def create_eeg_mesh(subject, excludes=[], overwrite_faces_verts=True):
try:
from scipy.spatial import Delaunay
from src.utils import trig_utils
input_file = op.join(MMVT_DIR, subject, 'eeg', 'eeg_positions.npz')
mesh_ply_fname = op.join(MMVT_DIR, subject, 'eeg', 'eeg_helmet.ply')
faces_verts_out_fname = op.join(MMVT_DIR, subject, 'eeg', 'eeg_faces_verts.npy')
f = np.load(input_file)
verts = f['pos']
excluded_inds = [np.where(f['names'] == e)[0] for e in excludes]
# verts = np.delete(verts, excluded_inds, 0)
verts_tup = [(x, y, z) for x, y, z in verts]
tris = Delaunay(verts_tup)
faces = tris.convex_hull
areas = [trig_utils.poly_area(verts[poly]) for poly in tris.convex_hull]
inds = [k for k, s in enumerate(areas) if s > np.percentile(areas, 97)]
faces = np.delete(faces, inds, 0)
utils.write_ply_file(verts, faces, mesh_ply_fname, True)
utils.calc_ply_faces_verts(verts, faces, faces_verts_out_fname, overwrite_faces_verts,
utils.namebase(faces_verts_out_fname))
np.savez(input_file, pos=f['pos'], names=f['names'], tri=faces, excludes=excludes)
except:
print('Error in create_eeg_mesh!')
print(traceback.format_exc())
return False
return True
def create_eeg_mesh(subject, excludes=[], overwrite_faces_verts=True):
try:
from scipy.spatial import Delaunay
from src.utils import trig_utils
input_file = op.join(MMVT_DIR, subject, 'eeg', 'eeg_positions.npz')
mesh_ply_fname = op.join(MMVT_DIR, subject, 'eeg', 'eeg_helmet.ply')
faces_verts_out_fname = op.join(MMVT_DIR, subject, 'eeg',
'eeg_faces_verts.npy')
f = np.load(input_file)
verts = f['pos']
excluded_inds = [np.where(f['names'] == e)[0] for e in excludes]
# verts = np.delete(verts, excluded_inds, 0)
verts_tup = [(x, y, z) for x, y, z in verts]
tris = Delaunay(verts_tup)
faces = tris.convex_hull
areas = [
trig_utils.poly_area(verts[poly]) for poly in tris.convex_hull
]
inds = [k for k, s in enumerate(areas) if s > np.percentile(areas, 97)]
faces = np.delete(faces, inds, 0)
utils.write_ply_file(verts, faces, mesh_ply_fname, True)
utils.calc_ply_faces_verts(verts, faces, faces_verts_out_fname,
overwrite_faces_verts,
utils.namebase(faces_verts_out_fname))
np.savez(input_file,
pos=f['pos'],
names=f['names'],
tri=faces,
excludes=excludes)
except:
print('Error in create_eeg_mesh!')
print(traceback.format_exc())
return False
return True
def create_eeg_mesh_from_obj(subject, obj_fname):
mesh_ply_fname = op.join(MMVT_DIR, subject, 'eeg', 'eeg_helmet.ply')
# mesh = obj.Obj(obj_fname)
# verts, faces = mesh.vertices, mesh.faces
verts, faces = utils.read_obj_file(obj_fname)
utils.write_ply_file(verts, faces, mesh_ply_fname)
faces_verts_out_fname = op.join(MMVT_DIR, subject, 'eeg', 'eeg_faces_verts.npy')
utils.calc_ply_faces_verts(verts, faces, faces_verts_out_fname, True,
utils.namebase(faces_verts_out_fname))
def calc_faces_verts_dic(subject, atlas, overwrite=False):
# hemis_plus = HEMIS + ['cortex']
ply_files = [op.join(MMVT_DIR, subject, 'surf', '{}.pial.npz'.format(hemi)) for hemi in utils.HEMIS]
out_files = [op.join(MMVT_DIR, subject, 'faces_verts_{}.npy'.format(hemi)) for hemi in utils.HEMIS]
subcortical_plys = glob.glob(op.join(MMVT_DIR, subject, 'subcortical', '*.ply'))
errors = {}
if len(subcortical_plys) > 0:
faces_verts_dic_fnames = [op.join(MMVT_DIR, subject, 'subcortical', '{}_faces_verts.npy'.format(
utils.namebase(ply))) for ply in subcortical_plys]
ply_files.extend(subcortical_plys)
out_files.extend(faces_verts_dic_fnames)
for hemi in utils.HEMIS:
labels_plys = glob.glob(op.join(MMVT_DIR, subject, '{}.pial.{}'.format(atlas, hemi), '*.ply'))
if len(labels_plys) > 0:
faces_verts_dic_fnames = [op.join(MMVT_DIR, subject, '{}.pial.{}'.format(atlas, hemi), '{}_faces_verts.npy'.format(
utils.namebase(ply))) for ply in labels_plys]
ply_files.extend(labels_plys)
out_files.extend(faces_verts_dic_fnames)
for ply_file, out_file in zip(ply_files, out_files):
if not overwrite and op.isfile(out_file):
# print('{} already exist.'.format(out_file))
continue
# ply_file = op.join(SUBJECTS_DIR, subject,'surf', '{}.pial.ply'.format(hemi))
# print('preparing a lookup table for {}'.format(ply_file))
verts, faces = utils.read_ply_file(ply_file)
errors = utils.calc_ply_faces_verts(verts, faces, out_file, overwrite, utils.namebase(ply_file), errors)
if len(errors) > 0:
for k, message in errors.items():
print('{}: {}'.format(k, message))
return len(errors) == 0
def create_faces_verts(subject):
skull_fol = op.join(MMVT_DIR, subject, 'skull')
errors = {}
for skull_surf in ['inner_skull', 'outer_skull']:
ply_fname = op.join(skull_fol, '{}.ply'.format(skull_surf))
verts, faces = utils.read_ply_file(ply_fname)
faces_verts_fname = op.join(skull_fol,
'faces_verts_{}.npy'.format(skull_surf))
errors = utils.calc_ply_faces_verts(verts, faces,
faces_verts_fname, False,
utils.namebase(ply_fname), errors)
if len(errors) > 0:
for k, message in errors.items():
print('{}: {}'.format(k, message))
def recreate_mesh_faces_verts(subject, ply_fname):
verts, faces = utils.read_ply_file(ply_fname)
faces_verts_out_fname = op.join(MMVT_DIR, subject, 'eeg', 'eeg_faces_verts.npy')
utils.calc_ply_faces_verts(verts, faces, faces_verts_out_fname, True,
utils.namebase(faces_verts_out_fname))