def test_anisotropic_normalized(self, sphere3_msh, tensor):
t = tensor
cond_list = [None, None, 2, 7, 9]
v = np.zeros((255, 255, 255, 6))
for i, j in enumerate([0, 1, 2, 4, 5, 8]):
v[..., i] = t.reshape(-1)[j]
affine = np.array([[-1, 0, 0, 128], [0, 1, 0, -128], [0, 0, 1, -127],
[0, 0, 0, 1]])
elmcond = cond.cond2elmdata(sphere3_msh,
cond_list,
v,
affine,
aniso_tissues=3,
normalize=True)
tensor = elmcond.value[sphere3_msh.elm.tag1 == 3].reshape(-1, 3, 3)
t = affine[:3, :3].dot(t).dot(affine[:3, :3])
assert np.allclose(np.linalg.det(tensor), 2**3)
assert np.allclose(
np.linalg.eig(tensor)[1][:, 0],
np.linalg.eig(t)[1][0])
assert np.allclose(
np.linalg.eig(tensor)[1][:, 1],
np.linalg.eig(t)[1][1])
assert np.allclose(
np.linalg.eig(tensor)[1][:, 2],
np.linalg.eig(t)[1][2])
assert np.allclose(elmcond.value[sphere3_msh.elm.tag1 == 4],
[7, 0, 0, 0, 7, 0, 0, 0, 7])
assert np.allclose(elmcond.value[sphere3_msh.elm.tag1 == 5],
[9, 0, 0, 0, 9, 0, 0, 0, 9])
def main():
args = parseArguments(sys.argv[1:])
if not os.path.isfile(args.fn_nifti):
raise IOError('Could not find file: {0}'.format(args.fn_nifti))
if not os.path.isfile(args.fn_mesh):
raise IOError('Could not find file: {0}'.format(args.fn_mesh))
image = nibabel.load(args.fn_nifti)
mesh = mesh_io.read_msh(args.fn_mesh)
vol = image.dataobj
affine = image.affine
if args.ev:
logger.info('Creating tensor visualization')
mesh = mesh.crop_mesh([1, 2, 1001, 1002])
cond_list = [c.value for c in cond.standard_cond()]
sigma = cond.cond2elmdata(mesh,
cond_list,
anisotropy_volume=vol,
affine=affine,
aniso_tissues=[1, 2])
views = cond.TensorVisualization(sigma, mesh)
mesh.nodedata = []
mesh.elmdata = views
mesh_io.write_msh(mesh, args.fn_out)
else:
logger.info('Interpolating data in NifTI file to mesh')
if args.type == 'elements':
ed = mesh_io.ElementData.from_data_grid(mesh, vol, affine,
'from_volume')
mesh.elmdata.append(ed)
if args.type == 'nodes':
nd = mesh_io.NodeData.from_data_grid(mesh, vol, affine,
'from_volume')
mesh.nodedata.append(nd)
mesh_io.write_msh(mesh, args.fn_out)
def test_isotropic(self, sphere3_msh):
cond_list = [None, None, 1, 2, 3]
c = cond.cond2elmdata(sphere3_msh, cond_list).value
assert np.all(c[sphere3_msh.elm.tag1 == 3] == 1)
assert np.all(c[sphere3_msh.elm.tag1 == 1003] == 1)
assert np.all(c[sphere3_msh.elm.tag1 == 4] == 2)
assert np.all(c[sphere3_msh.elm.tag1 == 1004] == 2)
assert np.all(c[sphere3_msh.elm.tag1 == 5] == 3)
assert np.all(c[sphere3_msh.elm.tag1 == 1005] == 3)
def test_anisotropic(self, sphere3_msh, tensor):
cond_list = [None, None, 1, 2, 3]
v = np.zeros((255, 255, 255, 6))
for i, j in enumerate([0, 1, 2, 4, 5, 8]):
v[:, :, :, i] = tensor.reshape(-1)[j]
affine = np.array([[-1, 0, 0, 128], [0, 1, 0, -128], [0, 0, 1, -127],
[0, 0, 0, 1]])
msh = sphere3_msh
elmcond = cond.cond2elmdata(msh,
cond_list,
v,
affine,
aniso_tissues=3,
max_cond=np.inf,
max_ratio=np.inf,
correct_intensity=False)
t = affine[:3, :3].dot(tensor).dot(affine[:3, :3])
assert np.allclose(elmcond.value[msh.elm.tag1 == 3], t.reshape(-1))
assert np.allclose(elmcond.value[msh.elm.tag1 == 4],
[2, 0, 0, 0, 2, 0, 0, 0, 2])
assert np.allclose(elmcond.value[msh.elm.tag1 == 5],
[3, 0, 0, 0, 3, 0, 0, 0, 3])
vol = np.linalg.eig(tensor)[0].prod()**(1. / 3.)
scaling = (vol * 1 + vol * 2) / (2 * (vol**2))
elmcond = cond.cond2elmdata(msh,
cond_list,
v,
affine,
aniso_tissues=[3, 4],
max_cond=np.inf,
max_ratio=np.inf,
correct_intensity=True)
assert np.allclose(elmcond.value[msh.elm.tag1 == 3],
scaling * t.reshape(-1))
assert np.allclose(elmcond.value[msh.elm.tag1 == 4],
scaling * t.reshape(-1))
assert np.allclose(elmcond.value[msh.elm.tag1 == 5],
[3, 0, 0, 0, 3, 0, 0, 0, 3])
def test_anisotropic_zero_region(self, sphere3_msh, tensor):
t = tensor
cond_list = [None, None, 2, 7, 9]
v = np.zeros((255, 255, 255, 6))
affine = np.array([[-1, 0, 0, 128],
[0, 1, 0, -128],
[0, 0, 1, -127],
[0, 0, 0, 1]])
elmcond = cond.cond2elmdata(sphere3_msh, cond_list, v, affine, aniso_tissues=3,
normalize=True)
assert np.allclose(elmcond.value[sphere3_msh.elm.tag1 == 3],
[2, 0, 0, 0, 2, 0, 0, 0, 2])
'''
def test_anisotropic_scale_excentricity(self, sphere3_msh, tensor):
t = tensor
cond_list = [None, None, 2, 7, 9]
v = np.zeros((255, 255, 255, 6))
for i, j in enumerate([0, 1, 2, 4, 5, 8]):
v[..., i] = t.reshape(-1)[j]
affine = np.array([[-1, 0, 0, 128],
[0, 1, 0, -128],
[0, 0, 1, -127],
[0, 0, 0, 1]])
elmcond = cond.cond2elmdata(sphere3_msh, cond_list, v, affine, aniso_tissues=3,
normalize=True, excentricity_scaling=0.)
tensor = elmcond.value[sphere3_msh.elm.tag1 == 3].reshape(-1, 3, 3)
t = affine[:3, :3].dot(t).dot(affine[:3, :3])
assert np.allclose(np.linalg.det(tensor), 2 ** 3)
assert np.allclose(tensor, 2 * np.eye(3))
args = parseArguments(sys.argv[1:])
if not os.path.isfile(args.fn_nifti):
raise IOError('Could not find file: {0}'.format(args.fn_nifti))
if not os.path.isfile(args.fn_mesh):
raise IOError('Could not find file: {0}'.format(args.fn_mesh))
image = nibabel.load(args.fn_nifti)
mesh = gmsh.read_msh(args.fn_mesh)
vol = image.dataobj
affine = image.affine
if args.ev:
logger.info('Creating tensor visualization')
mesh = mesh.crop_mesh([1, 2, 1001, 1002])
cond_list = [c.value for c in cond.standard_cond()]
sigma = cond.cond2elmdata(mesh,
cond_list,
anisotropy_volume=vol,
affine=affine,
aniso_tissues=[1, 2])
views = cond.TensorVisualization(sigma)
mesh.nodedata = []
mesh.elmdata = views
gmsh.write_msh(mesh, args.fn_out)
else:
logger.info('Interpolating data in NifTI file to mesh')
ed = gmsh.ElementData.from_data_grid(mesh,
vol,
affine,
'from_volume',
bounds_error=False,
fill_value=0)
mesh.nodedata = []