def test_odfdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
S, sticks = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
e1 = 15.0
e2 = 3.0
ratio = e2 / e1
csd = ConstrainedSDTModel(gtab, ratio, None)
csd_fit = csd.fit(S)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=10)
assert_equal(len(w) > 0, True)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=8)
assert_equal(len(w) > 0, False)
csd_fit = csd.fit(np.zeros_like(S))
fodf = csd_fit.odf(sphere)
assert_array_equal(fodf, np.zeros_like(fodf))
odf_sh = np.zeros_like(fodf)
odf_sh[1] = np.nan
fodf, it = odf_deconv(odf_sh, csd.R, csd.B_reg)
assert_array_equal(fodf, np.zeros_like(fodf))
def test_mapmri_odf(radial_order=6):
gtab = get_gtab_taiwan_dsi()
# load repulsion 724 sphere
sphere = default_sphere
# load icosahedron sphere
l1, l2, l3 = [0.0015, 0.0003, 0.0003]
data, golden_directions = generate_signal_crossing(gtab,
l1,
l2,
l3,
angle2=90)
mapmod = MapmriModel(gtab,
radial_order=radial_order,
laplacian_regularization=True,
laplacian_weighting=0.01)
# repulsion724
sphere2 = create_unit_sphere(5)
mapfit = mapmod.fit(data)
odf = mapfit.odf(sphere)
directions, _, _ = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
# 5 subdivisions
odf = mapfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
asmfit = mapmod.fit(data)
odf = asmfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
# for the isotropic implementation check if the odf spherical harmonics
# actually represent the discrete sphere function.
mapmod = MapmriModel(gtab,
radial_order=radial_order,
laplacian_regularization=True,
laplacian_weighting=0.01,
anisotropic_scaling=False)
mapfit = mapmod.fit(data)
odf = mapfit.odf(sphere)
odf_sh = mapfit.odf_sh()
odf_from_sh = sh_to_sf(odf_sh, sphere, radial_order, basis_type=None)
assert_almost_equal(odf, odf_from_sh, 10)
def test_odfdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
e1 = 15.0
e2 = 3.0
ratio = e2 / e1
csd = ConstrainedSDTModel(gtab, ratio, None)
csd_fit = csd.fit(S)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=10)
assert_equal(len(w) > 0, True)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=8)
assert_equal(len(w) > 0, False)
csd_fit = csd.fit(np.zeros_like(S))
fodf = csd_fit.odf(sphere)
assert_array_equal(fodf, np.zeros_like(fodf))
odf_sh = np.zeros_like(fodf)
odf_sh[1] = np.nan
fodf, it = odf_deconv(odf_sh, csd.R, csd.B_reg)
assert_array_equal(fodf, np.zeros_like(fodf))
def test_forecast_odf():
# check FORECAST fODF at different SH order
fm = ForecastModel(data.gtab,
sh_order=4,
dec_alg='CSD',
sphere=data.sphere)
f_fit = fm.fit(data.S)
sphere = default_sphere
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, data.sticks), 2, 1)
fm = ForecastModel(data.gtab,
sh_order=6,
dec_alg='CSD',
sphere=data.sphere)
f_fit = fm.fit(data.S)
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, data.sticks), 2, 1)
fm = ForecastModel(data.gtab,
sh_order=8,
dec_alg='CSD',
sphere=data.sphere)
f_fit = fm.fit(data.S)
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, data.sticks), 2, 1)
# stronger regularization is required for high order SH
fm = ForecastModel(data.gtab,
sh_order=10,
dec_alg='CSD',
sphere=sphere.vertices)
f_fit = fm.fit(data.S)
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, data.sticks), 2, 1)
fm = ForecastModel(data.gtab,
sh_order=12,
dec_alg='CSD',
sphere=sphere.vertices)
f_fit = fm.fit(data.S)
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, data.sticks), 2, 1)
def test_r2_term_odf_sharp():
SNR = None
S0 = 1
angle = 45 # 45 degrees is a very tight angle to disentangle
_, fbvals, fbvecs = get_data('small_64D') # get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
sphere = get_sphere('symmetric724')
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (angle, 0)]
S, sticks = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odfs_sh = sf_to_sh(odf_gt, sphere, sh_order=8, basis_type=None)
fodf_sh = odf_sh_to_sharp(odfs_sh,
sphere,
basis=None,
ratio=3 / 15.,
sh_order=8,
lambda_=1.,
tau=0.1,
r2_term=True)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
# This should pass as well
sdt_model = ConstrainedSDTModel(gtab, ratio=3 / 15., sh_order=8)
sdt_fit = sdt_model.fit(S)
fodf = sdt_fit.odf(sphere)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
def test_mapmri_odf(radial_order=6):
gtab = get_gtab_taiwan_dsi()
# load symmetric 724 sphere
sphere = get_sphere('symmetric724')
# load icosahedron sphere
l1, l2, l3 = [0.0015, 0.0003, 0.0003]
data, golden_directions = generate_signal_crossing(gtab, l1, l2, l3,
angle2=90)
mapmod = MapmriModel(gtab, radial_order=radial_order,
laplacian_regularization=True,
laplacian_weighting=0.01)
# symmetric724
sphere2 = create_unit_sphere(5)
mapfit = mapmod.fit(data)
odf = mapfit.odf(sphere)
directions, _, _ = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, golden_directions), 2, 1)
# 5 subdivisions
odf = mapfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, golden_directions), 2, 1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
asmfit = mapmod.fit(data)
odf = asmfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
# for the isotropic implementation check if the odf spherical harmonics
# actually represent the discrete sphere function.
mapmod = MapmriModel(gtab, radial_order=radial_order,
laplacian_regularization=True,
laplacian_weighting=0.01,
anisotropic_scaling=False)
mapfit = mapmod.fit(data)
odf = mapfit.odf(sphere)
odf_sh = mapfit.odf_sh()
odf_from_sh = sh_to_sf(odf_sh, sphere, radial_order, basis_type=None)
assert_almost_equal(odf, odf_from_sh, 10)
def test_shore_odf():
gtab = get_isbi2013_2shell_gtab()
# load repulsion 724 sphere
sphere = default_sphere
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
data, golden_directions = sticks_and_ball(gtab,
d=0.0015,
S0=100,
angles=[(0, 0), (90, 0)],
fractions=[50, 50],
snr=None)
asm = ShoreModel(gtab,
radial_order=6,
zeta=700,
lambdaN=1e-8,
lambdaL=1e-8)
# repulsion724
asmfit = asm.fit(data)
odf = asmfit.odf(sphere)
odf_sh = asmfit.odf_sh()
odf_from_sh = sh_to_sf(odf_sh, sphere, 6, basis_type=None, legacy=True)
npt.assert_almost_equal(odf, odf_from_sh, 10)
expected_phi = shore_matrix(radial_order=6, zeta=700, gtab=gtab)
npt.assert_array_almost_equal(np.dot(expected_phi, asmfit.shore_coeff),
asmfit.fitted_signal())
directions, _, _ = peak_directions(odf, sphere, .35, 25)
npt.assert_equal(len(directions), 2)
npt.assert_almost_equal(angular_similarity(directions, golden_directions),
2, 1)
# 5 subdivisions
odf = asmfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
npt.assert_equal(len(directions), 2)
npt.assert_almost_equal(angular_similarity(directions, golden_directions),
2, 1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
asmfit = asm.fit(data)
odf = asmfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
npt.assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
npt.assert_equal(gfa(odf) < 0.1, True)
def test_difference_with_minmax():
# Show difference with and without minmax normalization
# we create an odf here with 3 main peaks, 1 small sharp unwanted peak
# (noise) and an isotropic compartment.
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003], [0.0015, 0.00005, 0.00005],
[0.0015, 0.0015, 0.0015]])
angles = [(0, 0), (45, 0), (90, 0), (90, 90), (0, 0)]
fractions = [20, 20, 10, 1, 100 - 20 - 20 - 10 - 1]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
# We will show that when the minmax normalization is used we can remove
# the noisy peak using a lower threshold.
odf_gt_minmax = (odf_gt - odf_gt.min()) / (odf_gt.max() - odf_gt.min())
_, values_1, _ = peak_directions(odf_gt, sphere, .30, 25.)
assert_equal(len(values_1), 3)
_, values_2, _ = peak_directions(odf_gt_minmax, sphere, .30, 25.)
assert_equal(len(values_2), 3)
# Setting the smallest value of the odf to zero is like running
# peak_directions without the odf_min correction.
odf_gt[odf_gt.argmin()] = 0.
_, values_3, _ = peak_directions(
odf_gt,
sphere,
.30,
25.,
)
assert_equal(len(values_3), 4)
# we show here that to actually get that noisy peak out we need to
# increase the peak threshold considerably
directions, values_4, indices = peak_directions(
odf_gt,
sphere,
.60,
25.,
)
assert_equal(len(values_4), 3)
assert_almost_equal(values_1, values_4)
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_forecast_odf():
# check FORECAST fODF at different SH order
fm = ForecastModel(data.gtab, sh_order=4,
dec_alg='CSD', sphere=data.sphere)
f_fit = fm.fit(data.S)
sphere = get_sphere('repulsion724')
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, data.sticks), 2, 1)
fm = ForecastModel(data.gtab, sh_order=6,
dec_alg='CSD', sphere=data.sphere)
f_fit = fm.fit(data.S)
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, data.sticks), 2, 1)
fm = ForecastModel(data.gtab, sh_order=8,
dec_alg='CSD', sphere=data.sphere)
f_fit = fm.fit(data.S)
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, data.sticks), 2, 1)
# stronger regularization is required for high order SH
fm = ForecastModel(data.gtab, sh_order=10,
dec_alg='CSD', sphere=sphere.vertices)
f_fit = fm.fit(data.S)
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, data.sticks), 2, 1)
fm = ForecastModel(data.gtab, sh_order=12,
dec_alg='CSD', sphere=sphere.vertices)
f_fit = fm.fit(data.S)
fodf = f_fit.odf(sphere)
directions, _, _ = peak_directions(fodf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, data.sticks), 2, 1)
def test_shore_odf():
gtab = get_isbi2013_2shell_gtab()
# load symmetric 724 sphere
sphere = get_sphere('symmetric724')
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
data, golden_directions = SticksAndBall(gtab,
d=0.0015,
S0=100,
angles=[(0, 0), (90, 0)],
fractions=[50, 50],
snr=None)
asm = ShoreModel(gtab,
radial_order=6,
zeta=700,
lambdaN=1e-8,
lambdaL=1e-8)
# symmetric724
asmfit = asm.fit(data)
odf = asmfit.odf(sphere)
odf_sh = asmfit.odf_sh()
odf_from_sh = sh_to_sf(odf_sh, sphere, 6, basis_type=None)
assert_almost_equal(odf, odf_from_sh, 10)
directions, _, _ = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
# 5 subdivisions
odf = asmfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
asmfit = asm.fit(data)
odf = asmfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
def test_csd_superres():
""" Check the quality of csdfit with high SH order. """
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
# img, gtab = read_stanford_hardi()
evals = np.array([[1.5, .3, .3]]) * [[1.], [1.]] / 1000.
S, sticks = multi_tensor(gtab, evals, snr=None, fractions=[55., 45.])
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings(action="always",
message="Number of parameters required.*",
category=UserWarning)
model16 = ConstrainedSphericalDeconvModel(gtab, (evals[0], 3.),
sh_order=16)
assert_greater_equal(len(w), 1)
npt.assert_(issubclass(w[-1].category, UserWarning))
fit16 = model16.fit(S)
sphere = HemiSphere.from_sphere(get_sphere('symmetric724'))
# print local_maxima(fit16.odf(default_sphere), default_sphere.edges)
d, v, ind = peak_directions(fit16.odf(sphere), sphere,
relative_peak_threshold=.2,
min_separation_angle=0)
# Check that there are two peaks
assert_equal(len(d), 2)
# Check that peaks line up with sticks
cos_sim = abs((d * sticks).sum(1)) ** .5
assert_(all(cos_sim > .99))
def test_odf_sh_to_sharp():
SNR = None
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
S, _ = multi_tensor(gtab,
mevals,
S0,
angles=[(10, 0), (100, 0)],
fractions=[50, 50],
snr=SNR)
sphere = default_sphere
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
qb = QballModel(gtab, sh_order=8, assume_normed=True)
qbfit = qb.fit(S)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odf_gt = qbfit.odf(sphere)
Z = np.linalg.norm(odf_gt)
odfs_gt = np.zeros((3, 1, 1, odf_gt.shape[0]))
odfs_gt[:, :, :] = odf_gt[:]
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odfs_sh = sf_to_sh(odfs_gt, sphere, sh_order=8, basis_type=None)
odfs_sh /= Z
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
fodf_sh = odf_sh_to_sharp(odfs_sh,
sphere,
basis=None,
ratio=3 / 15.,
sh_order=8,
lambda_=1.,
tau=0.1)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions2, _, _ = peak_directions(fodf[0, 0, 0], sphere)
assert_equal(directions2.shape[0], 2)
def _peak_directions(self, blob):
"""Gets directions using parameters provided at init.
Blob can be any function defined on ``self.sphere``, ie an ODF, PMF,
FOD.
"""
return peak_directions(blob, self.sphere, **self._pf_kwargs)[0]
def _peak_directions(self, blob):
"""Gets directions using parameters provided at init.
Blob can be any function defined on ``self.sphere``, ie an ODF, PMF,
FOD.
"""
return peak_directions(blob, self.sphere, **self._pf_kwargs)[0]
def test_csd_superres():
""" Check the quality of csdfit with high SH order. """
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
# img, gtab = read_stanford_hardi()
evals = np.array([[1.5, .3, .3]]) * [[1.], [1.]] / 1000.
S, sticks = multi_tensor(gtab, evals, snr=None, fractions=[55., 45.])
model16 = ConstrainedSphericalDeconvModel(gtab, (evals[0], 3.),
sh_order=16)
fit16 = model16.fit(S)
# print local_maxima(fit16.odf(default_sphere), default_sphere.edges)
d, v, ind = peak_directions(fit16.odf(default_sphere),
default_sphere,
relative_peak_threshold=.2,
min_separation_angle=0)
# Check that there are two peaks
assert_equal(len(d), 2)
# Check that peaks line up with sticks
cos_sim = abs((d * sticks).sum(1))**.5
assert_(all(cos_sim > .99))
def test_single_voxel_fit(self):
signal, gtab, expected = make_fake_signal()
sphere = hemi_icosahedron.subdivide(4)
model = self.model(gtab, sh_order=4, min_signal=1e-5,
assume_normed=True)
fit = model.fit(signal)
odf = fit.odf(sphere)
assert_equal(odf.shape, sphere.phi.shape)
directions, _, _ = peak_directions(odf, sphere)
# Check the same number of directions
n = len(expected)
assert_equal(len(directions), n)
# Check directions are unit vectors
cos_similarity = (directions * directions).sum(-1)
assert_array_almost_equal(cos_similarity, np.ones(n))
# Check the directions == expected or -expected
cos_similarity = (directions * expected).sum(-1)
assert_array_almost_equal(abs(cos_similarity), np.ones(n))
# Test normalize data
model = self.model(gtab, sh_order=4, min_signal=1e-5,
assume_normed=False)
fit = model.fit(signal * 5)
odf_with_norm = fit.odf(sphere)
assert_array_almost_equal(odf, odf_with_norm)
def test_single_voxel_fit(self):
signal, gtab, expected = make_fake_signal()
sphere = hemi_icosahedron.subdivide(4)
model = self.model(gtab,
sh_order=4,
min_signal=1e-5,
assume_normed=True)
fit = model.fit(signal)
odf = fit.odf(sphere)
assert_equal(odf.shape, sphere.phi.shape)
directions, _, _ = peak_directions(odf, sphere)
# Check the same number of directions
n = len(expected)
assert_equal(len(directions), n)
# Check directions are unit vectors
cos_similarity = (directions * directions).sum(-1)
assert_array_almost_equal(cos_similarity, np.ones(n))
# Check the directions == expected or -expected
cos_similarity = (directions * expected).sum(-1)
assert_array_almost_equal(abs(cos_similarity), np.ones(n))
# Test normalize data
model = self.model(gtab,
sh_order=4,
min_signal=1e-5,
assume_normed=False)
fit = model.fit(signal * 5)
odf_with_norm = fit.odf(sphere)
assert_array_almost_equal(odf, odf_with_norm)
def test_csd_superres():
""" Check the quality of csdfit with high SH order. """
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
# img, gtab = read_stanford_hardi()
evals = np.array([[1.5, .3, .3]]) * [[1.], [1.]] / 1000.
S, sticks = multi_tensor(gtab, evals, snr=None, fractions=[55., 45.])
model16 = ConstrainedSphericalDeconvModel(gtab, (evals[0], 3.),
sh_order=16)
fit16 = model16.fit(S)
# print local_maxima(fit16.odf(default_sphere), default_sphere.edges)
d, v, ind = peak_directions(fit16.odf(default_sphere), default_sphere,
relative_peak_threshold=.2,
min_separation_angle=0)
# Check that there are two peaks
assert_equal(len(d), 2)
# Check that peaks line up with sticks
cos_sim = abs((d * sticks).sum(1)) ** .5
assert_(all(cos_sim > .99))
def test_dsi():
# load repulsion 724 sphere
sphere = default_sphere
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
btable = np.loadtxt(get_fnames('dsi515btable'))
gtab = gradient_table(btable[:, 0], btable[:, 1:])
data, golden_directions = sticks_and_ball(gtab,
d=0.0015,
S0=100,
angles=[(0, 0), (90, 0)],
fractions=[50, 50],
snr=None)
ds = DiffusionSpectrumDeconvModel(gtab)
# repulsion724
dsfit = ds.fit(data)
odf = dsfit.odf(sphere)
directions, _, _ = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
# 5 subdivisions
dsfit = ds.fit(data)
odf2 = dsfit.odf(sphere2)
directions, _, _ = peak_directions(odf2, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
assert_equal(dsfit.pdf().shape, 3 * (ds.qgrid_size, ))
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
odf = ds.fit(data).odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
assert_raises(ValueError,
DiffusionSpectrumDeconvModel,
gtab,
qgrid_size=16)
def test_single_voxel_fit(self):
signal, gtab, expected = make_fake_signal()
sphere = hemi_icosahedron.subdivide(4)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
model = self.model(gtab,
sh_order=4,
min_signal=1e-5,
assume_normed=True)
fit = model.fit(signal)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odf = fit.odf(sphere)
assert_equal(odf.shape, sphere.phi.shape)
directions, _, _ = peak_directions(odf, sphere)
# Check the same number of directions
n = len(expected)
assert_equal(len(directions), n)
# Check directions are unit vectors
cos_similarity = (directions * directions).sum(-1)
assert_array_almost_equal(cos_similarity, np.ones(n))
# Check the directions == expected or -expected
cos_similarity = (directions * expected).sum(-1)
assert_array_almost_equal(abs(cos_similarity), np.ones(n))
# Test normalize data
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
model = self.model(gtab,
sh_order=4,
min_signal=1e-5,
assume_normed=False)
fit = model.fit(signal * 5)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odf_with_norm = fit.odf(sphere)
assert_array_almost_equal(odf, odf_with_norm)
def test_shore_odf():
gtab = get_isbi2013_2shell_gtab()
# load symmetric 724 sphere
sphere = get_sphere('symmetric724')
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
data, golden_directions = SticksAndBall(gtab, d=0.0015,
S0=100, angles=[(0, 0), (90, 0)],
fractions=[50, 50], snr=None)
asm = ShoreModel(gtab, radial_order=6,
zeta=700, lambdaN=1e-8, lambdaL=1e-8)
# symmetric724
asmfit = asm.fit(data)
odf = asmfit.odf(sphere)
odf_sh = asmfit.odf_sh()
odf_from_sh = sh_to_sf(odf_sh, sphere, 6, basis_type=None)
assert_almost_equal(odf, odf_from_sh, 10)
directions, _ , _ = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, golden_directions), 2, 1)
# 5 subdivisions
odf = asmfit.odf(sphere2)
directions, _ , _ = peak_directions(odf, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, golden_directions), 2, 1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
asmfit = asm.fit(data)
odf = asmfit.odf(sphere2)
directions, _ , _ = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
def test_dsi():
# load symmetric 724 sphere
sphere = get_sphere('symmetric724')
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
btable = np.loadtxt(get_data('dsi515btable'))
gtab = gradient_table(btable[:, 0], btable[:, 1:])
data, golden_directions = SticksAndBall(gtab, d=0.0015,
S0=100, angles=[(0, 0), (90, 0)],
fractions=[50, 50], snr=None)
ds = DiffusionSpectrumModel(gtab)
# symmetric724
dsfit = ds.fit(data)
odf = dsfit.odf(sphere)
directions, _, _ = peak_directions(odf, sphere)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions),
2, 1)
# 5 subdivisions
dsfit = ds.fit(data)
odf2 = dsfit.odf(sphere2)
directions, _, _ = peak_directions(odf2, sphere2)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions),
2, 1)
assert_equal(dsfit.pdf().shape, 3 * (ds.qgrid_size, ))
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
odf = ds.fit(data).odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
assert_raises(ValueError, DiffusionSpectrumModel, gtab, qgrid_size=16)
def get_maximas(data,
sphere,
b_matrix,
threshold,
absolute_threshold,
min_separation_angle=25):
spherical_func = np.dot(data, b_matrix.T)
spherical_func[np.nonzero(spherical_func < absolute_threshold)] = 0.
return peak_directions(spherical_func, sphere, threshold,
min_separation_angle)
def test_r2_term_odf_sharp():
SNR = None
S0 = 1
angle = 45 # 45 degrees is a very tight angle to disentangle
_, fbvals, fbvecs = get_data('small_64D') # get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
sphere = get_sphere('symmetric724')
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (angle, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odfs_sh = sf_to_sh(odf_gt, sphere, sh_order=8, basis_type=None)
fodf_sh = odf_sh_to_sharp(odfs_sh, sphere, basis=None, ratio=3 / 15.,
sh_order=8, lambda_=1., tau=0.1, r2_term=True)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
# This should pass as well
sdt_model = ConstrainedSDTModel(gtab, ratio=3/15., sh_order=8)
sdt_fit = sdt_model.fit(S)
fodf = sdt_fit.odf(sphere)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
def test_gqi():
# load symmetric 724 sphere
sphere = get_sphere('symmetric724')
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
btable = np.loadtxt(get_fnames('dsi515btable'))
bvals = btable[:, 0]
bvecs = btable[:, 1:]
gtab = gradient_table(bvals, bvecs)
data, golden_directions = SticksAndBall(gtab,
d=0.0015,
S0=100,
angles=[(0, 0), (90, 0)],
fractions=[50, 50],
snr=None)
gq = GeneralizedQSamplingModel(gtab, method='gqi2', sampling_length=1.4)
# symmetric724
gqfit = gq.fit(data)
odf = gqfit.odf(sphere)
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
# 5 subdivisions
gqfit = gq.fit(data)
odf2 = gqfit.odf(sphere2)
directions, values, indices = peak_directions(odf2, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
odf = gq.fit(data).odf(sphere2)
directions, values, indices = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
def test_mapmri_odf():
gtab = get_3shell_gtab()
# load symmetric 724 sphere
sphere = get_sphere('symmetric724')
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
evals = np.array(([0.0017, 0.0003, 0.0003], [0.0017, 0.0003, 0.0003]))
data, golden_directions = MultiTensor(gtab,
evals,
S0=1.0,
angles=[(0, 0), (90, 0)],
fractions=[50, 50],
snr=None)
map_model = MapmriModel(gtab, radial_order=4)
# symmetric724
mapfit = map_model.fit(data)
odf = mapfit.odf(sphere)
directions, _, _ = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
# 5 subdivisions
odf = mapfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
mapfit = map_model.fit(data)
odf = mapfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
def test_difference_with_minmax():
# Show difference with and without minmax normalization
# we create an odf here with 3 main peaks, 1 small sharp unwanted peak
# (noise) and an isotropic compartment.
mevals = np.array([[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.00005, 0.00005],
[0.0015, 0.0015, 0.0015]])
angles = [(0, 0), (45, 0), (90, 0), (90, 90), (0, 0)]
fractions = [20, 20, 10, 1, 100 - 20 - 20 - 10 - 1]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions,
100, None)
# We will show that when the minmax normalization is used we can remove
# the noisy peak using a lower threshold.
odf_gt_minmax = (odf_gt - odf_gt.min()) / (odf_gt.max() - odf_gt.min())
_, values_1, _ = peak_directions(odf_gt, sphere, .30, 25.)
assert_equal(len(values_1), 3)
_, values_2, _ = peak_directions(odf_gt_minmax, sphere, .30, 25.)
assert_equal(len(values_2), 3)
# Setting the smallest value of the odf to zero is like running
# peak_directions without the odf_min correction.
odf_gt[odf_gt.argmin()] = 0.
_, values_3, _ = peak_directions(odf_gt, sphere, .30, 25.,)
assert_equal(len(values_3), 4)
# we show here that to actually get that noisy peak out we need to
# increase the peak threshold considerably
directions, values_4, indices = peak_directions(odf_gt, sphere, .60, 25.,)
assert_equal(len(values_4), 3)
assert_almost_equal(values_1, values_4)
def test_peak_directions():
model = SimpleOdfModel(_gtab)
fit = model.fit(None)
odf = fit.odf()
argmax = odf.argmax()
mx = odf.max()
sphere = fit.model.sphere
# Only one peak
dir, val, ind = peak_directions(odf, sphere, .5, 45)
dir_e = sphere.vertices[[argmax]]
assert_array_equal(ind, [argmax])
assert_array_equal(val, odf[ind])
assert_array_equal(dir, dir_e)
odf[0] = mx * .9
# Two peaks, relative_threshold
dir, val, ind = peak_directions(odf, sphere, 1., 0)
dir_e = sphere.vertices[[argmax]]
assert_array_equal(dir, dir_e)
assert_array_equal(ind, [argmax])
assert_array_equal(val, odf[ind])
dir, val, ind = peak_directions(odf, sphere, .8, 0)
dir_e = sphere.vertices[[argmax, 0]]
assert_array_equal(dir, dir_e)
assert_array_equal(ind, [argmax, 0])
assert_array_equal(val, odf[ind])
# Two peaks, angle_sep
dir, val, ind = peak_directions(odf, sphere, 0., 90)
dir_e = sphere.vertices[[argmax]]
assert_array_equal(dir, dir_e)
assert_array_equal(ind, [argmax])
assert_array_equal(val, odf[ind])
dir, val, ind = peak_directions(odf, sphere, 0., 0)
dir_e = sphere.vertices[[argmax, 0]]
assert_array_equal(dir, dir_e)
assert_array_equal(ind, [argmax, 0])
assert_array_equal(val, odf[ind])
def test_peak_directions():
model = SimpleOdfModel(_gtab)
fit = model.fit(None)
odf = fit.odf()
argmax = odf.argmax()
mx = odf.max()
sphere = fit.model.sphere
# Only one peak
dir, val, ind = peak_directions(odf, sphere, .5, 45)
dir_e = sphere.vertices[[argmax]]
assert_array_equal(ind, [argmax])
assert_array_equal(val, odf[ind])
assert_array_equal(dir, dir_e)
odf[0] = mx * .9
# Two peaks, relative_threshold
dir, val, ind = peak_directions(odf, sphere, 1., 0)
dir_e = sphere.vertices[[argmax]]
assert_array_equal(dir, dir_e)
assert_array_equal(ind, [argmax])
assert_array_equal(val, odf[ind])
dir, val, ind = peak_directions(odf, sphere, .8, 0)
dir_e = sphere.vertices[[argmax, 0]]
assert_array_equal(dir, dir_e)
assert_array_equal(ind, [argmax, 0])
assert_array_equal(val, odf[ind])
# Two peaks, angle_sep
dir, val, ind = peak_directions(odf, sphere, 0., 90)
dir_e = sphere.vertices[[argmax]]
assert_array_equal(dir, dir_e)
assert_array_equal(ind, [argmax])
assert_array_equal(val, odf[ind])
dir, val, ind = peak_directions(odf, sphere, 0., 0)
dir_e = sphere.vertices[[argmax, 0]]
assert_array_equal(dir, dir_e)
assert_array_equal(ind, [argmax, 0])
assert_array_equal(val, odf[ind])
def test_mapmri_odf():
gtab = get_3shell_gtab()
# load symmetric 724 sphere
sphere = get_sphere('symmetric724')
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
evals = np.array(([0.0017, 0.0003, 0.0003],
[0.0017, 0.0003, 0.0003]))
data, golden_directions = MultiTensor(
gtab, evals, S0=1.0, angles=[(0, 0), (90, 0)], fractions=[50, 50],
snr=None)
map_model = MapmriModel(gtab, radial_order=4)
# symmetric724
mapfit = map_model.fit(data)
odf = mapfit.odf(sphere)
directions, _, _ = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, golden_directions), 2, 1)
# 5 subdivisions
odf = mapfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(
angular_similarity(directions, golden_directions), 2, 1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
mapfit = map_model.fit(data)
odf = mapfit.odf(sphere2)
directions, _, _ = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
def test_gqi():
# load symmetric 724 sphere
sphere = get_sphere('symmetric724')
# load icosahedron sphere
sphere2 = create_unit_sphere(5)
btable = np.loadtxt(get_fnames('dsi515btable'))
bvals = btable[:, 0]
bvecs = btable[:, 1:]
gtab = gradient_table(bvals, bvecs)
data, golden_directions = SticksAndBall(gtab, d=0.0015,
S0=100, angles=[(0, 0), (90, 0)],
fractions=[50, 50], snr=None)
gq = GeneralizedQSamplingModel(gtab, method='gqi2', sampling_length=1.4)
# symmetric724
gqfit = gq.fit(data)
odf = gqfit.odf(sphere)
directions, values, indices = peak_directions(odf, sphere, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
# 5 subdivisions
gqfit = gq.fit(data)
odf2 = gqfit.odf(sphere2)
directions, values, indices = peak_directions(odf2, sphere2, .35, 25)
assert_equal(len(directions), 2)
assert_almost_equal(angular_similarity(directions, golden_directions), 2,
1)
sb_dummies = sticks_and_ball_dummies(gtab)
for sbd in sb_dummies:
data, golden_directions = sb_dummies[sbd]
odf = gq.fit(data).odf(sphere2)
directions, values, indices = peak_directions(odf, sphere2, .35, 25)
if len(directions) <= 3:
assert_equal(len(directions), len(golden_directions))
if len(directions) > 3:
assert_equal(gfa(odf) < 0.1, True)
def test_odf_sh_to_sharp():
SNR = None
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
S, sticks = multi_tensor(gtab,
mevals,
S0,
angles=[(10, 0), (100, 0)],
fractions=[50, 50],
snr=SNR)
sphere = get_sphere('symmetric724')
qb = QballModel(gtab, sh_order=8, assume_normed=True)
qbfit = qb.fit(S)
odf_gt = qbfit.odf(sphere)
Z = np.linalg.norm(odf_gt)
odfs_gt = np.zeros((3, 1, 1, odf_gt.shape[0]))
odfs_gt[:, :, :] = odf_gt[:]
odfs_sh = sf_to_sh(odfs_gt, sphere, sh_order=8, basis_type=None)
odfs_sh /= Z
fodf_sh = odf_sh_to_sharp(odfs_sh,
sphere,
basis=None,
ratio=3 / 15.,
sh_order=8,
lambda_=1.,
tau=0.1)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions2, _, _ = peak_directions(fodf[0, 0, 0], sphere)
assert_equal(directions2.shape[0], 2)
def test_degenerative_cases():
sphere = get_sphere('symmetric724')
# completely isotropic and degencase
odf = np.zeros(sphere.vertices.shape[0])
directions, values, indices = peak_directions(odf, sphere, .5, 25)
print(directions, values, indices)
assert_equal(len(values), 0)
assert_equal(len(directions), 0)
assert_equal(len(indices), 0)
odf = np.zeros(sphere.vertices.shape[0])
odf[0] = 0.020
odf[1] = 0.018
directions, values, indices = peak_directions(odf, sphere, .5, 25)
print(directions, values, indices)
assert_equal(values[0], 0.02)
odf = -np.ones(sphere.vertices.shape[0])
directions, values, indices = peak_directions(odf, sphere, .5, 25)
print(directions, values, indices)
assert_equal(len(values), 0)
odf = np.zeros(sphere.vertices.shape[0])
odf[0] = 0.020
odf[1] = 0.018
odf[2] = -0.018
directions, values, indices = peak_directions(odf, sphere, .5, 25)
assert_equal(values[0], 0.02)
odf = np.ones(sphere.vertices.shape[0])
odf += 0.1 * np.random.rand(odf.shape[0])
directions, values, indices = peak_directions(odf, sphere, .5, 25)
assert_(all(values > values[0] * .5))
assert_array_equal(values, odf[indices])
odf = np.ones(sphere.vertices.shape[0])
odf[1:] = np.finfo(np.float).eps * np.random.rand(odf.shape[0] - 1)
directions, values, indices = peak_directions(odf, sphere, .5, 25)
assert_equal(values[0], 1)
assert_equal(len(values), 1)
def test_degenerative_cases():
sphere = get_sphere('symmetric724')
# completely isotropic and degencase
odf = np.zeros(sphere.vertices.shape[0])
directions, values, indices = peak_directions(odf, sphere, .5, 25)
print(directions, values, indices)
assert_equal(len(values), 0)
assert_equal(len(directions), 0)
assert_equal(len(indices), 0)
odf = np.zeros(sphere.vertices.shape[0])
odf[0] = 0.020
odf[1] = 0.018
directions, values, indices = peak_directions(odf, sphere, .5, 25)
print(directions, values, indices)
assert_equal(values[0], 0.02)
odf = - np.ones(sphere.vertices.shape[0])
directions, values, indices = peak_directions(odf, sphere, .5, 25)
print(directions, values, indices)
assert_equal(len(values), 0)
odf = np.zeros(sphere.vertices.shape[0])
odf[0] = 0.020
odf[1] = 0.018
odf[2] = - 0.018
directions, values, indices = peak_directions(odf, sphere, .5, 25)
assert_equal(values[0], 0.02)
odf = np.ones(sphere.vertices.shape[0])
odf += 0.1 * np.random.rand(odf.shape[0])
directions, values, indices = peak_directions(odf, sphere, .5, 25)
assert_(all(values > values[0] * .5))
assert_array_equal(values, odf[indices])
odf = np.ones(sphere.vertices.shape[0])
odf[1:] = np.finfo(np.float).eps * np.random.rand(odf.shape[0] - 1)
directions, values, indices = peak_directions(odf, sphere, .5, 25)
assert_equal(values[0], 1)
assert_equal(len(values), 1)
def compute_peaks(odfs,
sphere,
relative_peak_threshold=.5,
peak_normalize=1,
min_separation_angle=45,
max_peak_number=5):
if odfs.shape[0] == sphere.vertices.shape[0]:
odfs = np.array(odfs.reshape(odfs.shape[0], -1).T, order='C')
num_peak_coeffs = max_peak_number * 3
peaks = np.zeros(odfs.shape[:-1] + (num_peak_coeffs, ))
for index in ndindex(odfs.shape[:-1]):
vox_peaks, values, _ = peak_directions(odfs[index], sphere,
float(relative_peak_threshold),
float(min_separation_angle))
if peak_normalize == 1:
values /= values[0]
vox_peaks = vox_peaks * values[:, None]
vox_peaks = vox_peaks.ravel()
m = vox_peaks.shape[0]
if m > num_peak_coeffs:
m = num_peak_coeffs
peaks[index][:m] = vox_peaks[:m]
return peaks
def peaks_from_sh_parallel(args):
shm_coeff = args[0]
B = args[1]
sphere = args[2]
relative_peak_threshold = args[3]
absolute_threshold = args[4]
min_separation_angle = args[5]
npeaks = args[6]
normalize_peaks = args[7]
chunk_id = args[8]
data_shape = shm_coeff.shape[0]
peak_dirs = np.zeros((data_shape, npeaks, 3))
peak_values = np.zeros((data_shape, npeaks))
peak_indices = np.zeros((data_shape, npeaks), dtype='int')
peak_indices.fill(-1)
for idx in range(len(shm_coeff)):
if shm_coeff[idx].any():
odf = np.dot(shm_coeff[idx], B)
odf[odf < absolute_threshold] = 0.
dirs, peaks, ind = peak_directions(odf, sphere,
relative_peak_threshold,
min_separation_angle)
if peaks.shape[0] != 0:
n = min(npeaks, peaks.shape[0])
peak_dirs[idx][:n] = dirs[:n]
peak_indices[idx][:n] = ind[:n]
peak_values[idx][:n] = peaks[:n]
if normalize_peaks:
peak_values[idx][:n] /= peaks[0]
peak_dirs[idx] *= peak_values[idx][:, None]
return chunk_id, peak_dirs, peak_values, peak_indices
def test_odf_sh_to_sharp():
SNR = None
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
S, sticks = multi_tensor(gtab, mevals, S0, angles=[(10, 0), (100, 0)],
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric724')
qb = QballModel(gtab, sh_order=8, assume_normed=True)
qbfit = qb.fit(S)
odf_gt = qbfit.odf(sphere)
Z = np.linalg.norm(odf_gt)
odfs_gt = np.zeros((3, 1, 1, odf_gt.shape[0]))
odfs_gt[:, :, :] = odf_gt[:]
odfs_sh = sf_to_sh(odfs_gt, sphere, sh_order=8, basis_type=None)
odfs_sh /= Z
fodf_sh = odf_sh_to_sharp(odfs_sh, sphere, basis=None, ratio=3 / 15.,
sh_order=8, lambda_=1., tau=0.1)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions2, _, _ = peak_directions(fodf[0, 0, 0], sphere)
assert_equal(directions2.shape[0], 2)
def test_csdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
response = (np.array([0.0015, 0.0003, 0.0003]), S0)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(S)
assert_equal(csd_fit.shm_coeff[0] > 0, True)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
ConstrainedSphericalDeconvModel(gtab, response, sh_order=10)
assert_equal(len(w) > 0, True)
with warnings.catch_warnings(record=True) as w:
ConstrainedSphericalDeconvModel(gtab, response, sh_order=8)
assert_equal(len(w) > 0, False)
mevecs = []
for s in sticks:
mevecs += [all_tensor_evecs(s).T]
S2 = single_tensor(gtab, 100, mevals[0], mevecs[0], snr=None)
big_S = np.zeros((10, 10, 10, len(S2)))
big_S[:] = S2
aresponse, aratio = auto_response(gtab,
big_S,
roi_center=(5, 5, 4),
roi_radius=3,
fa_thr=0.5)
assert_array_almost_equal(aresponse[0], response[0])
assert_almost_equal(aresponse[1], 100)
assert_almost_equal(aratio, response[0][1] / response[0][0])
aresponse2, aratio2 = auto_response(gtab, big_S, roi_radius=3, fa_thr=0.5)
assert_array_almost_equal(aresponse[0], response[0])
_, _, nvoxels = auto_response(gtab,
big_S,
roi_center=(5, 5, 4),
roi_radius=30,
fa_thr=0.5,
return_number_of_voxels=True)
assert_equal(nvoxels, 1000)
_, _, nvoxels = auto_response(gtab,
big_S,
roi_center=(5, 5, 4),
roi_radius=30,
fa_thr=1,
return_number_of_voxels=True)
assert_equal(nvoxels, 0)
def test_peak_directions_thorough():
# two equal fibers (creating a very sharp odf)
mevals = np.array([[0.0025, 0.0003, 0.0003],
[0.0025, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0)]
fractions = [50, 50]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions,
100, None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# two unequal fibers
fractions = [75, 25]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions,
100, None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 1, 2)
directions, values, indices = peak_directions(odf_gt, sphere, .20, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# two equal fibers short angle (simulating very sharp ODF)
mevals = np.array(([0.0045, 0.0003, 0.0003],
[0.0045, 0.0003, 0.0003]))
fractions = [50, 50]
angles = [(0, 0), (20, 0)]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles,
fractions, 100, None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 1, 2)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 15.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# 1 fiber
mevals = np.array([[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
fractions = [50, 50]
angles = [(15, 0), (15, 0)]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles,
fractions, 100, None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 15.)
assert_almost_equal(angular_similarity(directions, sticks), 1, 2)
AE = np.rad2deg(np.arccos(np.dot(directions[0], sticks[0])))
assert_(abs(AE) < 2. or abs(AE - 180) < 2.)
# two equal fibers and one small noisy one
mevals = np.array([[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (90, 0)]
fractions = [45, 45, 10]
odf_gt, sticks, sphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# two equal fibers and one faulty
mevals = np.array([[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (60, 0)]
fractions = [45, 45, 10]
odf_gt, sticks, sphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# two equal fibers and one very very annoying one
mevals = np.array([[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (60, 0)]
fractions = [40, 40, 20]
odf_gt, sticks, sphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# three peaks and one faulty
mevals = np.array([[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (90, 0), (90, 45)]
fractions = [35, 35, 20, 10]
odf_gt, sticks, sphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 3, 2)
# four peaks
mevals = np.array([[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (90, 0), (90, 45)]
fractions = [25, 25, 25, 25]
odf_gt, sticks, sphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .15, 5.)
assert_almost_equal(angular_similarity(directions, sticks), 4, 2)
# four difficult peaks
mevals = np.array([[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (90, 0), (90, 45)]
fractions = [30, 30, 20, 20]
odf_gt, sticks, sphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, 0, 0)
assert_almost_equal(angular_similarity(directions, sticks), 4, 1)
odf_gt, sticks, hsphere = _create_mt_sim(mevals, angles, fractions,
100, None, half_sphere=True)
directions, values, indices = peak_directions(odf_gt, hsphere, 0, 0)
assert_equal(angular_similarity(directions, sticks) < 4, True)
# four peaks and one them quite small
fractions = [35, 35, 20, 10]
odf_gt, sticks, sphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, 0, 0)
assert_equal(angular_similarity(directions, sticks) < 4, True)
odf_gt, sticks, hsphere = _create_mt_sim(mevals, angles, fractions,
100, None, half_sphere=True)
directions, values, indices = peak_directions(odf_gt, hsphere, 0, 0)
assert_equal(angular_similarity(directions, sticks) < 4, True)
# isotropic case
mevals = np.array([[0.0015, 0.0015, 0.0015]])
angles = [(0, 0)]
fractions = [100.]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions,
100, None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_equal(len(values) > 10, True)
def test_peak_directions_thorough():
# two equal fibers (creating a very sharp odf)
mevals = np.array([[0.0025, 0.0003, 0.0003], [0.0025, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0)]
fractions = [50, 50]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# two unequal fibers
fractions = [75, 25]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 1, 2)
directions, values, indices = peak_directions(odf_gt, sphere, .20, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# two equal fibers short angle (simulating very sharp ODF)
mevals = np.array(([0.0045, 0.0003, 0.0003], [0.0045, 0.0003, 0.0003]))
fractions = [50, 50]
angles = [(0, 0), (20, 0)]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 1, 2)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 15.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# 1 fiber
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]])
fractions = [50, 50]
angles = [(15, 0), (15, 0)]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 15.)
assert_almost_equal(angular_similarity(directions, sticks), 1, 2)
AE = np.rad2deg(np.arccos(np.dot(directions[0], sticks[0])))
assert_(abs(AE) < 2. or abs(AE - 180) < 2.)
# two equal fibers and one small noisy one
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (90, 0)]
fractions = [45, 45, 10]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# two equal fibers and one faulty
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (60, 0)]
fractions = [45, 45, 10]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# two equal fibers and one very very annoying one
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (60, 0)]
fractions = [40, 40, 20]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 2, 2)
# three peaks and one faulty
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (90, 0), (90, 45)]
fractions = [35, 35, 20, 10]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_almost_equal(angular_similarity(directions, sticks), 3, 2)
# four peaks
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (90, 0), (90, 45)]
fractions = [25, 25, 25, 25]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .15, 5.)
assert_almost_equal(angular_similarity(directions, sticks), 4, 2)
# four difficult peaks
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (45, 0), (90, 0), (90, 45)]
fractions = [30, 30, 20, 20]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, 0, 0)
assert_almost_equal(angular_similarity(directions, sticks), 4, 1)
odf_gt, sticks, hsphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None,
half_sphere=True)
directions, values, indices = peak_directions(odf_gt, hsphere, 0, 0)
assert_equal(angular_similarity(directions, sticks) < 4, True)
# four peaks and one them quite small
fractions = [35, 35, 20, 10]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, 0, 0)
assert_equal(angular_similarity(directions, sticks) < 4, True)
odf_gt, sticks, hsphere = _create_mt_sim(mevals,
angles,
fractions,
100,
None,
half_sphere=True)
directions, values, indices = peak_directions(odf_gt, hsphere, 0, 0)
assert_equal(angular_similarity(directions, sticks) < 4, True)
# isotropic case
mevals = np.array([[0.0015, 0.0015, 0.0015]])
angles = [(0, 0)]
fractions = [100.]
odf_gt, sticks, sphere = _create_mt_sim(mevals, angles, fractions, 100,
None)
directions, values, indices = peak_directions(odf_gt, sphere, .5, 25.)
assert_equal(len(values) > 10, True)
def test_csdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs, b0_threshold=0)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
response = (np.array([0.0015, 0.0003, 0.0003]), S0)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(S)
assert_equal(csd_fit.shm_coeff[0] > 0, True)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=UserWarning)
_ = ConstrainedSphericalDeconvModel(gtab, response, sh_order=10)
assert_greater(len([lw for lw in w if issubclass(lw.category,
UserWarning)]), 0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=UserWarning)
ConstrainedSphericalDeconvModel(gtab, response, sh_order=8)
assert_equal(len([lw for lw in w if issubclass(lw.category,
UserWarning)]), 0)
mevecs = []
for s in sticks:
mevecs += [all_tensor_evecs(s).T]
S2 = single_tensor(gtab, 100, mevals[0], mevecs[0], snr=None)
big_S = np.zeros((10, 10, 10, len(S2)))
big_S[:] = S2
aresponse, aratio = auto_response_ssst(gtab, big_S, roi_center=(5, 5, 4),
roi_radii=3, fa_thr=0.5)
assert_array_almost_equal(aresponse[0], response[0])
assert_almost_equal(aresponse[1], 100)
assert_almost_equal(aratio, response[0][1] / response[0][0])
auto_response_ssst(gtab, big_S, roi_radii=3, fa_thr=0.5)
assert_array_almost_equal(aresponse[0], response[0])
def test_recursive_response_calibration():
"""
Test the recursive response calibration method.
"""
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
sphere = default_sphere
gtab = gradient_table(bvals, bvecs)
evals = np.array([0.0015, 0.0003, 0.0003])
evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
where_dwi = lazy_index(~gtab.b0s_mask)
S_cross, _ = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
S_single = single_tensor(gtab, S0, evals, evecs, snr=SNR)
data = np.concatenate((np.tile(S_cross, (8, 1)), np.tile(S_single,
(2, 1))),
axis=0)
odf_gt_cross = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odf_gt_single = single_tensor_odf(sphere.vertices, evals, evecs)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
response = recursive_response(gtab,
data,
mask=None,
sh_order=8,
peak_thr=0.01,
init_fa=0.05,
init_trace=0.0021,
iter=8,
convergence=0.001,
parallel=False)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(data)
assert_equal(np.all(csd_fit.shm_coeff[:, 0] >= 0), True)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
fodf = csd_fit.odf(sphere)
directions_gt_single, _, _ = peak_directions(odf_gt_single, sphere)
directions_gt_cross, _, _ = peak_directions(odf_gt_cross, sphere)
directions_single, _, _ = peak_directions(fodf[8, :], sphere)
directions_cross, _, _ = peak_directions(fodf[0, :], sphere)
ang_sim = angular_similarity(directions_cross, directions_gt_cross)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions_cross.shape[0], 2)
assert_equal(directions_gt_cross.shape[0], 2)
ang_sim = angular_similarity(directions_single, directions_gt_single)
assert_equal(ang_sim > 0.9, True)
assert_equal(directions_single.shape[0], 1)
assert_equal(directions_gt_single.shape[0], 1)
with warnings.catch_warnings(record=True) as w:
sphere = Sphere(xyz=gtab.gradients[where_dwi])
npt.assert_equal(len(w), 1)
npt.assert_(issubclass(w[0].category, UserWarning))
npt.assert_("Vertices are not on the unit sphere" in str(w[0].message))
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
sf = response.on_sphere(sphere)
S = np.concatenate(([response.S0], sf))
tenmodel = TensorModel(gtab, min_signal=0.001)
tenfit = tenmodel.fit(S)
FA = fractional_anisotropy(tenfit.evals)
FA_gt = fractional_anisotropy(evals)
assert_almost_equal(FA, FA_gt, 1)
def test_csdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
response = (np.array([0.0015, 0.0003, 0.0003]), S0)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(S)
assert_equal(csd_fit.shm_coeff[0] > 0, True)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
ConstrainedSphericalDeconvModel(gtab, response, sh_order=10)
assert_equal(len(w) > 0, True)
with warnings.catch_warnings(record=True) as w:
ConstrainedSphericalDeconvModel(gtab, response, sh_order=8)
assert_equal(len(w) > 0, False)
mevecs = []
for s in sticks:
mevecs += [all_tensor_evecs(s).T]
S2 = single_tensor(gtab, 100, mevals[0], mevecs[0], snr=None)
big_S = np.zeros((10, 10, 10, len(S2)))
big_S[:] = S2
aresponse, aratio = auto_response(gtab, big_S, roi_center=(5, 5, 4),
roi_radius=3, fa_thr=0.5)
assert_array_almost_equal(aresponse[0], response[0])
assert_almost_equal(aresponse[1], 100)
assert_almost_equal(aratio, response[0][1] / response[0][0])
aresponse2, aratio2 = auto_response(gtab, big_S, roi_radius=3, fa_thr=0.5)
assert_array_almost_equal(aresponse[0], response[0])
_, _, nvoxels = auto_response(gtab, big_S, roi_center=(5, 5, 4),
roi_radius=30, fa_thr=0.5,
return_number_of_voxels=True)
assert_equal(nvoxels, 1000)
_, _, nvoxels = auto_response(gtab, big_S, roi_center=(5, 5, 4),
roi_radius=30, fa_thr=1,
return_number_of_voxels=True)
assert_equal(nvoxels, 0)
def test_odfdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
S, _ = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
e1 = 15.0
e2 = 3.0
ratio = e2 / e1
csd = ConstrainedSDTModel(gtab, ratio, None)
csd_fit = csd.fit(S)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=10)
w_count = len(w)
# A warning is expected from the ConstrainedSDTModel constructor
# and additionnal warnings should be raised where legacy SH bases
# are used
assert_equal(w_count > 1, True)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=8)
# Test that the warning from ConstrainedSDTModel
# constructor is no more raised
assert_equal(len(w) == w_count - 1, True)
csd_fit = csd.fit(np.zeros_like(S))
fodf = csd_fit.odf(sphere)
assert_array_equal(fodf, np.zeros_like(fodf))
odf_sh = np.zeros_like(fodf)
odf_sh[1] = np.nan
fodf, _ = odf_deconv(odf_sh, csd.R, csd.B_reg)
assert_array_equal(fodf, np.zeros_like(fodf))
def __call__(self, fit):
discrete_odf = fit.odf(self.sphere)
directions, _, _ = peak_directions(discrete_odf, self.sphere,
self.relative_peak_threshold,
self.min_seperation_angle)
return directions
def __call__(self, fit):
discrete_odf = fit.odf(self.sphere)
directions, _, _ = peak_directions(discrete_odf, self.sphere,
self.relative_peak_threshold,
self.min_seperation_angle)
return directions
def test_recursive_response_calibration():
"""
Test the recursive response calibration method.
"""
SNR = 100
S0 = 1
sh_order = 8
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
sphere = get_sphere('symmetric724')
gtab = gradient_table(bvals, bvecs)
evals = np.array([0.0015, 0.0003, 0.0003])
evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
where_dwi = lazy_index(~gtab.b0s_mask)
S_cross, sticks_cross = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
S_single = single_tensor(gtab, S0, evals, evecs, snr=SNR)
data = np.concatenate((np.tile(S_cross, (8, 1)),
np.tile(S_single, (2, 1))),
axis=0)
odf_gt_cross = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odf_gt_single = single_tensor_odf(sphere.vertices, evals, evecs)
response = recursive_response(gtab, data, mask=None, sh_order=8,
peak_thr=0.01, init_fa=0.05,
init_trace=0.0021, iter=8, convergence=0.001,
parallel=False)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(data)
assert_equal(np.all(csd_fit.shm_coeff[:, 0] >= 0), True)
fodf = csd_fit.odf(sphere)
directions_gt_single, _, _ = peak_directions(odf_gt_single, sphere)
directions_gt_cross, _, _ = peak_directions(odf_gt_cross, sphere)
directions_single, _, _ = peak_directions(fodf[8, :], sphere)
directions_cross, _, _ = peak_directions(fodf[0, :], sphere)
ang_sim = angular_similarity(directions_cross, directions_gt_cross)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions_cross.shape[0], 2)
assert_equal(directions_gt_cross.shape[0], 2)
ang_sim = angular_similarity(directions_single, directions_gt_single)
assert_equal(ang_sim > 0.9, True)
assert_equal(directions_single.shape[0], 1)
assert_equal(directions_gt_single.shape[0], 1)
sphere = Sphere(xyz=gtab.gradients[where_dwi])
sf = response.on_sphere(sphere)
S = np.concatenate(([response.S0], sf))
tenmodel = dti.TensorModel(gtab, min_signal=0.001)
tenfit = tenmodel.fit(S)
FA = fractional_anisotropy(tenfit.evals)
FA_gt = fractional_anisotropy(evals)
assert_almost_equal(FA, FA_gt, 1)
def test_recursive_response_calibration():
"""
Test the recursive response calibration method.
"""
SNR = 100
S0 = 1
sh_order = 8
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
sphere = get_sphere('symmetric724')
gtab = gradient_table(bvals, bvecs)
evals = np.array([0.0015, 0.0003, 0.0003])
evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
where_dwi = lazy_index(~gtab.b0s_mask)
S_cross, sticks_cross = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
S_single = single_tensor(gtab, S0, evals, evecs, snr=SNR)
data = np.concatenate((np.tile(S_cross, (8, 1)), np.tile(S_single,
(2, 1))),
axis=0)
odf_gt_cross = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odf_gt_single = single_tensor_odf(sphere.vertices, evals, evecs)
response = recursive_response(gtab,
data,
mask=None,
sh_order=8,
peak_thr=0.01,
init_fa=0.05,
init_trace=0.0021,
iter=8,
convergence=0.001,
parallel=False)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(data)
assert_equal(np.all(csd_fit.shm_coeff[:, 0] >= 0), True)
fodf = csd_fit.odf(sphere)
directions_gt_single, _, _ = peak_directions(odf_gt_single, sphere)
directions_gt_cross, _, _ = peak_directions(odf_gt_cross, sphere)
directions_single, _, _ = peak_directions(fodf[8, :], sphere)
directions_cross, _, _ = peak_directions(fodf[0, :], sphere)
ang_sim = angular_similarity(directions_cross, directions_gt_cross)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions_cross.shape[0], 2)
assert_equal(directions_gt_cross.shape[0], 2)
ang_sim = angular_similarity(directions_single, directions_gt_single)
assert_equal(ang_sim > 0.9, True)
assert_equal(directions_single.shape[0], 1)
assert_equal(directions_gt_single.shape[0], 1)
sphere = Sphere(xyz=gtab.gradients[where_dwi])
sf = response.on_sphere(sphere)
S = np.concatenate(([response.S0], sf))
tenmodel = dti.TensorModel(gtab, min_signal=0.001)
tenfit = tenmodel.fit(S)
FA = fractional_anisotropy(tenfit.evals)
FA_gt = fractional_anisotropy(evals)
assert_almost_equal(FA, FA_gt, 1)
