def test_calc_dadt(self, sphere3_msh):
phi = sphere3_msh.nodes.node_coord[:, 0] + \
2 * sphere3_msh.nodes.node_coord[:, 1] + \
-3 * sphere3_msh.nodes.node_coord[:, 2]
potential = mesh_io.NodeData(phi, mesh=sphere3_msh)
dadt = .2 * sphere3_msh.nodes.node_coord
dadt = mesh_io.NodeData(dadt, mesh=sphere3_msh)
E = np.zeros((sphere3_msh.elm.nr, 3))
E = [-1, -2, 3] - dadt.node_data2elm_data().value
E = mesh_io.ElementData(E, mesh=sphere3_msh)
E.assign_triangle_values()
cond = sphere3_msh.elm.tag1
cond = mesh_io.ElementData(cond, mesh=sphere3_msh)
m = fem.calc_fields(potential, 'vDJEgsej', cond, dadt=dadt,
units='m')
assert np.allclose(m.field['v'].value, potential.value)
assert np.allclose(m.field['D'].value, dadt.value)
assert np.allclose(m.field['g'].value, [1, 2, -3])
assert np.allclose(m.field['E'].value, E.value)
assert np.allclose(m.field['J'].value, cond.value[:, None] * E.value)
assert np.allclose(m.field['conductivity'].value, cond.value)
assert np.allclose(m.field['normE'].value, np.linalg.norm(E.value, axis=1))
assert np.allclose(m.field['normJ'].value,
np.linalg.norm(cond.value[:, None] * E.value, axis=1))
def test_calc_vEJgs(self, sphere3_msh):
phi = sphere3_msh.nodes.node_coord[:, 0] + \
2 * sphere3_msh.nodes.node_coord[:, 1] + \
-3 * sphere3_msh.nodes.node_coord[:, 2]
potential = mesh_io.NodeData(phi, mesh=sphere3_msh)
E = np.zeros((sphere3_msh.elm.nr, 3))
E[:] = [-1., -2., 3.]
E = mesh_io.ElementData(E, mesh=sphere3_msh)
cond = sphere3_msh.elm.tag1
cond = mesh_io.ElementData(cond, mesh=sphere3_msh)
m = fem.calc_fields(potential, 'vJEgsej', cond)
assert np.allclose(m.field['v'].value, potential.value)
assert np.allclose(m.field['E'].value, E.value * 1e3)
assert np.allclose(m.field['J'].value,
cond.value[:, None] * E.value * 1e3)
assert np.allclose(m.field['g'].value, -E.value * 1e3)
assert np.allclose(m.field['conductivity'].value, cond.value)
assert np.allclose(m.field['normE'].value,
np.linalg.norm(E.value, axis=1) * 1e3)
assert np.allclose(
m.field['normJ'].value,
np.linalg.norm(cond.value[:, None] * E.value, axis=1) * 1e3)
def test_tms_dadt(self, tms_sphere):
m, cond, dAdt, E_analytical = tms_sphere
v = fem.tms_dadt(m, cond, dAdt)
E = -v.gradient().value * 1e3 - dAdt.node_data2elm_data().value
m.elmdata = [mesh_io.ElementData(E_analytical, 'analytical'),
mesh_io.ElementData(E, 'E_FEM'),
mesh_io.ElementData(E_analytical + dAdt.node_data2elm_data().value, 'grad_analytical'),
dAdt]
#mesh_io.write_msh(m, '~/Tests/fem.msh')
assert rdm(E, E_analytical) < .2
assert np.abs(mag(E, E_analytical)) < np.log(1.1)
def test_single_dipole(self, dipole_direction, pos_target, sphere3_msh):
bar = sphere3_msh.elements_baricenters()[sphere3_msh.elm.tetrahedra]
vol = sphere3_msh.elements_volumes_and_areas()
dipole_th = np.argmin(np.linalg.norm(pos_target - bar, axis=1))
dipole_pos = bar[dipole_th]
dipole_th = sphere3_msh.elm.tetrahedra[dipole_th]
surface_nodes = np.unique(
sphere3_msh.elm[sphere3_msh.elm.tag1 == 1005, :3])
surface_nodes_pos = sphere3_msh.nodes[surface_nodes]
analytical_v = analytical_solutions.potential_dipole_3layers(
[85, 90, 95], 2, 0.1, dipole_pos, dipole_direction,
surface_nodes_pos)
# Relationship between primary current J and dipole vector p
# p = \int J dV
# p = J*V_i
# J = p/V_i
primary_j = mesh_io.ElementData(np.zeros((sphere3_msh.elm.nr, 3)))
primary_j[dipole_th] = dipole_direction / (vol[dipole_th] * 1e-9)
cond = 2 * np.ones(sphere3_msh.elm.nr)
cond[sphere3_msh.elm.tag1 == 4] = 0.1
S = fem.FEMSystem.electric_dipole(sphere3_msh, cond)
b = S.assemble_electric_dipole_rhs(primary_j)
numerical_v = S.solve(b)[surface_nodes - 1]
analytical_v -= np.average(analytical_v)
numerical_v -= np.average(numerical_v)
assert rdm(analytical_v, numerical_v) < 0.2
assert mag(analytical_v, numerical_v) < 0.15
def test_solve_petsc(self, tms_sphere):
m, cond, dAdt, E_analytical = tms_sphere
S = fem.FEMSystem.tms(m, cond)
b = S.assemble_tms_rhs(dAdt)
x = S.solve(b)
v = mesh_io.NodeData(x, 'FEM', mesh=m)
E = -v.gradient().value * 1e3 - dAdt.node_data2elm_data().value
m.elmdata = [mesh_io.ElementData(E_analytical, 'analytical'),
mesh_io.ElementData(E, 'E_FEM'),
mesh_io.ElementData(E_analytical + dAdt.node_data2elm_data().value, 'grad_analytical'),
dAdt]
m.nodedata = [mesh_io.NodeData(x, 'FEM')]
#mesh_io.write_msh(m, '~/Tests/fem.msh')
assert rdm(E, E_analytical) < .2
assert np.abs(mag(E, E_analytical)) < np.log(1.1)
def test_avoid_mean_field_norm_elm(self, sphere_surf):
a = opt_struct.TDCSavoid(tissues=[1003],
weight=1e4,
lf_type='element',
mesh=sphere_surf)
field = mesh_io.ElementData(np.ones((sphere_surf.elm.nr, 3)))
field[sphere_surf.elm.tag1 == 1003] = [2, 0, 0]
assert np.isclose(a.mean_field_norm_in_region(field), 2)
def calc_B(J, n_voxels, affine, calc_res=2., mask=False):
''' Calculates the magnetic field caused by a current density distribution J
Parameters
----------
J: simnibs.msh.ElementData
ElementData field with the current density field
n_voxels: list or tuple
number of voxels in x, y, and z directions for the output B
affine: ndarray
A 4x4 matrix specifying the transformation from voxels to xyz for the output B
calc_res: float (optional)
Resolution of the space used for the FFT calculations, in mm. Default: 2
mask: bool (optional)
Wether to mask the resul using the mesh. Default: False
Returns
--------
B: ndarray
numpy array of size n_voxesx3 with the magnetic field
Reference
----------
Yazdanian, H., Saturnino, G. B., Thielscher, A., & Knudsen, K. (2020).
Fast evaluation of the Biot-Savart integral using FFT for electrical conductivity imaging.
Journal of Computational Physics, 109408.
https://doi.org/10.1016/j.jcp.2020.109408
Example
---------
Load a simulation result with a 'J' field can calculate B in an ROI
Defined by a nifti file
>>> import simnibs
>>> import nibabel
>>> simulation_J = simnibs.read_msh('simulation_result_with_J.msh')
>>> reference_nifti = nibabel.load('reference.nii)
>>> B = simnibs.simulation.calc_B(simulation_J.field['J'], reference_nifti.shape, reference_nifti.affine)
'''
mesh = J.mesh
# Computational Domain (before zero-padding)
domain = _comp_domain(mesh, n_voxels, affine)
# Voxelize J
J_vol, affine_vol = _voxelize(J, domain, calc_res)
# Calculate B in the whole domain
B_vol = _bs_ft(J_vol, calc_res)
# Interpolate B to the domain of interest
B = transformations.volumetric_affine((B_vol, affine_vol),
np.eye(4),
affine,
n_voxels,
intorder=1,
keep_vector_length=False)
if mask:
msk = mesh_io.ElementData(np.ones(mesh.elm.nr), mesh=mesh)
msk = msk.interpolate_to_grid(n_voxels, affine, method='assign')
B *= msk[..., None]
return B
def test_mean_angle(self, sphere_vol):
t = opt_struct.TDCStarget(indexes=[1, 2],
directions=[[1, 0, 0], [0, 1, 0]],
mesh=sphere_vol,
lf_type='element',
radius=0)
f = mesh_io.ElementData(np.zeros((sphere_vol.elm.nr, 3)))
f[1] = [1, 1, 0]
f[2] = [2, 2, 0]
assert np.isclose(t.mean_angle(f), 45)
def test_leadfield(self, input_type, n_workers, field, post_pro, cube_msh):
if sys.platform == 'win32' and n_workers > 1:
''' Same as above, does not work on windows '''
return
m = cube_msh
cond = np.ones(m.elm.nr)
cond[m.elm.tag1 > 5] = 1e3
cond = mesh_io.ElementData(cond, mesh=m)
if input_type == 'tag':
el = [1100, 1101, 1101]
elif input_type == 'node':
el = [
np.unique(m.elm[m.elm.tag1 == 1100, :3]),
np.unique(m.elm[m.elm.tag1 == 1101, :3]),
np.unique(m.elm[m.elm.tag1 == 1101, :3])
]
fn_hdf5 = tempfile.NamedTemporaryFile(delete=False).name
dataset = 'leadfield'
if post_pro:
def post(E):
return E[:10] * 2
else:
post = None
fem.tdcs_leadfield(m,
cond,
el,
fn_hdf5,
dataset,
roi=[5],
field=field,
post_pro=post,
n_workers=n_workers,
input_type=input_type)
if not post_pro:
n_roi = np.sum(m.elm.tag1 == 5)
with h5py.File(fn_hdf5) as f:
assert f[dataset].shape == (2, n_roi, 3)
assert rdm(f[dataset][0, ...],
np.tile([0., 100, 0.], (n_roi, 1))) < .2
assert mag(f[dataset][0, ...],
np.tile([0., 100, 0.], (n_roi, 1))) < np.log(1.1)
if post_pro:
with h5py.File(fn_hdf5) as f:
assert f[dataset].shape == (2, 10, 3)
assert rdm(f[dataset][0, ...], np.tile([0., 200, 0.],
(10, 1))) < .2
assert mag(f[dataset][0, ...], np.tile([0., 200, 0.],
(10, 1))) < np.log(1.1)
os.remove(fn_hdf5)
def test_mean_intensity_none(self, sphere_vol):
t = opt_struct.TDCStarget(indexes=[1, 2],
directions=None,
mesh=sphere_vol,
lf_type='element',
radius=0)
f = mesh_io.ElementData(np.zeros((sphere_vol.elm.nr, 3)))
f[1] = [np.sqrt(2), np.sqrt(2), 0]
f[2] = [np.sqrt(3), np.sqrt(3), np.sqrt(3)]
vols = sphere_vol.elements_volumes_and_areas()[:]
m = np.average([2, 3], weights=vols[:2])
assert np.isclose(t.mean_intensity(f), m)
def test_tdcs_neumann_3_el(self, cube_msh):
m = cube_msh
cond = np.ones(m.elm.nr)
cond[m.elm.tag1 > 5] = 1e3
cond = mesh_io.ElementData(cond)
el_tags = [1100, 1101, 1101]
currents = [.5, -1.5, 1.]
x = fem.tdcs_neumann(m, cond, currents, el_tags)
sol = (m.nodes.node_coord[:, 1] - 50) / 20
m.nodedata = [x, mesh_io.NodeData(sol, 'Analytical')]
#mesh_io.write_msh(m, '~/Tests/fem.msh')
assert rdm(sol, x.value) < .1
assert np.abs(mag(x.value, sol)) < np.log(1.1)
def test_solve_dirichlet_petsc(self, cube_msh):
m = cube_msh
cond = np.ones(m.elm.nr)
cond[m.elm.tag1 > 5] = 1e3
cond = mesh_io.ElementData(cond)
el_tags = [1100, 1101]
potentials = [1, -1]
S = fem.FEMSystem.tdcs(m, cond, el_tags, potentials)
x = S.solve()
sol = m.nodes.node_coord[:, 1]/50.
m.nodedata = [mesh_io.NodeData(x, 'FEM'), mesh_io.NodeData(sol, 'Analytical')]
#mesh_io.write_msh(m, '~/Tests/fem.msh')
assert rdm(sol, x.T) < .1
assert np.abs(mag(x, sol)) < np.log(1.1)
def test_visualization(self, tensor):
eig_val, eig_vec = np.linalg.eig(tensor)
max_eig = eig_val.argmax()
min_eig = eig_val.argmin()
t = np.tile(tensor, [10, 1, 1])
factor = np.arange(1, 11)
t *= factor[:, None, None]
t = mesh_io.ElementData(t.reshape(-1, 9))
fields = cond.TensorVisualization(t, None, all_compoents=True)
assert np.allclose(fields[0].value / factor[:, None],
eig_val[max_eig] * eig_vec[:, max_eig])
assert np.allclose(fields[2].value / factor[:, None],
eig_val[min_eig] * eig_vec[:, min_eig])
assert np.allclose(fields[3].value / factor,
np.prod(eig_val) ** (1.0/3.0))
def test_solve_assemble_neumann_petsc(self, cube_msh):
m = cube_msh
cond = np.ones(m.elm.nr)
cond[m.elm.tag1 > 5] = 25
cond = mesh_io.ElementData(cond)
el_tags = [1100, 1101]
currents = [1, -1]
S = fem.FEMSystem.tdcs_neumann(m, cond, el_tags[0])
b = S.assemble_tdcs_neumann_rhs(el_tags[1:], currents[1:])
x = S.solve(b)
sol = (m.nodes.node_coord[:, 1] - 50) / 10
m.nodedata = [mesh_io.NodeData(x, 'FEM'), mesh_io.NodeData(sol, 'Analytical')]
#mesh_io.write_msh(m, '~/Tests/fem.msh')
assert rdm(sol, x.T) < .1
assert np.abs(mag(x, sol)) < np.log(1.5)
def tms_sphere(sphere3_msh):
m = sphere3_msh.crop_mesh(elm_type=4)
dipole_pos = np.array([0., 0., 300])
dipole_moment = np.array([1., 0., 0.])
didt = 1e6
r = (m.nodes.node_coord - dipole_pos) * 1e-3
dAdt = 1e-7 * didt * np.cross(dipole_moment, r) / (np.linalg.norm(r, axis=1)[:, None] ** 3)
dAdt = mesh_io.NodeData(dAdt, mesh=m)
dAdt.field_name = 'dAdt'
dAdt.mesh = m
pos = m.elements_baricenters().value
E_analytical = analytical_solutions.tms_E_field(dipole_pos * 1e-3,
dipole_moment, didt,
pos * 1e-3)
cond = mesh_io.ElementData(np.ones(m.elm.nr))
cond.mesh = m
return m, cond, dAdt, E_analytical
def test_solve_assemble_aniso(self, cube_msh):
m = cube_msh
cond = np.tile(np.eye(3), (m.elm.nr, 1, 1))
cond[m.elm.tag1 > 5] *= 100
cond[m.elm.tag1 < 5, 0, :] = 0.01
cond[m.elm.tag1 < 5, 1, :] = 0.1
cond = mesh_io.ElementData(cond.reshape(-1, 9))
el_tags = [1100, 1101]
currents = [1, -1]
S = fem.FEMSystem.tdcs_neumann(m, cond, el_tags[0])
b = S.assemble_tdcs_neumann_rhs(el_tags[1:], currents[1:])
x = S.solve(b)
sol = (m.nodes.node_coord[:, 1] - 50) / 10
m.nodedata = [mesh_io.NodeData(x, 'FEM'), mesh_io.NodeData(sol, 'Analytical')]
#mesh_io.write_msh(m, '~/Tests/fem.msh')
assert rdm(sol, x.T) < .1
assert np.abs(mag(x, sol)) < np.log(1.5)
def test_calc_tensor(self, sphere3_msh):
phi = sphere3_msh.nodes.node_coord[:, 0] + \
2 * sphere3_msh.nodes.node_coord[:, 1] + \
-3 * sphere3_msh.nodes.node_coord[:, 2]
potential = mesh_io.NodeData(phi, mesh=sphere3_msh)
o = np.ones(sphere3_msh.elm.nr)
z = np.zeros(sphere3_msh.elm.nr)
cond = np.reshape(np.eye(3) * np.array([1, 2, 3]), -1)
cond = np.tile(cond, [sphere3_msh.elm.nr, 1])
cond = mesh_io.ElementData(cond, mesh=sphere3_msh)
m = fem.calc_fields(potential, 'vJEgsej', cond, units='m')
assert np.allclose(m.field['v'].value, potential.value)
assert np.allclose(m.field['g'].value, [1, 2, -3])
assert np.allclose(m.field['E'].value, [-1, -2, 3])
assert np.allclose(m.field['J'].value, [-1, -4, 9])
def test_calc_gradient(self, cube_msh):
m = cube_msh
cond = np.ones(m.elm.nr)
cond = mesh_io.ElementData(cond)
S = fem.FEMSystem.tdcs_neumann(m, cond, 1100)
z = m.nodes.node_coord[:, 0]
assert np.allclose(S.calc_gradient(z), [1, 0, 0])
z = m.nodes.node_coord[:, 1]
assert np.allclose(S.calc_gradient(z), [0, 1, 0])
z = m.nodes.node_coord[:, 2]
assert np.allclose(S.calc_gradient(z), [0, 0, 1])
z = m.nodes.node_coord
grad = S.calc_gradient(z) * [2, 3, 1]
assert np.allclose(grad[:, :, 0], [2, 0, 0])
assert np.allclose(grad[:, :, 1], [0, 3, 0])
assert np.allclose(grad[:, :, 2], [0, 0, 1])
def test_solve_assemble_neumann_nodes(self, cube_msh):
m = cube_msh
cond = np.ones(m.elm.nr)
cond[m.elm.tag1 > 5] = 25
cond = mesh_io.ElementData(cond)
currents = [1, -1]
nodes_top = np.unique(m.elm[m.elm.tag1 == 1100, :3])
nodes_bottom = np.unique(m.elm[m.elm.tag1 == 1101, :3])
S = fem.FEMSystem.tdcs_neumann(m, cond, nodes_top, input_type='node')
b = S.assemble_tdcs_neumann_rhs(nodes_bottom,
currents[1:],
input_type='node')
x = S.solve(b)
sol = (m.nodes.node_coord[:, 1] - 50) / 10
m.nodedata = [
mesh_io.NodeData(x, 'FEM'),
mesh_io.NodeData(sol, 'Analytical')
]
#mesh_io.write_msh(m, '~/Tests/fem.msh')
assert rdm(sol, x.T) < .1
assert np.abs(mag(x, sol)) < np.log(1.5)