zero
data[2] = 0.
tensor_model = dti.TensorModel(gtab)
fit = tensor_model.fit(data)
assert_array_almost_equal(fit[0].evals, evals)
# Evals should be high for high diffusion voxel
assert_(all(fit[1].evals > evals[0] * .9))
# Evals should be zero where data is masked
assert_array_almost_equal(fit[2].evals, 0.)
def test_TensorModel():
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.5, True)
dm = dti.TensorModel(gtab, 'WLS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.5, True)
sphere = create_unit_sphere(4)
assert_equal(len(dtifit.odf(sphere)), len(sphere.vertices))
assert_almost_equal(dtifit.fa, gfa(dtifit.odf(sphere)), 1)
# Check that the multivoxel case works:
dtifit = dm.fit(data)
# And smoke-test that all these operations return sensibly-shaped arrays:
assert_equal(dtifit.fa.shape, data.shape[:3])
assert_equal(dtifit.ad.shape, data.shape[:3])
assert_equal(dtifit.md.shape, data.shape[:3])
assert_equal(dtifit.rd.shape, data.shape[:3])
assert_equal(dtifit.trace.shape, data.shape[:3])
assert_equal(dtifit.mode.shape, data.shape[:3])
assert_equal(dtifit.linearity.shape, data.shape[:3])
assert_equal(dtifit.planarity.shape, data.shape[:3])
assert_equal(dtifit.sphericity.shape, data.shape[:3])
# Test for the shape of the mask
assert_raises(ValueError, dm.fit, np.ones((10, 10, 3)), np.ones((3, 3)))
# Make some synthetic data
b0 = 1000.
bvecs, bvals = read_bvec_file(get_data('55dir_grad.bvec'))
gtab = grad.gradient_table_from_bvals_bvecs(bvals, bvecs.T)
# The first b value is 0., so we take the second one:
B = bvals[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)
A_squiggle = tensor - (1 / 3.0) * np.trace(tensor) * np.eye(3)
mode = 3 * np.sqrt(6) * np.linalg.det(
A_squiggle / np.linalg.norm(A_squiggle))
evecs = np.linalg.eigh(tensor)[1]
# Design Matrix
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1, ) + Y.shape
# Test fitting with different methods:
for fit_method in ['OLS', 'WLS', 'NLLS']:
tensor_model = dti.TensorModel(gtab, fit_method=fit_method)
tensor_fit = tensor_model.fit(Y)
assert_true(tensor_fit.model is tensor_model)
assert_equal(tensor_fit.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_fit.evals[0], evals)
assert_array_almost_equal(tensor_fit.quadratic_form[0], tensor,
err_msg=\
"Calculation of tensor from Y does not compare to analytical solution")
assert_almost_equal(tensor_fit.md[0], md)
assert_array_almost_equal(tensor_fit.mode, mode, decimal=5)
assert_equal(tensor_fit.directions.shape[-2], 1)
assert_equal(tensor_fit.directions.shape[-1], 3)
# Test error-handling:
assert_raises(ValueError, dti.TensorModel, gtab, fit_method='crazy_method')
def test_TensorModel():
data, gtab = dsi_voxels()
dm = dti.TensorModel(gtab, 'LS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.5, True)
dm = dti.TensorModel(gtab, 'WLS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.5, True)
sphere = create_unit_sphere(4)
assert_equal(len(dtifit.odf(sphere)), len(sphere.vertices))
assert_almost_equal(dtifit.fa, gfa(dtifit.odf(sphere)), 1)
# Check that the multivoxel case works:
dtifit = dm.fit(data)
# And smoke-test that all these operations return sensibly-shaped arrays:
assert_equal(dtifit.fa.shape, data.shape[:3])
assert_equal(dtifit.ad.shape, data.shape[:3])
assert_equal(dtifit.md.shape, data.shape[:3])
assert_equal(dtifit.rd.shape, data.shape[:3])
assert_equal(dtifit.trace.shape, data.shape[:3])
assert_equal(dtifit.mode.shape, data.shape[:3])
assert_equal(dtifit.linearity.shape, data.shape[:3])
assert_equal(dtifit.planarity.shape, data.shape[:3])
assert_equal(dtifit.sphericity.shape, data.shape[:3])
# Test for the shape of the mask
assert_raises(ValueError, dm.fit, np.ones((10, 10, 3)), np.ones((3,3)))
# Make some synthetic data
b0 = 1000.
bvecs, bvals = read_bvec_file(get_data('55dir_grad.bvec'))
gtab = grad.gradient_table_from_bvals_bvecs(bvals, bvecs.T)
# The first b value is 0., so we take the second one:
B = bvals[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)
A_squiggle = tensor - (1 / 3.0) * np.trace(tensor) * np.eye(3)
mode = 3 * np.sqrt(6) * np.linalg.det(A_squiggle / np.linalg.norm(A_squiggle))
evecs = np.linalg.eigh(tensor)[1]
# Design Matrix
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
# Test fitting with different methods:
for fit_method in ['OLS', 'WLS', 'NLLS']:
tensor_model = dti.TensorModel(gtab,
fit_method=fit_method)
tensor_fit = tensor_model.fit(Y)
assert_true(tensor_fit.model is tensor_model)
assert_equal(tensor_fit.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_fit.evals[0], evals)
assert_array_almost_equal(tensor_fit.quadratic_form[0], tensor,
err_msg=\
"Calculation of tensor from Y does not compare to analytical solution")
assert_almost_equal(tensor_fit.md[0], md)
assert_array_almost_equal(tensor_fit.mode, mode, decimal=5)
assert_equal(tensor_fit.directions.shape[-2], 1)
assert_equal(tensor_fit.directions.shape[-1], 3)
# Test error-handling:
assert_raises(ValueError,
dti.TensorModel,
gtab,
fit_method='crazy_method')
def test_tensor_model():
fdata, fbval, fbvec = get_data('small_25')
data1 = nib.load(fdata).get_data()
gtab1 = grad.gradient_table(fbval, fbvec)
data2, gtab2 = dsi_voxels()
for data, gtab in zip([data1, data2], [gtab1, gtab2]):
dm = dti.TensorModel(gtab, 'LS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.9, True)
dm = dti.TensorModel(gtab, 'WLS')
dtifit = dm.fit(data[0, 0, 0])
assert_equal(dtifit.fa < 0.9, True)
assert_equal(dtifit.fa > 0, True)
sphere = create_unit_sphere(4)
assert_equal(len(dtifit.odf(sphere)), len(sphere.vertices))
# Check that the multivoxel case works:
dtifit = dm.fit(data)
# Check that it works on signal that has already been normalized to S0:
dm_to_relative = dti.TensorModel(gtab)
if np.any(gtab.b0s_mask):
relative_data = (data[0, 0, 0]/np.mean(data[0, 0, 0,
gtab.b0s_mask]))
dtifit_to_relative = dm_to_relative.fit(relative_data)
npt.assert_almost_equal(dtifit.fa[0,0,0], dtifit_to_relative.fa,
decimal=3)
# And smoke-test that all these operations return sensibly-shaped arrays:
assert_equal(dtifit.fa.shape, data.shape[:3])
assert_equal(dtifit.ad.shape, data.shape[:3])
assert_equal(dtifit.md.shape, data.shape[:3])
assert_equal(dtifit.rd.shape, data.shape[:3])
assert_equal(dtifit.trace.shape, data.shape[:3])
assert_equal(dtifit.mode.shape, data.shape[:3])
assert_equal(dtifit.linearity.shape, data.shape[:3])
assert_equal(dtifit.planarity.shape, data.shape[:3])
assert_equal(dtifit.sphericity.shape, data.shape[:3])
# Test for the shape of the mask
assert_raises(ValueError, dm.fit, np.ones((10, 10, 3)), np.ones((3,3)))
# Make some synthetic data
b0 = 1000.
bvecs, bvals = read_bvec_file(get_data('55dir_grad.bvec'))
gtab = grad.gradient_table_from_bvals_bvecs(bvals, bvecs.T)
# The first b value is 0., so we take the second one:
B = bvals[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)
A_squiggle = tensor - (1 / 3.0) * np.trace(tensor) * np.eye(3)
mode = 3 * np.sqrt(6) * np.linalg.det(A_squiggle / np.linalg.norm(A_squiggle))
evecs = np.linalg.eigh(tensor)[1]
# Design Matrix
X = dti.design_matrix(gtab)
# Signals
Y = np.exp(np.dot(X, D))
assert_almost_equal(Y[0], b0)
Y.shape = (-1,) + Y.shape
# Test fitting with different methods:
for fit_method in ['OLS', 'WLS', 'NLLS']:
tensor_model = dti.TensorModel(gtab,
fit_method=fit_method)
tensor_fit = tensor_model.fit(Y)
assert_true(tensor_fit.model is tensor_model)
assert_equal(tensor_fit.shape, Y.shape[:-1])
assert_array_almost_equal(tensor_fit.evals[0], evals)
assert_array_almost_equal(tensor_fit.quadratic_form[0], tensor,
err_msg=\
"Calculation of tensor from Y does not compare to analytical solution")
assert_almost_equal(tensor_fit.md[0], md)
assert_array_almost_equal(tensor_fit.mode, mode, decimal=5)
assert_equal(tensor_fit.directions.shape[-2], 1)
assert_equal(tensor_fit.directions.shape[-1], 3)
# Test error-handling:
assert_raises(ValueError,
dti.TensorModel,
gtab,
fit_method='crazy_method')
# Test multi-voxel data
data = np.zeros((3, Y.shape[1]))
# Normal voxel
data[0] = Y
# High diffusion voxel, all diffusing weighted signal equal to zero
data[1, gtab.b0s_mask] = b0
data[1, ~gtab.b0s_mask] = 0
# Masked voxel, all data set to zero
data[2] = 0.
tensor_model = dti.TensorModel(gtab)
fit = tensor_model.fit(data)
assert_array_almost_equal(fit[0].evals, evals)
# Evals should be high for high diffusion voxel
assert_(all(fit[1].evals > evals[0] * .9))
# Evals should be zero where data is masked
assert_array_almost_equal(fit[2].evals, 0.)