def _get_geom(bem_model, mri_trans, head_trans):
surf_names = ['cortex', 'skull', 'scalp'][::-1]
# meshes = []
for surf_name, surf in zip(surf_names, bem_model):
surf = _convert_bem_surf(surf, mri_trans, head_trans)
points, faces, normals = surf['rr'], surf['tris'], surf['nn']
write_tri('%s.tri' % surf_name, points, swap_faces(faces), normals)
# mesh = om.Mesh('%s.tri' % surf_name)
# mesh = om.Mesh(np.asfortranarray(points),
# np.asfortranarray(swap_faces(faces)).astype(np.int64))
# mesh.update()
# mesh.setName(surf_name)
# meshes.append(mesh)
# cortex, skull, scalp = meshes[::-1]
cortex = om.Mesh("cortex.tri")
cortex.setName("cortex")
skull = om.Mesh("skull.tri")
skull.setName("skull")
scalp = om.Mesh("scalp.tri")
scalp.setName("scalp")
# cortex = om.Mesh("cortex.1.tri")
# cortex.setName("cortex")
# skull = om.Mesh("skull.1.tri")
# skull.setName("skull")
# scalp = om.Mesh("scalp.1.tri")
# scalp.setName("scalp")
# geom_fname = 'model.geom'
# cond_fname = 'model.cond'
conductivity = [s['sigma'] for s in bem_model]
interfaces = {
"interface1": [(cortex, om.OrientedMesh.Normal)],
"interface2": [(skull, om.OrientedMesh.Normal)],
"interface3": [(scalp, om.OrientedMesh.Normal)]
}
domains = {
"Scalp": ([('interface2', om.SimpleDomain.Outside),
('interface3', om.SimpleDomain.Inside)], conductivity[0]),
"Brain": ([('interface1', om.SimpleDomain.Inside)], conductivity[2]),
"Air": ([('interface3', om.SimpleDomain.Outside)], 0.0),
"Skull": ([('interface2', om.SimpleDomain.Inside),
('interface1', om.SimpleDomain.Outside)], conductivity[1])
}
geom = om.make_geometry(interfaces, domains)
return geom
def python_mesh(name, path):
mesh = om.Mesh(path)
mesh_vertices = mesh.geometry().vertices()
vertices = np.array([vertex.array() for vertex in mesh_vertices])
mesh_triangles = mesh.triangles()
triangles = np.array(
[mesh.triangle(triangle).array() for triangle in mesh_triangles])
return vertices, triangles
def test_mesh(name, vertices, triangles, expected_result):
try:
mesh = om.Mesh(vertices, triangles)
mesh.info()
except:
if expected_result:
print("Test", name, "--> Failed")
assert False
else:
print("Test", name, "--> Expected failure")
return
if not expected_result:
print("Test", name, "--> Unexpected success")
assert False
print("Test", name, "--> Expected success")
def create_om_sources(self): #TODO: Prob. should make file names specifiable
"""
Take a TVB Connectivity or Cortex object and return an OpenMEEG object
that specifies sources, a Matrix object for region level sources or a
Mesh object for a cortical surface source.
"""
if isinstance(self.sources, connectivity_module.Connectivity):
sources_file = self._tvb_connectivity_to_txt("sources.txt")
om_sources = om.Matrix()
elif isinstance(self.sources, Cortex):
sources_file = self._tvb_surface_to_tri("sources.tri")
om_sources = om.Mesh()
else:
LOG.error("sources must be either a Connectivity or Cortex.")
om_sources.load(sources_file)
return om_sources
############################################################################### # Load data subject = 'Head1' cond_file = op.join(data_path, subject, subject + '.cond') geom_file = op.join(data_path, subject, subject + '.geom') source_mesh_file = op.join(data_path, subject, subject + '.tri') dipole_file = op.join(data_path, subject, subject + '.dip') squidsFile = op.join(data_path, subject, subject + '.squids') patches_file = op.join(data_path, subject, subject + '.patches') geom = om.Geometry() geom.read(geom_file, cond_file) mesh = om.Mesh() mesh.load(source_mesh_file) dipoles = om.Matrix() dipoles.load(dipole_file) sensors = om.Sensors() sensors.load(squidsFile) patches = om.Sensors() patches.load(patches_file) ############################################################################### # Compute forward problem (Build Gain Matrices) gauss_order = 3
options, args = parser.parse_args() data_path = options.data_path # Load data subject = "Head1" cond_file = op.join(data_path, subject, subject + ".cond") geom_file = op.join(data_path, subject, subject + ".geom") source_mesh_file = op.join(data_path, subject, subject + ".tri") dipole_file = op.join(data_path, subject, subject + ".dip") squidsFile = op.join(data_path, subject, subject + ".squids") patches_file = op.join(data_path, subject, subject + ".patches") geom = om.Geometry(geom_file, cond_file) mesh = om.Mesh(source_mesh_file) dipoles = om.Matrix() dipoles.load(dipole_file) sensors = om.Sensors() sensors.load(squidsFile) patches = om.Sensors() patches.load(patches_file) # Compute forward problem (Build Gain Matrices) gauss_order = 3 use_adaptive_integration = True dipole_in_cortex = True
bad_vertices = np.array([0.0, 0.0])
test_mesh("6", bad_vertices, triangles, False)
bad_triangles = np.array([1, 2, 3])
test_mesh("7", vertices, bad_triangles, False)
triangles = np.array([[1, 2, 3], [2, 3, 0]], dtype=np.uint64)
test_mesh("8", vertices, triangles, True)
triangles = np.array([[1, 2, 3], [2, 3, 0]], dtype=np.int64)
test_mesh("9", vertices, triangles, True)
# test X -> should be OK
# TODO: Does not work if not jls....
data_file = path.join(data_path, "Head1", "Head1.tri")
mesh_X = om.Mesh()
mesh_X.load(data_file)
mesh_X.update()
# test Y -> redo with np.array()
V_Y = mesh_X.vertices()
# T6 = mesh_6.triangles()
# mesh_7 = om.Mesh(V6, T6)
# mesh_7.info()
# TODO
#
# mesh_6.nb_vertices() == mesh_7.nb_vertices()
# mesh_6.nb_triangles() == mesh_7.nb_triangles()
# V7 = mesh_6.vertices()
# T7 = mesh_6.triangles()
#!/usr/bin/env python
import numpy as np
import openmeeg as om
vertices = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [1.0, 1.0, 0.0],
[0.0, 1.0, 0.0]])
triangles = np.array([[1, 2, 3], [2, 3, 0]])
mesh = om.Mesh(vertices, triangles)
g = om.Geometry()
assert g.check(mesh)
g.import_meshes([mesh])
assert not g.check(mesh)
#!/usr/bin/env python
import numpy as np
import openmeeg as om
vertices = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [1.0, 1.0, 0.0],
[0.0, 1.0, 0.0]])
triangles = np.array([[1, 2, 3], [2, 3, 0]])
g = om.Geometry()
mesh = om.Mesh(vertices, triangles, "test", g)
assert mesh.geometry().check(mesh)
[0.5501, 0.2101, -0.34, -0.808998, -0.309019, 0.50003],
[0.5501, -0.2101, -0.34, -0.808998, 0.309019, 0.50003],
[0.2101, 0.34, -0.5501, -0.309019, -0.50003, 0.808998],
[-0.2101, 0.34, -0.5501, 0.309019, -0.50003, 0.808998],
[0, 0, -0.68, 0, 0, 1],
[-0.2101, -0.34, -0.5501, 0.309019, 0.50003, 0.808998],
[0.2101, -0.34, -0.5501, -0.309019, 0.50003, 0.808998],
[0.34, -0.5501, -0.2101, -0.50003, 0.808998, 0.309019],
[0, -0.68, 0, 0, 1, 0],
[0.34, -0.5501, 0.2101, -0.50003, 0.808998, -0.309019],
[-0.34, -0.5501, -0.2101, 0.50003, 0.808998, 0.309019],
[-0.34, -0.5501, 0.2101, 0.50003, 0.808998, -0.309019],
[-0.5501, -0.2101, 0.34, 0.808998, 0.309019, -0.50003],
[-0.2101, -0.34, 0.5501, 0.309019, 0.50003, -0.808998],
[0.2101, -0.34, 0.5501, -0.309019, 0.50003, -0.808998],
[0.68, 0, 0, 1, 0, 0],
[-0.5501, -0.2101, -0.34, 0.808998, 0.309019, 0.50003],
[-0.5501, 0.2101, -0.34, 0.808998, -0.309019, 0.50003],
])
I = np.array([[1, 3, 4], [2, 4, 5], [10, 3, 5], [21, 4, 5]])
mesh_1 = om.Mesh(V, I)
mesh_1.info()
# TODO: mesh.read() using numpy arrays
# TODO: mesh == [ double ] , [ int ]
# mesh = om.Mesh()
# mesh.load( fileskel + "tri")
# TODO: V = [...]
# TODO: I = [...]
# TODO: mesh_1 = om.Mesh(V, I)
