def test_prepare_set_mesh_vol(self, fn_vol, sphere_surf):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_vol)
p.mesh = sphere_surf
assert np.all(
np.isclose(p.mesh.nodes.node_coord, sphere_surf.nodes.node_coord))
assert np.all(
p.mesh.elm.node_number_list == sphere_surf.elm.node_number_list)
def test_optimize(self, intensity, max_el_c, max_tot_c, max_ac, max_angle,
n_targets, sphere_surf, fn_surf, leadfield_surf):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_surf,
max_individual_current=max_el_c,
max_total_current=max_tot_c,
max_active_electrodes=max_ac)
for i in range(n_targets):
t = p.add_target()
t.indexes = i + 1
t.directions = [1., 0., 0.]
t.intensity = intensity
if max_el_c is None and max_tot_c is None:
pass
elif n_targets > 1 and max_angle is not None:
pass
else:
currents = p.optimize()
assert np.isclose(np.sum(currents), 0, atol=1e-6)
if max_el_c is not None:
assert np.max(np.abs(currents)) < max_el_c * 1.05
if max_tot_c is not None:
assert np.linalg.norm(currents, 1) < 2 * max_tot_c * 1.05
if max_ac is not None:
assert np.linalg.norm(currents, 0) <= max_ac
for i in range(n_targets):
field = currents[1:].dot(leadfield_surf[:, i, :])
assert np.sign(field[0]) == np.sign(intensity)
def test_optimize_norm(self, max_el_c, max_tot_c, max_ac, n_targets,
sphere_surf, fn_surf, leadfield_surf):
intensity = 3e-5
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_surf,
max_individual_current=max_el_c,
max_total_current=max_tot_c,
max_active_electrodes=max_ac)
for i in range(n_targets):
t = p.add_target()
t.indexes = i + 1
t.directions = None
t.intensity = intensity
if max_el_c is None and max_tot_c is None:
pass
else:
currents = p.optimize()
assert np.isclose(np.sum(currents), 0, atol=1e-6)
if max_el_c is not None:
assert np.max(np.abs(currents)) < max_el_c * 1.05
if max_tot_c is not None:
assert np.linalg.norm(currents, 1) < 2 * max_tot_c * 1.05
if max_ac is not None:
assert np.linalg.norm(currents, 0) <= max_ac
def test_get_avoid_field_vol(self, fn_vol, sphere_vol):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_vol)
t = p.add_avoid()
t.tissues = 4
t.weight = 1e5
avoid_field = p._get_avoid_field()
assert np.allclose(avoid_field[sphere_vol.elm.tag1 == 4], 1e5)
assert np.allclose(avoid_field[sphere_vol.elm.tag1 != 4], 1)
def test_calc_energy_matrix_surf(self, fn_surf, sphere_surf,
leadfield_surf):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_surf)
p.mesh = sphere_surf
energy_mat = p.calc_energy_matrix()
areas = sphere_surf.nodes_volumes_or_areas().value
e_matrix = methods.energy_matrix(leadfield_surf, areas)
assert np.all(np.isclose(energy_mat, e_matrix))
def test_currents_csv(self, names, fn_elec):
csv_fn = 'test.csv'
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_elec)
currents = [-0.2, 0.2]
p.write_currents_csv(currents, csv_fn, electrode_names=names)
with open(csv_fn) as f:
reader = csv.reader(f)
csv_rows = [row for row in reader]
os.remove(csv_fn)
assert csv_rows[0][0] == 'A'
assert np.isclose(float(csv_rows[0][1]), currents[0])
assert csv_rows[1][0] == 'B'
assert np.isclose(float(csv_rows[1][1]), currents[1])
def test_create_mat_struct(self):
p = opt_struct.TDCSoptimize(leadfield_hdf='a.hdf5',
max_total_current=2.,
max_individual_current=.1,
max_active_electrodes=3,
name='a',
open_in_gmsh=False)
m = p.to_mat()
assert m['leadfield_hdf'] == 'a.hdf5'
assert m['max_total_current'] == 2.
assert m['max_individual_current'] == .1
assert m['max_active_electrodes'] == 3
assert m['name'] == 'a'
assert m['open_in_gmsh'] == False
def test_mat_io(self, max_active_electrodes):
p = opt_struct.TDCSoptimize(
leadfield_hdf='a.hdf5',
max_total_current=2.,
max_individual_current=.1,
max_active_electrodes=max_active_electrodes,
name='aaa')
m = p.to_mat()
scipy.io.savemat('tmp.mat', m)
m = scipy.io.loadmat('tmp.mat',
struct_as_record=True,
squeeze_me=False)
os.remove('tmp.mat')
p = opt_struct.TDCSoptimize.read_mat_struct(m)
assert p.leadfield_hdf == 'a.hdf5'
assert p.max_total_current == 2.
assert p.max_individual_current == .1
assert p.max_active_electrodes == max_active_electrodes
assert p.name == 'aaa'
def test_add_target(self):
p = opt_struct.TDCSoptimize()
t = p.add_target()
assert t is p.target[-1]
def test_field_elm(self, leadfield_vol, fn_vol):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_vol)
c = [1., -1., 0, 0., 0.]
E = p.field(c)
assert isinstance(E, mesh_io.ElementData)
assert np.allclose(E.value, -leadfield_vol[0])
def test_field_node(self, leadfield_surf, fn_surf):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_surf)
c = [1., -1., 0, 0., 0.]
E = p.field(c)
assert isinstance(E, mesh_io.NodeData)
assert np.allclose(E.value, -leadfield_surf[0])
def test_read_lf(self, fn_surf, leadfield_surf):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_surf)
assert np.all(np.isclose(p.leadfield, leadfield_surf))
p.leadfield
def test_set_lf(self, fn_surf, leadfield_vol):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_surf)
p.leadfield = leadfield_vol
assert np.all(np.isclose(p.leadfield, leadfield_vol))
def test_add_target_arg(self):
t = 'taget'
p = opt_struct.TDCSoptimize()
p.add_target(t)
assert t is p.target[-1]
def test_read_lftype(self, fn_surf):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_surf)
assert p.lf_type == 'node'
def test_read_lftype_elm(self, fn_vol):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_vol)
assert p.lf_type == 'element'
def test_read_lftype_wrong(self, fn_vol, sphere_surf):
p = opt_struct.TDCSoptimize(leadfield_hdf=fn_vol)
p.mesh = sphere_surf
with pytest.raises(ValueError):
p.lf_type
