def test_sf_to_sh():
# Subdividing a hemi_icosahedron twice produces 81 unique points, which
# is more than enough to fit a order 8 (45 coefficients) spherical harmonic
sphere = hemi_icosahedron.subdivide(2)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
mevecs = [np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]])]
odf = multi_tensor_odf(sphere.vertices, [0.5, 0.5], mevals, mevecs)
# 1D case with the 3 bases functions
odf_sh = sf_to_sh(odf, sphere, 8)
odf2 = sh_to_sf(odf_sh, sphere, 8)
assert_array_almost_equal(odf, odf2, 2)
odf_sh = sf_to_sh(odf, sphere, 8, "mrtrix")
odf2 = sh_to_sf(odf_sh, sphere, 8, "mrtrix")
assert_array_almost_equal(odf, odf2, 2)
odf_sh = sf_to_sh(odf, sphere, 8, "fibernav")
odf2 = sh_to_sf(odf_sh, sphere, 8, "fibernav")
assert_array_almost_equal(odf, odf2, 2)
# 2D case
odf2d = np.vstack((odf2, odf))
odf2d_sh = sf_to_sh(odf2d, sphere, 8)
odf2d_sf = sh_to_sf(odf2d_sh, sphere, 8)
assert_array_almost_equal(odf2d, odf2d_sf, 2)
def create_anisopowermap(bvec_path, diffdata):
import os
import nibabel as nib
from dipy.reconst.shm import anisotropic_power
import numpy as np
from dipy.core.sphere import HemiSphere
from dipy.reconst.shm import sf_to_sh
bvecs_xyz = np.loadtxt(bvec_path)
bvecs_xyz_array = np.array(bvecs_xyz[:,1:]).transpose()
gtab_hemisphere = HemiSphere(xyz=bvecs_xyz_array)
img = nib.load(diffdata)
diffdata = img.get_data()
diffdatashell = diffdata[:,:,:,1:]
aff = img.get_affine()
myshs = sf_to_sh(diffdatashell, gtab_hemisphere, sh_order=2)
anisomap = anisotropic_power(myshs)
#Add in a brain masking step here, if beneficial to end result
anisopwr_savepath = os.path.abspath('anisotropic_power_map.nii.gz')
img = nib.Nifti1Image(anisomap, aff)
img.to_filename(anisopwr_savepath)
return anisopwr_savepath
def test_r2_term_odf_sharp():
SNR = None
S0 = 1
angle = 75
_, 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]))
S, sticks = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (angle, 0)],
fractions=[50, 50], snr=SNR)
mevecs = [all_tensor_evecs(sticks[0]).T,
all_tensor_evecs(sticks[1]).T]
odf_gt = multi_tensor_odf(sphere.vertices, [0.5, 0.5], mevals, mevecs)
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)
def sh_estimate(inFile, dirsInFile, outFile, rank=4, smoothness=0.0):
in_nifti = nib.load(inFile)
refaff = in_nifti.get_affine()
data=in_nifti.get_data()
vertices = np.loadtxt( dirsInFile )
sphere = Sphere( xyz=vertices )
odf_sh = sf_to_sh( data, sphere, int(rank), "mrtrix", smoothness )
sh_out = nib.Nifti1Image(odf_sh.astype('float32'), refaff)
nib.save(sh_out, outFile)
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)
def save_odfs_peaks(training, odf, affine, sphere, dres, prefix):
nib.save(nib.Nifti1Image(odf, affine), dres + prefix + 'odf.nii.gz')
peaks_extract(dres + prefix + 'peaks.nii.gz',
odf, affine, sphere,
relative_peak_threshold=.3,
peak_normalize=1,
min_separation_angle=25,
max_peak_number=5)
odf_sh = sf_to_sh(odf, sphere, sh_order=8, basis_type='mrtrix')
nib.save(nib.Nifti1Image(odf_sh, affine), dres + prefix + 'odf_sh.nii.gz')
if training == True:
return training_check(dres, prefix)
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_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_sf_to_sh():
# Subdividing a hemi_icosahedron twice produces 81 unique points, which
# is more than enough to fit a order 8 (45 coefficients) spherical harmonic
sphere = hemi_icosahedron.subdivide(2)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
odf = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
# 1D case with the 3 bases functions
odf_sh = sf_to_sh(odf, sphere, 8)
odf2 = sh_to_sf(odf_sh, sphere, 8)
assert_array_almost_equal(odf, odf2, 2)
odf_sh = sf_to_sh(odf, sphere, 8, "tournier07")
odf2 = sh_to_sf(odf_sh, sphere, 8, "tournier07")
assert_array_almost_equal(odf, odf2, 2)
# Test the basis naming deprecation
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", DeprecationWarning)
odf_sh_mrtrix = sf_to_sh(odf, sphere, 8, "mrtrix")
odf2_mrtrix = sh_to_sf(odf_sh_mrtrix, sphere, 8, "mrtrix")
assert_array_almost_equal(odf, odf2_mrtrix, 2)
assert len(w) != 0
assert issubclass(w[-1].category, DeprecationWarning)
warnings.simplefilter("default", DeprecationWarning)
odf_sh = sf_to_sh(odf, sphere, 8, "descoteaux07")
odf2 = sh_to_sf(odf_sh, sphere, 8, "descoteaux07")
assert_array_almost_equal(odf, odf2, 2)
# Test the basis naming deprecation
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", DeprecationWarning)
odf_sh_fibernav = sf_to_sh(odf, sphere, 8, "fibernav")
odf2_fibernav = sh_to_sf(odf_sh_fibernav, sphere, 8, "fibernav")
assert_array_almost_equal(odf, odf2_fibernav, 2)
assert len(w) != 0
assert issubclass(w[-1].category, DeprecationWarning)
warnings.simplefilter("default", DeprecationWarning)
# 2D case
odf2d = np.vstack((odf2, odf))
odf2d_sh = sf_to_sh(odf2d, sphere, 8)
odf2d_sf = sh_to_sf(odf2d_sh, sphere, 8)
assert_array_almost_equal(odf2d, odf2d_sf, 2)
def test_normalization():
""" Test the normalization routine applied after a convolution"""
# create kernel
D33 = 1.0
D44 = 0.04
t = 1
num_orientations = 5
k = EnhancementKernel(D33, D44, t, orientations=num_orientations, force_recompute=True)
# create a constant dataset
numorientations = k.get_orientations().shape[0]
spike = np.ones((7, 7, 7, numorientations), dtype=np.float64)
# convert dataset to SH
spike_sh = sf_to_sh(spike, k.get_sphere(), sh_order=8)
# convolve kernel with delta spike and apply normalization
csd_enh = convolve(spike_sh, k, sh_order=8, test_mode=True, normalize=True)
# convert dataset to DSF
csd_enh_dsf = sh_to_sf(csd_enh, k.get_sphere(), sh_order=8, basis_type=None)
# test if the normalization is performed correctly
npt.assert_almost_equal(np.amax(csd_enh_dsf), np.amax(spike))
We can now express this signal as a series of SH coefficients using
``sf_to_sh``. This function converts a series of SF coefficients in a series of
SH coefficients. For more information on SH basis, see :ref:`sh-basis`. For
this example, we will use the ``descoteaux07`` basis up to a maximum SH order
of 8.
"""
from dipy.reconst.shm import sf_to_sh
# Change this value to try out other bases
sh_basis = 'descoteaux07'
# Change this value to try other maximum orders
sh_order = 8
sh_coeffs = sf_to_sh(odf, sph, sh_order, sh_basis)
"""
``sh_coeffs`` is an array containing the SH coefficients multiplying the SH
functions of the chosen basis. We can use it as input of ``sh_to_sf`` to
reconstruct our original signal. We will now reproject our signal on a high
resolution sphere using ``sh_to_sf``.
"""
from dipy.data import get_sphere
from dipy.reconst.shm import sh_to_sf
high_res_sph = get_sphere('symmetric724').subdivide(2)
reconst = sh_to_sf(sh_coeffs, high_res_sph, sh_order, sh_basis)
scene.clear()
odf_actor = actor.odf_slicer(reconst[None, None, None, :], sphere=high_res_sph)
sphere = get_sphere('symmetric724')
for NC in [1, 2, 3]:
for iso in [0, 1]:
for fr in [0, 1]:
for snr in [30, 10]:
for typ in [1]:
for ang_t in [23,33,25,35]:#[0, 10, 20, 30]:
for category in ['dti', 'hardi']:
filename = '{}_pso_odf_sf_sel={}_NC={}_iso={}_fr={}_Np={}_Ni={}_snr={}_type={}'.format(category, ang_t, NC, iso, fr, Np, Ni, snr, typ)
filepath = '/media/Data/work/isbi2013/pso_odf_sf/' + filename + '.nii.gz'
if os.path.exists(filepath):
odf = nib.load(filepath)
affine = odf.get_affine()
odf = odf.get_data()
print(filename)
odf_sh = sf_to_sh(odf, sphere, sh_order=8,basis_type='mrtrix')
filename2 = '{}_pso_odf_sh_sel={}_NC={}_iso={}_fr={}_Np={}_Ni={}_snr={}_type={}'.format(category, ang_t, NC, iso, fr, Np, Ni, snr, typ)
nib.save(nib.Nifti1Image(odf_sh, affine), '/media/Data/work/isbi2013/pso_odf_sh/' + filename2 + '.nii.gz')
def compute_sh_coefficients(dwi,
gradient_table,
sh_order=4,
basis_type='descoteaux07',
smooth=0.006,
use_attenuation=False,
force_b0_threshold=False,
mask=None,
sphere=None):
"""Fit a diffusion signal with spherical harmonics coefficients.
Parameters
----------
dwi : nib.Nifti1Image object
Diffusion signal as weighted images (4D).
gradient_table : GradientTable
Dipy object that contains all bvals and bvecs.
sh_order : int, optional
SH order to fit, by default 4.
smooth : float, optional
Lambda-regularization coefficient in the SH fit, by default 0.006.
basis_type: str
Either 'tournier07' or 'descoteaux07'
use_attenuation: bool, optional
If true, we will use DWI attenuation. [False]
force_b0_threshold : bool, optional
If set, will continue even if the minimum bvalue is suspiciously high.
mask: nib.Nifti1Image object, optional
Binary mask. Only data inside the mask will be used for computations
and reconstruction.
sphere: Sphere
Dipy object. If not provided, will use Sphere(xyz=bvecs).
Returns
-------
sh_coeffs : np.ndarray with shape (X, Y, Z, #coeffs)
Spherical harmonics coefficients at every voxel. The actual number
of coefficients depends on `sh_order`.
"""
# Extracting infos
b0_mask = gradient_table.b0s_mask
bvecs = gradient_table.bvecs
bvals = gradient_table.bvals
# Checks
if not is_normalized_bvecs(bvecs):
logging.warning("Your b-vectors do not seem normalized...")
bvecs = normalize_bvecs(bvecs)
check_b0_threshold(force_b0_threshold, bvals.min())
# Ensure that this is on a single shell.
shell_values, _ = identify_shells(bvals)
shell_values.sort()
if force_b0_threshold:
b0_threshold = bvals.min()
else:
b0_threshold = DEFAULT_B0_THRESHOLD
if shell_values.shape[0] != 2 or shell_values[0] > b0_threshold:
raise ValueError("Can only work on single shell signals.")
# Keeping b0-based infos
bvecs = bvecs[np.logical_not(b0_mask)]
weights = dwi[..., np.logical_not(b0_mask)]
# Compute attenuation using the b0.
if use_attenuation:
b0 = dwi[..., b0_mask].mean(axis=3)
weights = compute_dwi_attenuation(weights, b0)
# Get cartesian coords from bvecs
if sphere is None:
sphere = Sphere(xyz=bvecs)
# Fit SH
sh = sf_to_sh(weights, sphere, sh_order, basis_type, smooth=smooth)
# Apply mask
if mask is not None:
sh *= mask[..., None]
return sh
def test_sf_to_sh():
# Subdividing a hemi_icosahedron twice produces 81 unique points, which
# is more than enough to fit a order 8 (45 coefficients) spherical harmonic
hemisphere = hemi_icosahedron.subdivide(2)
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (60, 0)]
odf = multi_tensor_odf(hemisphere.vertices, mevals, angles, [50, 50])
# 1D case with the 2 symmetric bases functions
# Tournier basis
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=tournier07_legacy_msg,
category=PendingDeprecationWarning)
odf_sh = sf_to_sh(odf, hemisphere, 8, "tournier07")
odf_reconst = sh_to_sf(odf_sh, hemisphere, 8, "tournier07")
assert_array_almost_equal(odf, odf_reconst, 2)
# Legacy definition
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=tournier07_legacy_msg,
category=PendingDeprecationWarning)
odf_sh = sf_to_sh(odf, hemisphere, 8, "tournier07", legacy=True)
odf_reconst = sh_to_sf(odf_sh,
hemisphere,
8,
"tournier07",
legacy=True)
assert_array_almost_equal(odf, odf_reconst, 2)
# Descoteaux basis
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odf_sh = sf_to_sh(odf, hemisphere, 8, "descoteaux07")
odf_reconst = sh_to_sf(odf_sh, hemisphere, 8, "descoteaux07")
assert_array_almost_equal(odf, odf_reconst, 2)
# Legacy definition
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odf_sh = sf_to_sh(odf, hemisphere, 8, "descoteaux07", legacy=True)
odf_reconst = sh_to_sf(odf_sh,
hemisphere,
8,
"descoteaux07",
legacy=True)
assert_array_almost_equal(odf, odf_reconst, 2)
# We now create an asymmetric signal
# to try out our full SH basis
mevals = np.array([[0.0015, 0.0003, 0.0003]])
angles = [(0, 0)]
odf2 = multi_tensor_odf(hemisphere.vertices, mevals, angles, [100])
# We simulate our asymmetric signal by using a different ODF
# per hemisphere. The sphere used is a concatenation of the
# vertices of our hemisphere, for a total of 162 vertices.
sphere = Sphere(xyz=np.vstack((hemisphere.vertices, -hemisphere.vertices)))
asym_odf = np.append(odf, odf2)
# Try out full bases with order 10 (121 coefficients)
# Tournier basis
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=tournier07_legacy_msg,
category=PendingDeprecationWarning)
odf_sh = sf_to_sh(asym_odf, sphere, 10, 'tournier07', full_basis=True)
odf_reconst = sh_to_sf(odf_sh,
sphere,
10,
'tournier07',
full_basis=True)
assert_array_almost_equal(odf_reconst, asym_odf, 2)
# Legacy definition
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=tournier07_legacy_msg,
category=PendingDeprecationWarning)
odf_sh = sf_to_sh(asym_odf,
sphere,
10,
'tournier07',
full_basis=True,
legacy=True)
odf_reconst = sh_to_sf(odf_sh,
sphere,
10,
'tournier07',
full_basis=True,
legacy=True)
assert_array_almost_equal(odf_reconst, asym_odf, 2)
# Descoteaux basis
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odf_sh = sf_to_sh(asym_odf,
sphere,
10,
'descoteaux07',
full_basis=True)
odf_reconst = sh_to_sf(odf_sh,
sphere,
10,
'descoteaux07',
full_basis=True)
assert_array_almost_equal(odf_reconst, asym_odf, 2)
# Legacy definition
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odf_sh = sf_to_sh(asym_odf,
sphere,
10,
'descoteaux07',
full_basis=True,
legacy=True)
odf_reconst = sh_to_sf(odf_sh,
sphere,
10,
'descoteaux07',
full_basis=True,
legacy=True)
assert_array_almost_equal(odf_reconst, asym_odf, 2)
# An invalid basis name should raise an error
assert_raises(ValueError, sh_to_sf, odf, hemisphere, basis_type="")
assert_raises(ValueError, sf_to_sh, odf_sh, hemisphere, basis_type="")
# 2D case
odf2d = np.vstack((odf, odf))
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odf2d_sh = sf_to_sh(odf2d, hemisphere, 8)
odf2d_sf = sh_to_sf(odf2d_sh, hemisphere, 8)
assert_array_almost_equal(odf2d, odf2d_sf, 2)
We can now express this signal as a series of SH coefficients using
``sf_to_sh``. This function converts a series of SF coefficients in a series of
SH coefficients. For more information on SH basis, see :ref:`sh-basis`. For
this example, we will use the ``descoteaux07`` basis up to a maximum SH order
of 8.
"""
from dipy.reconst.shm import sf_to_sh
# Change this value to try out other bases
sh_basis = 'descoteaux07'
# Change this value to try other maximum orders
sh_order = 8
sh_coeffs = sf_to_sh(odf, sph, sh_order, sh_basis)
"""
``sh_coeffs`` is an array containing the SH coefficients multiplying the SH
functions of the chosen basis. We can use it as input of ``sh_to_sf`` to
reconstruct our original signal. We will now reproject our signal on a high
resolution sphere using ``sh_to_sf``.
"""
from dipy.data import get_sphere
from dipy.reconst.shm import sh_to_sf
high_res_sph = get_sphere('symmetric724').subdivide(2)
reconst = sh_to_sf(sh_coeffs, high_res_sph, sh_order, sh_basis)
window.rm_all(ren)
odf_actor = actor.odf_slicer(reconst[None, None, None, :], sphere=high_res_sph)
def test_convert_sh_to_legacy():
hemisphere = hemi_icosahedron.subdivide(2)
mevals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]])
angles = [(0, 0), (60, 0)]
odf = multi_tensor_odf(hemisphere.vertices, mevals, angles, [50, 50])
sh_coeffs = sf_to_sh(odf, hemisphere, 8, legacy=False)
converted_coeffs = convert_sh_to_legacy(sh_coeffs, 'descoteaux07')
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
expected_coeffs = sf_to_sh(odf, hemisphere, 8, legacy=True)
assert_array_almost_equal(converted_coeffs, expected_coeffs, 2)
sh_coeffs = sf_to_sh(odf,
hemisphere,
8,
basis_type='tournier07',
legacy=False)
converted_coeffs = convert_sh_to_legacy(sh_coeffs, 'tournier07')
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=tournier07_legacy_msg,
category=PendingDeprecationWarning)
expected_coeffs = sf_to_sh(odf,
hemisphere,
8,
basis_type='tournier07',
legacy=True)
assert_array_almost_equal(converted_coeffs, expected_coeffs, 2)
# 2D case
odfs = np.array([odf, odf])
sh_coeffs = sf_to_sh(odfs,
hemisphere,
8,
basis_type='tournier07',
full_basis=True,
legacy=False)
converted_coeffs = convert_sh_to_legacy(sh_coeffs,
'tournier07',
full_basis=True)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=tournier07_legacy_msg,
category=PendingDeprecationWarning)
expected_coeffs = sf_to_sh(odfs,
hemisphere,
8,
basis_type='tournier07',
legacy=True,
full_basis=True)
assert_array_almost_equal(converted_coeffs, expected_coeffs, 2)
assert_raises(ValueError, convert_sh_to_legacy, sh_coeffs, '', True)
def main():
logging.basicConfig(level=logging.INFO)
parser = _build_arg_parser()
args = parser.parse_args()
required = [args.in_bundle, args.in_fodf, args.in_mask]
assert_inputs_exist(parser, required)
out_efod = os.path.join(args.out_dir,
'{0}efod.nii.gz'.format(args.out_prefix))
out_priors = os.path.join(args.out_dir,
'{0}priors.nii.gz'.format(args.out_prefix))
out_todi_mask = os.path.join(args.out_dir,
'{0}todi_mask.nii.gz'.format(args.out_prefix))
out_endpoints_mask = os.path.join(args.out_dir,
'{0}endpoints_mask.nii.gz'.format(
args.out_prefix))
if args.out_dir and not os.path.isdir(args.out_dir):
os.mkdir(args.out_dir)
required = [out_efod, out_priors, out_todi_mask, out_endpoints_mask]
assert_outputs_exist(parser, args, required)
img_sh = nib.load(args.in_fodf)
sh_shape = img_sh.shape
sh_order = find_order_from_nb_coeff(sh_shape)
img_mask = nib.load(args.in_mask)
sft = load_tractogram(args.in_bundle, args.in_fodf,
trk_header_check=True)
sft.to_vox()
streamlines = sft.streamlines
if len(streamlines) < 1:
raise ValueError('The input bundle contains no streamline.')
# Compute TODI from streamlines
with TrackOrientationDensityImaging(img_mask.shape,
'repulsion724') as todi_obj:
todi_obj.compute_todi(streamlines, length_weights=True)
todi_obj.smooth_todi_dir()
todi_obj.smooth_todi_spatial(sigma=args.todi_sigma)
# Fancy masking of 1d indices to limit spatial dilation to WM
sub_mask_3d = np.logical_and(get_data_as_mask(img_mask),
todi_obj.reshape_to_3d(todi_obj.get_mask()))
sub_mask_1d = sub_mask_3d.flatten()[todi_obj.get_mask()]
todi_sf = todi_obj.get_todi()[sub_mask_1d] ** 2
# The priors should always be between 0 and 1
# A minimum threshold is set to prevent misaligned FOD from disappearing
todi_sf /= np.max(todi_sf, axis=-1, keepdims=True)
todi_sf[todi_sf < args.sf_threshold] = args.sf_threshold
# Memory friendly saving, as soon as possible saving then delete
priors_3d = np.zeros(sh_shape)
sphere = get_sphere('repulsion724')
priors_3d[sub_mask_3d] = sf_to_sh(todi_sf, sphere,
sh_order=sh_order,
basis_type=args.sh_basis)
nib.save(nib.Nifti1Image(priors_3d, img_mask.affine), out_priors)
del priors_3d
input_sh_3d = img_sh.get_fdata(dtype=np.float32)
input_sf_1d = sh_to_sf(input_sh_3d[sub_mask_3d],
sphere, sh_order=sh_order, basis_type=args.sh_basis)
# Creation of the enhanced-FOD (direction-wise multiplication)
mult_sf_1d = input_sf_1d * todi_sf
del todi_sf
input_max_value = np.max(input_sf_1d, axis=-1, keepdims=True)
mult_max_value = np.max(mult_sf_1d, axis=-1, keepdims=True)
mult_positive_mask = np.squeeze(mult_max_value) > 0.0
mult_sf_1d[mult_positive_mask] = mult_sf_1d[mult_positive_mask] * \
input_max_value[mult_positive_mask] / \
mult_max_value[mult_positive_mask]
# Memory friendly saving
input_sh_3d[sub_mask_3d] = sf_to_sh(mult_sf_1d, sphere,
sh_order=sh_order,
basis_type=args.sh_basis)
nib.save(nib.Nifti1Image(input_sh_3d, img_mask.affine), out_efod)
del input_sh_3d
nib.save(nib.Nifti1Image(sub_mask_3d.astype(
np.int16), img_mask.affine), out_todi_mask)
endpoints_mask = np.zeros(img_mask.shape, dtype=np.int16)
for streamline in streamlines:
if get_data_as_mask(img_mask)[tuple(streamline[0].astype(np.int16))]:
endpoints_mask[tuple(streamline[0].astype(np.int16))] = 1
endpoints_mask[tuple(streamline[-1].astype(np.int16))] = 1
nib.save(nib.Nifti1Image(endpoints_mask,
img_mask.affine), out_endpoints_mask)
def create_anisopowermap(gtab_file, dwi_file, B0_mask):
'''
Estimate an anisotropic power map image to use for registrations.
Parameters
----------
gtab_file : str
File path to pickled DiPy gradient table object.
dwi_file : str
File path to diffusion weighted image.
B0_mask : str
File path to B0 brain mask.
Returns
-------
anisopwr_path : str
File path to the anisotropic power Nifti1Image.
B0_mask : str
File path to B0 brain mask Nifti1Image.
gtab_file : str
File path to pickled DiPy gradient table object.
dwi_file : str
File path to diffusion weighted Nifti1Image.
'''
import os
from dipy.io import load_pickle
from dipy.reconst.shm import anisotropic_power
from dipy.core.sphere import HemiSphere
from dipy.reconst.shm import sf_to_sh
gtab = load_pickle(gtab_file)
gtab_hemisphere = HemiSphere(xyz=gtab.bvecs[np.where(
gtab.b0s_mask == False)])
img = nib.load(dwi_file)
aff = img.affine
anisopwr_path = "%s%s" % (os.path.dirname(B0_mask), '/aniso_power.nii.gz')
if os.path.isfile(anisopwr_path):
pass
else:
print('Generating anisotropic power map to use for registrations...')
nodif_B0_img = nib.load(B0_mask)
dwi_data = np.asarray(img.dataobj)
for b0 in sorted(list(np.where(gtab.b0s_mask == True)[0]),
reverse=True):
dwi_data = np.delete(dwi_data, b0, 3)
anisomap = anisotropic_power(
sf_to_sh(dwi_data, gtab_hemisphere, sh_order=2))
anisomap[np.isnan(anisomap)] = 0
masked_data = anisomap * np.asarray(
nodif_B0_img.dataobj).astype('bool')
img = nib.Nifti1Image(masked_data.astype(np.float32), aff)
img.to_filename(anisopwr_path)
nodif_B0_img.uncache()
del anisomap
return anisopwr_path, B0_mask, gtab_file, dwi_file
def main():
parser = buildArgsParser()
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
if not args.not_all:
if not args.odf:
args.odf = 'shore_dodf.nii.gz'
if not args.rtop:
args.rtop = 'rtop.nii.gz'
if not args.msd:
args.msd = 'msd.nii.gz'
if not args.pa:
args.pa = 'pa.nii.gz'
arglist = [args.odf, args.rtop, args.msd, args.pa]
if args.not_all and not any(arglist):
parser.error('When using --not_all, you need to specify at least ' +
'one file to output.')
for out in arglist:
if os.path.isfile(out):
if args.overwrite:
logging.info('Overwriting "{0}".'.format(out))
else:
parser.error(
'"{0}" already exists! Use -f to overwrite it.'.format(
out))
vol = nib.load(args.input)
data = vol.get_data()
affine = vol.get_affine()
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
if bvals.min() != 0:
if bvals.min() > 20:
raise ValueError('The minimal bvalue is greater than 20. ' +
'This is highly suspicious. Please check ' +
'your data to ensure everything is correct.\n' +
'Value found: {0}'.format(bvals.min()))
else:
logging.warning('Warning: no b=0 image. Setting b0_threshold to ' +
'bvals.min() = {0}'.format(bvals.min()))
gtab = gradient_table(bvals, bvecs, b0_threshold=bvals.min())
else:
gtab = gradient_table(bvals, bvecs)
if args.mask is None:
mask = None
else:
mask = nib.load(args.mask).get_data().astype(np.bool)
voxels_with_values_mask = data[:, :, :, 0] > 0
mask = voxels_with_values_mask * mask
sphere = get_sphere('repulsion100')
if args.regul_weighting <= 0:
logging.info('Now computing SHORE ODF of radial order {0}'.format(
args.radial_order) + ' and Laplacian generalized cross-validation')
shore_model = ShoreOzarslanModel(gtab,
radial_order=args.radial_order,
laplacian_regularization=True,
laplacian_weighting='GCV')
else:
logging.info('Now computing SHORE ODF of radial order {0}'.format(
args.radial_order) +
' and Laplacian regularization weight of {0}'.format(
args.regul_weighting))
shore_model = ShoreOzarslanModel(
gtab,
radial_order=args.radial_order,
laplacian_regularization=True,
laplacian_weighting=args.regul_weighting)
smfit = shore_model.fit(data, mask)
odf = smfit.odf(sphere, radial_moment=args.radial_moment)
odf_sh = sf_to_sh(odf,
sphere,
sh_order=8,
basis_type=args.basis,
smooth=0.0)
rtop = smfit.rtop()
msd = smfit.msd()
pa = smfit.propagator_anisotropy()
if args.odf:
nib.save(nib.Nifti1Image(odf_sh.astype(np.float32), affine), args.odf)
if args.rtop:
nib.save(nib.Nifti1Image(rtop.astype(np.float32), affine), args.rtop)
if args.msd:
nib.save(nib.Nifti1Image(msd.astype(np.float32), affine), args.msd)
if args.pa:
nib.save(nib.Nifti1Image(pa.astype(np.float32), affine), args.pa)
t = 1
k = EnhancementKernel(D33, D44, t)
"""
Visualize the kernel
"""
from dipy.viz import fvtk
from dipy.data import get_sphere
from dipy.reconst.shm import sf_to_sh, sh_to_sf
ren = fvtk.ren()
# convolve kernel with delta spike
spike = np.zeros((7, 7, 7, k.get_orientations().shape[0]), dtype=np.float64)
spike[3, 3, 3, 0] = 1
spike_shm_conv = convolve(sf_to_sh(spike, k.get_sphere(), sh_order=8), k,
sh_order=8, test_mode=True)
sphere = get_sphere('symmetric724')
spike_sf_conv = sh_to_sf(spike_shm_conv, sphere, sh_order=8)
model_kernel = fvtk.sphere_funcs((spike_sf_conv * 6)[3,:,:,:],
sphere,
norm=False,
radial_scale=True)
fvtk.add(ren, model_kernel)
fvtk.camera(ren, pos=(30, 0, 0), focal=(0, 0, 0), viewup=(0, 0, 1), verbose=False)
fvtk.record(ren, out_path='kernel.png', size=(900, 900))
"""
.. figure:: kernel.png
:align: center
def create_anisopowermap(gtab_file, dwi_file, B0_mask):
"""
Estimate an anisotropic power map image to use for registrations.
Parameters
----------
gtab_file : str
File path to pickled DiPy gradient table object.
dwi_file : str
File path to diffusion weighted image.
B0_mask : str
File path to B0 brain mask.
Returns
-------
anisopwr_path : str
File path to the anisotropic power Nifti1Image.
B0_mask : str
File path to B0 brain mask Nifti1Image.
gtab_file : str
File path to pickled DiPy gradient table object.
dwi_file : str
File path to diffusion weighted Nifti1Image.
References
----------
.. [1] Chen, D. Q., Dell’Acqua, F., Rokem, A., Garyfallidis, E., Hayes, D.,
Zhong, J., & Hodaie, M. (2018). Diffusion Weighted Image Co-registration:
Investigation of Best Practices. PLoS ONE.
"""
import os
from dipy.io import load_pickle
from dipy.reconst.shm import anisotropic_power
from dipy.core.sphere import HemiSphere, Sphere
from dipy.reconst.shm import sf_to_sh
gtab = load_pickle(gtab_file)
dwi_vertices = gtab.bvecs[np.where(gtab.b0s_mask == False)]
gtab_hemisphere = HemiSphere(xyz=gtab.bvecs[np.where(
gtab.b0s_mask == False)])
try:
assert len(gtab_hemisphere.vertices) == len(dwi_vertices)
except BaseException:
gtab_hemisphere = Sphere(xyz=gtab.bvecs[np.where(
gtab.b0s_mask == False)])
img = nib.load(dwi_file)
aff = img.affine
anisopwr_path = f"{os.path.dirname(B0_mask)}{'/aniso_power.nii.gz'}"
if os.path.isfile(anisopwr_path):
pass
else:
print("Generating anisotropic power map to use for registrations...")
nodif_B0_img = nib.load(B0_mask)
dwi_data = img.get_fdata(dtype=np.float32)
for b0 in sorted(list(np.where(gtab.b0s_mask)[0]), reverse=True):
dwi_data = np.delete(dwi_data, b0, 3)
anisomap = anisotropic_power(
sf_to_sh(dwi_data, gtab_hemisphere, sh_order=2))
anisomap[np.isnan(anisomap)] = 0
masked_data = anisomap * \
np.asarray(nodif_B0_img.dataobj).astype("bool")
img = nib.Nifti1Image(masked_data.astype(np.float32), aff)
img.to_filename(anisopwr_path)
nodif_B0_img.uncache()
del anisomap
img.uncache()
return anisopwr_path, B0_mask, gtab_file, dwi_file
t = 1
k = EnhancementKernel(D33, D44, t)
"""
Visualize the kernel
"""
from dipy.viz import window, actor
from dipy.data import get_sphere
from dipy.reconst.shm import sf_to_sh, sh_to_sf
ren = window.Renderer()
# convolve kernel with delta spike
spike = np.zeros((7, 7, 7, k.get_orientations().shape[0]), dtype=np.float64)
spike[3, 3, 3, 0] = 1
spike_shm_conv = convolve(sf_to_sh(spike, k.get_sphere(), sh_order=8),
k,
sh_order=8,
test_mode=True)
sphere = get_sphere('symmetric724')
spike_sf_conv = sh_to_sf(spike_shm_conv, sphere, sh_order=8)
model_kernel = actor.odf_slicer(spike_sf_conv * 6,
sphere=sphere,
norm=False,
scale=0.4)
model_kernel.display(x=3)
ren.add(model_kernel)
ren.set_camera(position=(30, 0, 0), focal_point=(0, 0, 0), view_up=(0, 0, 1))
window.record(ren, out_path='kernel.png', size=(900, 900))
if interactive: