def add_electrodes(mesh_filename):
fwd_dir = os.environ['FWD_DIR']
electrode_location_file = op.join(fwd_dir, 'etc', 'ElectrodeLocations_TMS007.txt')
electrode_name_file = op.join(fwd_dir, 'etc', 'ElectrodeNames_BESA256.txt')
points = np.loadtxt(electrode_location_file, delimiter=',')
electrode_names = np.loadtxt(electrode_name_file, dtype='str')
write_electrode_labels(points, electrode_names, out_file="BESA256.geo")
mesh_id = 1005
out_file = rewrite_mesh_with_electrodes(electrode_location_file, electrode_name_file, mesh_filename, mesh_id)
return out_file
def add_electrodes(mesh_filename):
fwd_dir = os.environ['FWD_DIR']
electrode_location_file = op.join(fwd_dir, 'etc',
'ElectrodeLocations_TMS007.txt')
electrode_name_file = op.join(fwd_dir, 'etc', 'ElectrodeNames_BESA256.txt')
points = np.loadtxt(electrode_location_file, delimiter=',')
electrode_names = np.loadtxt(electrode_name_file, dtype='str')
write_electrode_labels(points, electrode_names, out_file="BESA256.geo")
mesh_id = 1005
out_file = rewrite_mesh_with_electrodes(electrode_location_file,
electrode_name_file, mesh_filename,
mesh_id)
return out_file
def add_sensors(electrode_location_file, mesh_file, radii):
points = np.loadtxt(electrode_location_file, delimiter=",")
points = np.max(radii) * points
new_electrode_location_file = op.abspath("electrode_locations.txt")
np.savetxt(new_electrode_location_file, points, delimiter=",")
elec_name_file = op.abspath(
op.basename(electrode_location_file) + "_names.txt")
f = open(elec_name_file, "w")
for idx in range(0, len(points)):
name = "vertex%03d" % (idx + 1)
f.write("%s\n" % name)
f.close()
print('Rewriting mesh with sensors')
print(new_electrode_location_file, elec_name_file, mesh_file)
out_file = rewrite_mesh_with_electrodes(
new_electrode_location_file,
electrode_name_file=elec_name_file,
mesh_file=mesh_file,
mesh_id=1004)
return op.abspath(out_file), elec_name_file, new_electrode_location_file
electrode_position_file = op.join(data_path, subject_id,
"ElectrodePositions.txt")
electrode_name_file = op.join(data_path, subject_id, "ElectrodeNames.txt")
# If you want to use the structural mesh, rather than the mesh including the conductivity
# tensors, you should uncomment the following line, and comment the one below it.
#mesh_path = op.abspath("structural_datasink/subject/volume_mesh/")
mesh_path = op.abspath("diffusion_datasink/subject/mesh_file/")
assert (op.exists(mesh_path))
search_string = "/*%s/%s*.msh" % (subject_id, subject_id)
try:
mesh_file = glob.glob(mesh_path + search_string)[0]
except IndexError:
raise IOError("Mesh file not found. You must run step1 and/or step2 \
before trying to add electrodes to the mesh.")
'''
We use the element ID for the scalp volume in the Gmsh mesh
'''
mesh_id = 1005
import time
start = time.time()
out_file = rewrite_mesh_with_electrodes(electrode_position_file,
electrode_name_file, mesh_file,
mesh_id)
end = time.time()
print(start)
print(end)
print(end - start)
electrode_position_file = op.join(data_path, subject_id, "ElectrodePositions.txt")
electrode_name_file = op.join(data_path, subject_id, "ElectrodeNames.txt")
# If you want to use the structural mesh, rather than the mesh including the conductivity
# tensors, you should uncomment the following line, and comment the one below it.
#mesh_path = op.abspath("structural_datasink/subject/volume_mesh/")
mesh_path = op.abspath("diffusion_datasink/subject/mesh_file/")
assert(op.exists(mesh_path))
search_string = "/*%s/%s*.msh" % (subject_id, subject_id)
try:
mesh_file = glob.glob(mesh_path + search_string)[0]
except IndexError:
raise IOError("Mesh file not found. You must run step1 and/or step2 \
before trying to add electrodes to the mesh.")
'''
We use the element ID for the scalp volume in the Gmsh mesh
'''
mesh_id = 1005
import time
start = time.time()
out_file = rewrite_mesh_with_electrodes(electrode_position_file, electrode_name_file,
mesh_file, mesh_id)
end = time.time()
print(start)
print(end)
print(end-start)
