def calc_surface_potential_fn(dipole_file, dipole_row, leadfield, mesh_file,
mesh_id):
import os.path as op
import numpy as np
import h5py
from forward.mesh import get_closest_element_to_point
from nipype import logging
iflogger = logging.getLogger('interface')
dipole_data = np.loadtxt(dipole_file)
if len(dipole_data.shape) == 1:
dipole_data = [dipole_data]
dip = dipole_data[int(dipole_row)]
x, y, z = [float(i) for i in dip[2:5]]
q_x, q_y, q_z = [float(j) for j in dip[6:9]]
_, element_idx, centroid, element_data, lf_idx = get_closest_element_to_point(
mesh_file, mesh_id, [[x, y, z]])
lf_data_file = h5py.File(leadfield, "r")
lf_data = lf_data_file.get("leadfield")
leadfield_matrix = lf_data.value
L = np.transpose(leadfield_matrix[lf_idx * 3:lf_idx * 3 + 3])
J = np.array([q_x, q_y, q_z])
potential = np.dot(L, J)
out_potential = op.abspath("potential.npy")
np.save(out_potential, potential)
return out_potential
def calc_surface_potential_fn(dipole_file, dipole_row, leadfield, mesh_file, mesh_id):
import os.path as op
import numpy as np
import h5py
from forward.mesh import get_closest_element_to_point
from nipype import logging
iflogger = logging.getLogger('interface')
dipole_data = np.loadtxt(dipole_file)
if len(dipole_data.shape) == 1:
dipole_data = [dipole_data]
dip = dipole_data[int(dipole_row)]
x, y, z = [float(i) for i in dip[2:5]]
q_x, q_y, q_z = [float(j) for j in dip[6:9]]
_, element_idx, centroid, element_data, lf_idx = get_closest_element_to_point(mesh_file, mesh_id, [[x, y, z]])
lf_data_file = h5py.File(leadfield, "r")
lf_data = lf_data_file.get("leadfield")
leadfield_matrix = lf_data.value
L = np.transpose(leadfield_matrix[lf_idx * 3:lf_idx * 3 + 3])
J = np.array([q_x,q_y,q_z])
potential = np.dot(L,J)
out_potential = op.abspath("potential.npy")
np.save(out_potential,potential)
return out_potential
def single_dipole_search(electrode_potential, leadfield, mesh_file, elements_to_consider=[1002]):
from forward.mesh import read_mesh, get_closest_element_to_point
from nipype import logging
iflogger = logging.getLogger('interface')
geo_file = op.abspath("search_points.geo")
data_name = "leadfield"
lf_data_file = h5py.File(leadfield, "r")
lf_data = lf_data_file.get(data_name)
leadfield_matrix = lf_data.value
_, lf_name, _ = split_filename(leadfield)
bounds = (0,leadfield_matrix.shape[0]/3)
mesh_data, _, _, _ = read_mesh(mesh_file, elements_to_consider)
centroids = []
element_ids = []
for poly in mesh_data:
element_ids.append(poly["element_id"])
centroids.append(poly["centroid"])
p0, bounds = random_initial_guess(centroids)
#p0 = np.array([0,0,60])
mw = {}
args = (leadfield_matrix, electrode_potential, centroids, element_ids)
mw['args'] = args
#mw['bounds'] = bounds
#res = so.basinhopping(calculate_element_cost, p0, T=0.01, stepsize = 3, minimizer_kwargs=mw, disp=True, niter_success=20)
# Perform downhill search, minimizing cost function
xopt, fopt, n_iter, funcalls, _, allvecs = so.fmin(calculate_element_cost, p0, ftol=0.00000001, args=(leadfield_matrix, electrode_potential, centroids, element_ids), xtol = 1, disp=True, full_output=True, retall=True)
write_search_points(allvecs, geo_file)
# Need to minimize cost by changing values of orientation and magnitude:
_, element_idx, centroid, element_data, lf_idx = get_closest_element_to_point(mesh_file, elements_to_consider, np.array([xopt]))
L = np.transpose(leadfield_matrix[lf_idx * 3:lf_idx * 3 + 3])
V = electrode_potential
qopt, _, _, _ = np.linalg.lstsq(L, V)
return xopt, qopt, element_data, geo_file
def get_rdm_and_mags(mesh_file, mesh_id, probe_dipole, probe_dipole_orientation, radii, cond, n=42, nMax=60):
four = pe.Node(interface=FourShellAnalyticalModel(), name="four")
name = str(probe_dipole[0]).replace(" ", "")
name = name.replace("[", "")
name = name.replace("]", "")
out_directory = op.abspath("dipole" + name)
if not op.exists(out_directory):
os.makedirs(out_directory)
four.base_dir = out_directory
four.inputs.probe_dipole_location = probe_dipole[0].tolist()
four.inputs.probe_dipole_orientation = probe_dipole_orientation[0].tolist()
four.inputs.script = "pyscript.m"
four.inputs.sphere_radii = radii
four.inputs.shell_conductivity = cond
four.inputs.icosahedron_sides = n
four.inputs.number_of_analytical_terms = nMax
four.inputs.fieldtrip_path = "/Developer/fieldtrip"
analytical_solution = op.join(out_directory, "four", "analytical.txt")
if not op.exists(analytical_solution):
four.run()
# Re-reference to ground electrode
lf_sphere = np.loadtxt(analytical_solution, delimiter=",")
lf_sphere = lf_sphere - lf_sphere[ground_idx]
lf_sphere = np.delete(lf_sphere, (ground_idx), axis=0)
lf_sphere = lf_sphere * probe_dipole_orientation
mesh_data, closest_element_idx, centroid, closest_element_data, lf_idx = get_closest_element_to_point(
mesh_file, mesh_id, probe_dipole
)
lf_getdp = np.transpose(leadfield_matrix[lf_idx * 3 : lf_idx * 3 + 3])
lf_getdp = lf_getdp * probe_dipole_orientation
rdms = np.empty((np.shape(lf_getdp)[1], 1))
rows = np.shape(lf_getdp)[1]
for idx in xrange(0, rows):
rdms[idx, :] = norm(lf_getdp[:, idx] / norm(lf_getdp[:, idx]) - lf_sphere[:, idx] / norm(lf_sphere[:, idx]))
mags = np.divide(np.sqrt(np.sum(lf_getdp ** 2, 0)), np.sqrt(np.sum(lf_sphere ** 2, 0)))
rdm_singlevalue = norm(lf_getdp / norm(lf_getdp) - lf_sphere / norm(lf_sphere))
mag_singlevalue = np.divide(norm(lf_getdp), norm(lf_sphere))
print ("RDMs %s" % str(rdms))
print rdm_singlevalue
print ("MAGs %s" % str(mags))
print mag_singlevalue
openmeeg_solution = op.join(out_directory, "four", "openmeeg.txt")
lf_openmeeg = np.loadtxt(openmeeg_solution, delimiter=",")
lf_openmeeg = lf_openmeeg * probe_dipole_orientation
try:
lf_openmeeg = lf_openmeeg - lf_openmeeg[ground_idx]
lf_openmeeg = np.delete(lf_openmeeg, (ground_idx), axis=0)
rdm_openmeeg = norm(lf_openmeeg / norm(lf_openmeeg) - lf_sphere / norm(lf_sphere))
mag_openmeeg = np.divide(norm(lf_openmeeg), norm(lf_sphere))
except IndexError:
rdm_openmeeg = None
mag_openmeeg = None
return (rdms, mags, rdm_singlevalue, mag_singlevalue, rdm_openmeeg, mag_openmeeg, lf_getdp, lf_sphere)
def get_rdm_and_mags(mesh_file, mesh_id, probe_dipole, probe_dipole_orientation, radii, cond, n=42, nMax=60):
four = pe.Node(interface=FourShellAnalyticalModel(), name="four")
name = str(probe_dipole[0]).replace(" ","")
name = name.replace('[','')
name = name.replace(']','')
out_directory = op.abspath("dipole" + name)
if not op.exists(out_directory):
os.makedirs(out_directory)
four.base_dir = out_directory
four.inputs.probe_dipole_location = probe_dipole[0].tolist()
four.inputs.probe_dipole_orientation = probe_dipole_orientation[0].tolist()
four.inputs.script = "pyscript.m"
four.inputs.sphere_radii = radii
four.inputs.shell_conductivity = cond
four.inputs.icosahedron_sides = n
four.inputs.number_of_analytical_terms = nMax
four.inputs.fieldtrip_path = "/Developer/fieldtrip"
analytical_solution = op.join(out_directory, "four", "analytical.txt")
if not op.exists(analytical_solution):
four.run()
# Re-reference to ground electrode
lf_sphere = np.loadtxt(analytical_solution, delimiter=",")
lf_sphere = lf_sphere - lf_sphere[ground_idx]
lf_sphere = np.delete(lf_sphere, (ground_idx), axis=0)
lf_sphere = lf_sphere * probe_dipole_orientation
mesh_data, closest_element_idx, centroid, closest_element_data, lf_idx = get_closest_element_to_point(mesh_file, mesh_id, probe_dipole)
lf_getdp = np.transpose(leadfield_matrix[lf_idx * 3:lf_idx * 3 + 3])
lf_getdp = lf_getdp * probe_dipole_orientation
rdms = np.empty((np.shape(lf_getdp)[1], 1))
rows = np.shape(lf_getdp)[1]
for idx in xrange(0, rows):
rdms[idx, :] = norm(lf_getdp[:, idx] / norm(lf_getdp[:, idx]) -
lf_sphere[:, idx] / norm(lf_sphere[:, idx]))
mags = np.divide(np.sqrt(np.sum(lf_getdp ** 2, 0)),
np.sqrt(np.sum(lf_sphere ** 2, 0)) )
rdm_singlevalue = norm( lf_getdp / norm(lf_getdp) - lf_sphere / norm(lf_sphere) )
mag_singlevalue = np.divide(norm(lf_getdp),norm(lf_sphere))
print("RDMs %s" % str(rdms))
print rdm_singlevalue
print("MAGs %s" % str(mags))
print mag_singlevalue
openmeeg_solution = op.join(out_directory, "four", "openmeeg.txt")
lf_openmeeg = np.loadtxt(openmeeg_solution, delimiter=",")
lf_openmeeg = lf_openmeeg * probe_dipole_orientation
try:
lf_openmeeg = lf_openmeeg - lf_openmeeg[ground_idx]
lf_openmeeg = np.delete(lf_openmeeg, (ground_idx), axis=0)
rdm_openmeeg = norm( lf_openmeeg / norm(lf_openmeeg) - lf_sphere / norm(lf_sphere) )
mag_openmeeg = np.divide(norm(lf_openmeeg),norm(lf_sphere))
except IndexError:
rdm_openmeeg = None
mag_openmeeg = None
return (rdms, mags, rdm_singlevalue, mag_singlevalue, rdm_openmeeg,
mag_openmeeg, lf_getdp, lf_sphere)