def LFcomputing(condFile, geomFile, dipoleFile, electrodesFile, savedir):
"""
condFile = 'om_demo.cond'
geomFile = 'om_demo.geom'
dipoleFile = 'cortex.dip'
squidsFile = 'meg_squids.txt'
electrodesFile = 'eeg_electrodes.txt'
"""
# Load data
geom = om.Geometry()
geom.read(geomFile, condFile)
dipoles = om.Matrix()
dipoles.load(dipoleFile)
#squids = om.Sensors()
#squids.load(squidsFile)
electrodes = om.Sensors()
electrodes.load(electrodesFile)
# Compute forward problem
gaussOrder = 3
use_adaptive_integration = True
hm = om.HeadMat(geom, gaussOrder)
hminv = hm.inverse()
dsm = om.DipSourceMat(geom, dipoles, gaussOrder, use_adaptive_integration)
#ds2mm = om.DipSource2MEGMat (dipoles, squids)
#h2mm = om.Head2MEGMat (geom, squids)
h2em = om.Head2EEGMat(geom, electrodes)
#gain_meg = om.GainMEG (hminv, dsm, h2mm, ds2mm)
gain_eeg = om.GainEEG(hminv, dsm, h2em)
gain_eeg.save(savedir)
return gain_eeg
def create_om_head(self): #TODO: Prob. need to make file names specifiable
"""
Generates 5 files::
skull_skin.tri
skin_air.tri
brain_skull.tri
head_model.geom
head_model.cond
Containing the specification of a head in a form that can be read by
OpenMEEG, then creates and returns an OpenMEEG Geometry object containing
this information.
"""
surface_files = []
surface_files.append(self._tvb_surface_to_tri("skull_skin.tri"))
surface_files.append(self._tvb_surface_to_tri("brain_skull.tri"))
surface_files.append(self._tvb_surface_to_tri("skin_air.tri"))
geometry_file = self._write_head_geometry(surface_files,
"head_model.geom")
conductances_file = self._write_conductances("head_model.cond")
LOG.info("Creating OpenMEEG Geometry object for the head...")
om_head = om.Geometry()
om_head.read(geometry_file, conductances_file)
#om_head.selfCheck() #Didn't catch bad order...
LOG.info("OpenMEEG Geometry object for the head successfully created.")
return om_head
def _get_geom_files(bem_model, mri_trans, head_trans):
surf_names = ['inner_skull', 'outer_skull', 'outer_skin'][::-1]
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']
# mlab.triangular_mesh(points[:, 0], points[:, 1], points[:, 2],
# faces, colormap='RdBu', opacity=0.5)
write_tri('%s.tri' % surf_name, points, swap_faces(faces), normals)
geom_fname = 'model.geom'
cond_fname = 'model.cond'
conductivity = [s['sigma'] for s in bem_model]
write_geom(geom_fname, surf_names)
write_cond(cond_fname, conductivity)
coord_frame = 'head'
trans = mne.read_trans(trans_fname)
head_trans, meg_trans, mri_trans = _prepare_trans(info, trans, coord_frame)
surf_names = ['inner_skull', 'outer_skull', 'outer_skin'][::-1]
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']
# mlab.triangular_mesh(points[:, 0], points[:, 1], points[:, 2],
# faces, colormap='RdBu', opacity=0.5)
write_tri('%s.tri' % surf_name, points, swap_faces(faces), normals)
write_geom(geom_fname, surf_names)
write_cond(cond_fname, conductivity)
# OpenMEEG
geom = om.Geometry(geom_fname, cond_fname)
return geom
default=data_path) 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.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) ###############################################################################
default=data_path, ) 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
meshes["skull"] = python_mesh("skull", op.join(dirpath, "skull.1.tri"))
meshes["scalp"] = python_mesh("scalp", op.join(dirpath, "scalp.1.tri"))
# It should be possible to have multiple oriented meshes per interface. e.g.
# interface1 = [(m1,om.OrientedMesh.Normal), (m2,om.OrientedMesh.Opposite), (m3,om.OrientedMesh.Normal)]
# It should also be possible to have a name added at the beginning of the
# tuple.
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)], 1.0),
"Brain": ([('interface1', om.SimpleDomain.Inside)], 1.0),
"Air": ([('interface3', om.SimpleDomain.Outside)], 0.0),
"Skull": ([('interface2', om.SimpleDomain.Inside),
('interface1', om.SimpleDomain.Outside)], 0.0125)
}
g1 = om.make_geometry(meshes, interfaces, domains)
g2 = om.Geometry(op.join(dirpath, subject + ".geom"),
op.join(dirpath, subject + ".cond"))
assert g1.is_nested()
assert g2.is_nested()
assert g1.__class__ == g2.__class__
#!/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)