def test_real_sph_harm_fibernav():
# This test should do for now
# The mrtrix basis should be the same as re-ordering and re-scaling the
# fibernav basis
new_order = [0, 5, 4, 3, 2, 1, 14, 13, 12, 11, 10, 9, 8, 7, 6]
sphere = hemi_icosahedron.subdivide(2)
basis, m, n = real_sph_harm_mrtrix(4, sphere.theta, sphere.phi)
expected = basis[:, new_order]
expected *= np.where(m == 0, 1., np.sqrt(2))
fibernav_basis, m, n = real_sph_harm_fibernav(4, sphere.theta, sphere.phi)
assert_array_almost_equal(fibernav_basis, expected)
def gqi(training, category, snr, denoised, odeconv, tv, method, weight=0.1, sl=3.):
data, affine, gtab, mask, evals, S0, prefix = prepare(training,
category,
snr,
denoised,
odeconv,
tv,
method)
model = GeneralizedQSamplingModel(gtab,
method='gqi2',
sampling_length=sl,
normalize_peaks=False)
fit = model.fit(data, mask)
sphere = get_sphere('symmetric724')
odf = fit.odf(sphere)
if odeconv == True:
odf_sh = sf_to_sh(odf, sphere, sh_order=8,
basis_type='mrtrix')
# # nib.save(nib.Nifti1Image(odf_sh, affine), model_tag + 'odf_sh.nii.gz')
reg_sphere = get_sphere('symmetric724')
fodf_sh = odf_sh_to_sharp(odf_sh,
reg_sphere, basis='mrtrix', ratio=3.8 / 16.6,
sh_order=8, Lambda=1., tau=1.)
# # nib.save(nib.Nifti1Image(odf_sh, affine), model_tag + 'fodf_sh.nii.gz')
fodf_sh[np.isnan(fodf_sh)]=0
r, theta, phi = cart2sphere(sphere.x, sphere.y, sphere.z)
B_regul, m, n = real_sph_harm_mrtrix(8, theta[:, None], phi[:, None])
fodf = np.dot(fodf_sh, B_regul.T)
odf = fodf
if tv == True:
odf = tv_denoise_4d(odf, weight=weight)
save_odfs_peaks(training, odf, affine, sphere, dres, prefix)
from dipy.reconst.csdeconv import odf_sh_to_sharp
reg_sphere = get_sphere('symmetric724')
fodf_sh = odf_sh_to_sharp(odf_sh,
reg_sphere, basis='mrtrix', ratio=3.8 / 16.6,
sh_order=8, Lambda=1., tau=1.)
# nib.save(nib.Nifti1Image(odf_sh, affine), model_tag + 'fodf_sh.nii.gz')
from dipy.reconst.shm import real_sph_harm_mrtrix
from dipy.data import get_sphere
from dipy.core.geometry import cart2sphere
r, theta, phi = cart2sphere(sphere.x, sphere.y, sphere.z)
B_regul, m, n = real_sph_harm_mrtrix(8, theta[:, None], phi[:, None])
fodf = np.dot(fodf_sh, B_regul.T)
from dipy.viz import fvtk
#odf = odf[25 - 10:25 + 10, 25 - 10:25 + 10, 25]
r = fvtk.ren()
fvtk.add(r, fvtk.sphere_funcs(odf, sphere))
fvtk.show(r)
fvtk.clear(r)
# odf_var = tv_denoise_4d(odf, weight=0.1)
# fvtk.add(r, fvtk.sphere_funcs(odf_var, sphere))
# fvtk.show(r)
# fvtk.clear(r)
def test_real_sph_harm_mrtrix():
coef, expected, sphere = mrtrix_spherical_functions()
basis, m, n = real_sph_harm_mrtrix(8, sphere.theta, sphere.phi)
func = np.dot(coef, basis.T)
assert_array_almost_equal(func, expected, 4)
