def test_patch(subject, **kargs):
from src.utils import preproc_utils as pu
SUBJECTS_DIR, MMVT_DIR, FREESURFER_HOME = pu.get_links()
flat_patch_cut_vertices = utils.load(op.join(MMVT_DIR, subject, 'flat_patch_cut_vertices.pkl'))
for hemi in utils.HEMIS:
# verts, faces = read_patch(hemi, SUBJECTS_DIR)
# write_patch(op.join(MMVT_DIR, 'fsaverage', 'surf', '{}.flat.test.pial'.format(hemi)), verts, faces)
# fs_verts, fs_faces = utils.read_pial('fsaverage', MMVT_DIR, hemi, surface_type='inflated')
print('Reading inflated surf')
fs_verts, fs_faces = nib.freesurfer.read_geometry(op.join(SUBJECTS_DIR, subject, 'surf', '{}.inflated'.format(hemi)))
# flat_verts, flat_faces = read_patch(hemi, SUBJECTS_DIR, surface_type='inflated')
# good_verts = set(np.unique(flat_faces))
# bad_verts = np.setdiff1d(np.arange(0, flat_verts.shape[0]), good_verts)
# bad_faces_inds = set(utils.flat_list_of_lists([verts_faces_lookup[hemi][v] for v in bad_verts]))
patch_fname = op.join(SUBJECTS_DIR, subject, 'surf', '{}.inflated.patch'.format(hemi))
print('Writing patch')
flat_patch_cut_vertices_hemi = set(flat_patch_cut_vertices[hemi])
write_patch(patch_fname, [(ind, v) for ind, v in enumerate(fs_verts) if ind not in flat_patch_cut_vertices_hemi], set())#flat_faces)
print('Reading patch')
patch_verts, patch_faces = read_patch(subject, hemi, SUBJECTS_DIR, surface_type='inflated', patch_fname=patch_fname)
print('Writing ply')
patch_verts *= 0.1
utils.write_ply_file(patch_verts, patch_faces, op.join(MMVT_DIR, subject, 'surf', '{}.flat.pial.test.ply').format(hemi))
print('Finish!')
def writing_ply_files(subject, surface_type, lab, facL_lab, vtx, vtxL, labels,
hemi, output_fol):
# Vertices for the current label
nV = vtx.shape[0]
facL_lab_flat = utils.list_flatten(facL_lab)
if len(facL_lab_flat) == 0:
print("Cant write {}, no vertices!".format(labels[lab]))
return True
vidx = list(set(facL_lab_flat))
vtxL[lab] = vtx[vidx]
# Reindex the faces
tmp = np.zeros(nV, dtype=np.int)
tmp[vidx] = np.arange(len(vidx))
try:
facL_lab = np.reshape(tmp[facL_lab_flat],
(len(facL_lab), len(facL_lab[0])))
except:
print(traceback.format_exc())
dumps_fol = utils.make_dir(op.join(MMVT_DIR, subject, 'dumps'))
utils.save((lab, facL_lab, vtx, vtxL, labels, hemi, output_fol),
op.join(dumps_fol,
'parcelate_cortex_writing_ply_files.pkl'))
return False
# Save the resulting surface
label_name = '{}-{}.ply'.format(
lu.get_label_hemi_invariant_name(labels[lab].name), hemi)
# print('Writing {}'.format(op.join(output_fol, label_name)))
# todo: add distance between hemis if inflated like with the activity surfaces
if surface_type == 'inflated':
verts_offset = 55 if hemi == 'rh' else -55
vtxL[lab][:, 0] = vtxL[lab][:, 0] + verts_offset
utils.write_ply_file(vtxL[lab], facL_lab, op.join(output_fol, label_name),
True)
return op.isfile(op.join(output_fol, label_name))
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_skull_plys(subject):
for skull_surf in ['inner_skull', 'outer_skull']:
ply_fname = op.join(SUBJECTS_DIR, subject, 'bem',
'{}.ply'.format(skull_surf))
surf_fname = op.join(SUBJECTS_DIR, subject, 'bem',
'{}.surf'.format(skull_surf))
verts, faces = nib_fs.read_geometry(surf_fname)
utils.write_ply_file(verts, faces, ply_fname, True)
def transform_to_another_subject(subject, region, subjects_dir):
colin27_xfm = tu.get_talxfm('colin27', subjects_dir)
xfm = tu.get_talxfm('colin27', subjects_dir)
for hemi in ['lh', 'rh']:
verts, faces = utils.read_ply_file(op.join(MMVT_DIR, 'colin27', 'subcortical', '{}_{}.ply'.format(region, hemi)))
verts = tu.apply_trans(colin27_xfm, verts)
verts = tu.apply_trans(np.linalg.inv(xfm), verts)
utils.write_ply_file(verts, faces, op.join(MMVT_DIR, subject, 'subcortical', '{}_{}.ply'.format(region, hemi)))
def transform_to_another_subject(subject, region, subjects_dir):
colin27_xfm = tu.get_talxfm('colin27', subjects_dir)
xfm = tu.get_talxfm('colin27', subjects_dir)
for hemi in ['lh', 'rh']:
verts, faces = utils.read_ply_file(op.join(MMVT_DIR, 'colin27', 'subcortical', '{}_{}.ply'.format(region, hemi)))
verts = tu.apply_trans(colin27_xfm, verts)
verts = tu.apply_trans(np.linalg.inv(xfm), verts)
utils.write_ply_file(verts, faces, op.join(MMVT_DIR, subject, 'subcortical', '{}_{}.ply'.format(region, hemi)))
def obj_to_ply():
fol = '/homes/5/npeled/space1/Angelique/Lionel Recon/blender/objs'
files = glob.glob(op.join(fol, '*.obj'))
for f in files:
print(f)
verts, faces = utils.read_obj_file(f)
ply_fname = utils.change_fname_extension(f, 'ply')
utils.write_ply_file(verts, faces, ply_fname, True)
def convert(subject, surfaces_fnames):
for surf_fname in surfaces_fnames:
ply_fname = op.join(SUBJECTS_DIR, subject, 'surf',
'{}.ply'.format(utils.namebase(surf_fname)))
if op.isfile(ply_fname):
continue
verts, faces = nib_fs.read_geometry(surf_fname)
utils.write_ply_file(verts, faces, ply_fname)
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 transform_to_another_subject(subject, region, subjects_dir):
import mne.source_space
import mne.transforms
colin27_xfm = mne.source_space._read_talxfm('colin27', subjects_dir, 'nibabel')
xfm = mne.source_space._read_talxfm(subject, subjects_dir, 'nibabel')
for hemi in ['lh', 'rh']:
verts, faces = utils.read_ply_file(op.join(MMVT_DIR, 'colin27', 'subcortical', '{}_{}.ply'.format(region, hemi)))
verts = apply_trans(colin27_xfm['trans'], verts)
verts = apply_trans(np.linalg.inv(xfm['trans']), verts)
utils.write_ply_file(verts, faces, op.join(MMVT_DIR, subject, 'subcortical', '{}_{}.ply'.format(region, hemi)))
def writing_ply_files_parallel(p):
facL_lab, vtxL_lab, vidx, nV, label_name, hemi, output_fol = p
# Reindex the faces
tmp = np.zeros(nV, dtype=np.int)
tmp[vidx] = np.arange(len(vidx))
facL_lab_flat = utils.list_flatten(facL_lab)
facL_lab = np.reshape(tmp[facL_lab_flat], (len(facL_lab), len(facL_lab[0])))
# Save the resulting surface
label_name = '{}-{}.ply'.format(lu.get_label_hemi_invariant_name(label_name), hemi)
# print('Writing {}'.format(op.join(output_fol, label_name)))
utils.write_ply_file(vtxL_lab, facL_lab, op.join(output_fol, label_name), True)
def create_surf(subject, subcortical_code, subcortical_name):
aseg = nib.load(op.join(SUBJECTS_DIR, subject, 'mri',
'aseg.mgz')).get_data()
t1_header = nib.load(op.join(SUBJECTS_DIR, subject, 'mri',
'T1.mgz')).header
aseg[aseg != subcortical_code] = 255
aseg[aseg == subcortical_code] = 10
aseg = np.array(aseg, dtype=np.float)
aseg_smooth = scipy.ndimage.gaussian_filter(aseg, sigma=1)
verts_vox, faces, _, _ = measure.marching_cubes(aseg_smooth, 100)
# Doesn't seem to fix the normals directions that should be out...
faces = measure.correct_mesh_orientation(aseg_smooth, verts_vox, faces)
verts = utils.apply_trans(t1_header.get_vox2ras_tkr(), verts_vox)
fol = utils.make_dir(op.join(MMVT_DIR, subject, 'subcortical_test'))
ply_file_name = op.join(fol, '{}.ply'.format(subcortical_name))
utils.write_ply_file(verts, faces, ply_file_name, False)
def aseg_to_srf(subject,
subjects_dir,
output_fol,
region_id,
lookup,
mask_fname,
norm_fname,
overwrite_subcortical_objs=False,
**kargs):
from src.utils import geometry_utils as gu
ret = True
tmp_fol = op.join(subjects_dir, subject, 'tmp', utils.rand_letters(6))
utils.make_dir(tmp_fol)
rs = utils.partial_run_script(locals())
# output_fname = op.join(output_fol, '{}.srf'.format(region_id))
# tmp_output_fname = op.join(tmp_fol, '{}.asc'.format(region_id))
# if overwrite_subcortical_objs:
# utils.remove_file(output_fname)
try:
rs(mri_pretess)
rs(mri_tessellate)
rs(mris_smooth)
fs_file = op.join(tmp_fol, '{}_smooth'.format(region_id))
verts, faces = gu.read_surface(fs_file)
# verts, faces = nib_fs.read_geometry(fs_file)
num = int(op.basename(fs_file).split('_')[0])
if num not in lookup:
print('Error in the subcorticals lookup table!')
return False
new_name = lookup.get(num, '')
utils.write_ply_file(verts, faces,
op.join(output_fol, '{}.ply'.format(new_name)),
True)
# mris_convert = 'mris_convert {tmp_fol}/{region_id}_smooth {tmp_fol}/{region_id}.asc'
# rs(mris_convert)
# if op.isfile(tmp_output_fname):
# shutil.move(tmp_output_fname, output_fname)
if op.isdir(tmp_fol):
shutil.rmtree(tmp_fol)
else:
ret = False
except:
print('Error in aseg_to_srf! subject: {}'.format(subject))
print(traceback.format_exc())
ret = False
return ret
def convert_perecelated_cortex(subject, aparc_name, surf_type='pial', overwrite_ply_files=False, hemi='both'):
lookup = {}
for hemi in utils.get_hemis(hemi):
lookup[hemi] = create_labels_lookup(subject, hemi, aparc_name)
if len(lookup[hemi]) == 0:
continue
srf_fol = op.join(SUBJECTS_DIR, subject,'{}.{}.{}'.format(aparc_name, surf_type, hemi))
ply_fol = op.join(SUBJECTS_DIR, subject,'{}_{}_{}_ply'.format(aparc_name, surf_type, hemi))
blender_fol = op.join(MMVT_DIR, subject,'{}.{}.{}'.format(aparc_name, surf_type, hemi))
utils.convert_srf_files_to_ply(srf_fol, overwrite_ply_files)
rename_cortical(lookup, srf_fol, ply_fol)
if surf_type == 'inflated':
for ply_fname in glob.glob(op.join(ply_fol, '*.ply')):
verts, faces = utils.read_ply_file(ply_fname)
verts_offset = 5.5 if hemi == 'rh' else -5.5
verts[:, 0] = verts[:, 0] + verts_offset
utils.write_ply_file(verts, faces, ply_fname)
utils.rmtree(blender_fol)
shutil.copytree(ply_fol, blender_fol)
return lookup
def convert_perecelated_cortex(subject, aparc_name, surf_type='pial', overwrite_ply_files=False, hemi='both'):
lookup = {}
for hemi in utils.get_hemis(hemi):
lookup[hemi] = create_labels_lookup(subject, hemi, aparc_name)
if len(lookup[hemi]) == 0:
continue
srf_fol = op.join(SUBJECTS_DIR, subject,'{}.{}.{}'.format(aparc_name, surf_type, hemi))
ply_fol = op.join(SUBJECTS_DIR, subject,'{}_{}_{}_ply'.format(aparc_name, surf_type, hemi))
blender_fol = op.join(MMVT_DIR, subject,'{}.{}.{}'.format(aparc_name, surf_type, hemi))
utils.convert_srf_files_to_ply(srf_fol, overwrite_ply_files)
rename_cortical(lookup, srf_fol, ply_fol)
if surf_type == 'inflated':
for ply_fname in glob.glob(op.join(ply_fol, '*.ply')):
verts, faces = utils.read_ply_file(ply_fname)
verts_offset = 5.5 if hemi == 'rh' else -5.5
verts[:, 0] = verts[:, 0] + verts_offset
utils.write_ply_file(verts, faces, ply_fname)
utils.rmtree(blender_fol)
shutil.copytree(ply_fol, blender_fol)
return lookup
def mat_to_ply():
fol = '/homes/5/npeled/space1/Angelique/Lionel Recon/'
files = glob.glob(op.join(fol, 'Iso*.mat'))
avg_fname = op.join(fol, 'blender', 'mean_vertices.npy')
if not op.isfile(avg_fname):
vertices_avg = []
for f in files:
print(f)
m = utils.read_mat_file_into_bag(f)
vertices_avg.append(np.mean(m.vertices.T / 10, 0))
m.clear()
vertices_avg = np.mean(vertices_avg)
np.save(avg_fname, vertices_avg)
else:
vertices_avg = np.load(avg_fname)
for f in files:
print(f)
m = utils.read_mat_file_into_bag(f)
ply_fname = utils.change_fname_extension(f, 'ply')
utils.write_ply_file(m.vertices.T / 10.0 - vertices_avg , m.faces.T, ply_fname, True)
m.clear()
def convert_to_ply(srf_fname, ply_fname, org_vox2ras_tkr, shifter_vox2tk_ras):
verts, faces, verts_num, faces_num = utils.read_srf_file(srf_fname)
verts = tu.apply_trans(np.linalg.inv(org_vox2ras_tkr), verts)
verts = tu.apply_trans(shifter_vox2tk_ras, verts)
utils.write_ply_file(verts, faces, ply_fname)
import glob
import re
from src.utils import utils
fol = '/home/npeled/Angelique/Niles'
tar_fol = ' '
npz_files = glob.glob(op.join(fol, 'npzs_center', '*.npz'))
utils.make_dir(op.join(fol, 'plys'))
electrodes_coords, electrodes_names = [], []
for npz_fname in npz_files:
d = np.load(npz_fname)
vertices, faces = d['vertices'], d['faces']
ply_fname = op.join(fol, 'plys',
'{}.ply'.format(utils.namebase(npz_fname)))
if op.isfile(ply_fname):
os.remove(ply_fname)
if faces.ndim == 1:
print('{} is an electrode'.format(ply_fname))
name = utils.namebase(npz_fname).replace('Electrode', '')
num = re.sub('\D', ',', name).split(',')[-1]
if not '.' in name and num == '':
continue
electrodes_coords.append(np.mean(vertices, 0))
electrodes_names.append(name)
else:
print('Writing {}'.format(ply_fname))
utils.write_ply_file(vertices, faces, ply_fname, False)
np.savez(op.join(fol, 'electrodes.npz'),
pos=electrodes_coords,
names=electrodes_names)
def convert_to_ply(srf_fname, ply_fname, org_vox2ras_tkr, shifter_vox2tk_ras):
verts, faces, verts_num, faces_num = utils.read_srf_file(srf_fname)
verts = apply_trans(np.linalg.inv(org_vox2ras_tkr), verts)
verts = apply_trans(shifter_vox2tk_ras, verts)
utils.write_ply_file(verts, faces, ply_fname)